Contacts of the helix formed by residues 82 - 111 (chain Y) in PDB entry 2X17
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 82 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Y TYR* 3.3 8.5 + - - -
80Y TRP* 3.3 1.6 - - - +
81Y GLU* 1.3 80.5 - - - +
83Y PRO* 1.4 71.4 - - - +
84Y LEU* 3.7 13.0 + - - +
85Y LYS* 3.0 28.2 + - - +
86Y ALA* 2.9 27.9 + - - +
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Residues in contact with PRO 83 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30Y TYR* 3.6 8.0 - - + +
31Y PHE* 3.7 22.9 - - + -
34Y LEU* 4.1 20.4 - - + -
36Y LEU* 4.1 14.6 - - + -
39Y PHE* 5.1 1.1 - - + -
82Y SER* 1.4 86.3 - - - +
84Y LEU* 1.3 60.7 + - - +
86Y ALA* 3.4 5.1 + - + +
87Y PHE* 3.3 19.2 + - - -
141Y LEU* 3.5 17.7 - - + +
151Y LEU* 4.2 27.6 - - + -
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Residues in contact with LEU 84 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82Y SER* 3.1 11.8 + - - +
83Y PRO* 1.3 78.4 - - - +
85Y LYS* 1.3 65.9 + - + +
86Y ALA 3.4 0.2 + - - -
87Y PHE* 3.4 5.0 + - - +
88Y GLU* 3.2 44.5 + - + +
138Y LEU* 4.1 5.1 - - + +
141Y LEU* 3.8 28.8 - - + +
142Y LYS* 3.7 44.2 - - + +
145Y LYS* 4.9 15.9 - - + -
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Residues in contact with LYS 85 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80Y TRP* 3.8 11.8 - - + -
81Y GLU* 4.2 33.0 - - + +
82Y SER* 3.0 27.5 + - - +
84Y LEU* 1.3 81.3 - - + +
86Y ALA* 1.3 64.0 + - - +
87Y PHE 3.4 0.2 - - - -
88Y GLU* 3.4 30.0 + - - +
89Y ALA* 3.3 16.8 + - - +
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Residues in contact with ALA 86 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Y MET* 3.5 19.2 - - + +
30Y TYR* 4.1 9.0 - - + -
31Y PHE* 3.7 24.0 - - + -
80Y TRP* 3.8 26.2 - - + +
82Y SER 2.9 11.8 + - - +
83Y PRO 3.5 10.1 - - - +
84Y LEU 3.2 0.2 - - - -
85Y LYS* 1.3 78.3 - - - +
87Y PHE* 1.3 58.1 + - - +
89Y ALA* 3.5 2.1 + - - +
90Y ALA* 3.3 18.2 + - - +
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Residues in contact with PHE 87 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31Y PHE* 3.7 12.8 - + - -
39Y PHE* 3.7 30.5 - + - -
42Y TRP* 4.4 14.6 - + + -
43Y MET* 3.7 24.7 - - + -
83Y PRO 3.3 8.4 + - - -
84Y LEU 3.4 2.9 + - - +
86Y ALA* 1.3 75.9 - - - +
88Y GLU* 1.3 60.5 + - - +
89Y ALA 3.3 0.2 - - - -
90Y ALA* 3.6 6.4 - - + +
91Y TYR* 3.0 23.4 + - - +
134Y VAL* 3.9 30.7 - - + +
137Y ILE* 3.7 39.3 - - + -
138Y LEU* 3.4 19.3 - - - +
141Y LEU* 3.6 27.8 - - + -
158Y LEU* 4.7 1.8 - - + -
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Residues in contact with GLU 88 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Y LEU* 3.2 40.5 + - - +
85Y LYS* 3.4 41.2 + - + +
86Y ALA 3.3 0.4 - - - -
87Y PHE* 1.3 78.5 - - - +
89Y ALA* 1.3 56.8 + - - +
91Y TYR* 3.7 3.3 + - - +
92Y GLU* 3.2 25.9 + - - +
138Y LEU* 3.7 23.3 - - + -
142Y LYS* 4.3 11.5 - - - -
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Residues in contact with ALA 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23Y LEU* 5.4 0.5 - - - +
27Y MET* 4.3 6.6 - - + +
80Y TRP* 3.4 30.5 - - + +
85Y LYS 3.3 6.6 + - - +
86Y ALA 3.8 4.7 - - - +
87Y PHE 3.3 0.2 - - - -
88Y GLU* 1.3 76.9 - - - +
90Y ALA* 1.3 60.5 + - - +
92Y GLU* 3.6 13.2 + - - +
93Y HIS* 3.0 27.7 + - - +
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Residues in contact with ALA 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Y TYR* 3.7 24.3 + - + +
27Y MET* 3.9 13.2 - - + +
43Y MET* 4.9 2.2 - - + -
86Y ALA 3.3 12.0 + - - +
87Y PHE* 3.6 15.9 - - + +
88Y GLU 3.3 0.4 - - - -
89Y ALA* 1.3 77.4 - - - +
91Y TYR* 1.3 58.7 + - - +
93Y HIS* 3.3 6.3 + - - +
94Y GLU* 2.8 32.9 + - - +
134Y VAL* 4.0 14.1 - - + -
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Residues in contact with TYR 91 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13 MET 5.5 1.6 + - - -
653 ASN* 4.5 4.9 - - - +
11743 AG 2.8 27.9 - - - -
87Y PHE 3.0 17.0 + - - +
88Y GLU 4.0 3.6 - - - +
90Y ALA* 1.3 72.8 - - - +
92Y GLU* 1.3 61.3 + - - +
94Y GLU* 3.8 2.5 - - - +
95Y LYS* 3.1 52.0 + - + +
131Y GLU* 3.8 43.7 + - + -
134Y VAL* 3.8 9.8 - - + +
135Y LYS* 3.6 46.6 - - + +
138Y LEU* 3.6 17.7 - - + -
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Residues in contact with GLU 92 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88Y GLU 3.2 17.0 + - - +
89Y ALA* 3.7 14.3 - - - +
91Y TYR* 1.3 77.6 - - - +
93Y HIS* 1.3 56.3 + - - +
95Y LYS* 3.4 15.8 + - - +
96Y PHE* 3.0 25.0 + - - +
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Residues in contact with HIS 93 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Y TYR* 3.8 29.9 - + - -
20Y SER* 2.8 34.7 + - - -
23Y LEU* 3.5 26.5 - - + +
24Y TYR* 4.2 14.4 - + - -
89Y ALA 3.0 18.6 + - - +
90Y ALA* 3.6 5.6 - - - +
92Y GLU* 1.3 75.2 - - - +
94Y GLU* 1.3 61.3 + - - +
96Y PHE* 3.1 22.0 + + - +
97Y ILE* 2.9 44.9 + - + +
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Residues in contact with GLU 94 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Y SER* 5.7 0.3 - - - -
24Y TYR* 2.5 34.5 + - - +
50Y GLU* 3.7 5.2 - - - +
90Y ALA 2.8 14.5 + - - +
91Y TYR* 3.8 7.6 - - - +
92Y GLU 3.4 0.4 - - - -
93Y HIS* 1.3 80.6 - - - +
95Y LYS* 1.3 52.8 + - - +
97Y ILE* 4.5 5.1 - - - +
98Y SER* 2.7 37.0 + - - -
127Y GLN* 2.8 32.8 + - - +
130Y GLU* 3.0 36.1 - - - +
131Y GLU* 4.0 16.6 - - + -
134Y VAL* 4.2 16.4 - - + -
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Residues in contact with LYS 95 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13 MET 5.6 7.4 - - - +
91Y TYR* 3.1 48.8 + - + +
92Y GLU* 3.7 13.9 - - - +
94Y GLU* 1.3 73.6 - - - +
96Y PHE* 1.3 60.4 + - - +
98Y SER* 3.9 1.5 - - - -
99Y LYS* 3.0 29.3 + - - +
102Y TYR* 5.8 0.2 - - - -
131Y GLU* 4.0 25.8 - - - +
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Residues in contact with PHE 96 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Y ARG* 4.3 26.2 - - + -
19Y TYR* 6.0 2.7 - + - -
92Y GLU 3.0 13.9 + - - +
93Y HIS* 3.3 32.5 - + - +
95Y LYS* 1.3 74.7 - - - +
97Y ILE* 1.3 77.3 + - + +
99Y LYS* 3.5 8.9 + - + +
100Y SER* 3.2 22.7 + - - -
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Residues in contact with ILE 97 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Y GLN* 3.9 7.6 - - - +
16Y ARG* 4.0 26.7 - - + +
17Y GLU* 3.9 17.5 - - - +
20Y SER* 3.4 20.6 - - - +
50Y GLU* 5.7 1.3 - - - +
93Y HIS* 2.9 42.5 + - + +
94Y GLU* 4.0 9.4 - - - +
96Y PHE* 1.3 81.6 - - + +
98Y SER* 1.3 62.4 + - - +
100Y SER* 2.6 20.1 + - - +
101Y ILE* 3.0 13.2 + - + +
127Y GLN* 3.6 28.7 - - - +
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Residues in contact with SER 98 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94Y GLU 2.7 22.3 + - - -
95Y LYS* 3.9 4.3 - - - -
96Y PHE 3.4 0.2 - - - -
97Y ILE* 1.3 76.4 - - - +
99Y LYS* 1.3 56.8 + - - +
101Y ILE* 3.2 9.5 + - - +
102Y TYR* 3.0 51.1 + - - -
127Y GLN* 3.3 27.4 + - - +
131Y GLU* 2.8 23.3 + - - -
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Residues in contact with LYS 99 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95Y LYS 3.0 19.5 + - - +
96Y PHE* 3.7 9.6 - - + +
97Y ILE 3.2 0.2 - - - -
98Y SER* 1.3 75.2 - - - +
100Y SER* 1.3 58.7 + - - +
102Y TYR* 3.2 17.4 + - + +
103Y GLU* 3.1 48.6 + - + +
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Residues in contact with SER 100 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Y GLN* 2.9 26.4 + - - +
16Y ARG* 3.9 26.9 + - - -
96Y PHE* 3.2 15.3 + - - -
97Y ILE* 2.6 27.1 + - - -
99Y LYS* 1.3 75.1 - - - +
101Y ILE* 1.3 59.2 + - - +
103Y GLU* 4.0 13.7 - - - +
104Y LEU* 3.3 24.1 + - - +
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Residues in contact with ILE 101 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Y GLN* 3.7 32.1 - - + +
17Y GLU* 4.5 4.5 - - - +
57Y PHE* 4.3 9.6 - - + -
97Y ILE* 3.0 25.4 + - + +
98Y SER* 3.4 11.4 - - - +
99Y LYS 3.2 0.2 - - - -
100Y SER* 1.3 76.2 - - - +
102Y TYR* 1.3 65.9 + - + +
103Y GLU 3.2 0.2 - - - -
104Y LEU* 3.3 4.9 + - - +
105Y ALA* 3.0 22.3 + - - +
120Y LEU* 4.3 11.5 - - + +
123Y PHE* 4.0 32.3 - - + +
124Y ILE* 3.8 30.1 - - + +
127Y GLN* 4.5 7.2 - - + -
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Residues in contact with TYR 102 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643 ARG* 3.3 17.6 + - - -
1123 LYS 5.6 2.5 - - - -
1133 ASP* 5.7 1.1 - - - -
1143 TYR* 3.5 53.4 - + + -
1153 SER* 2.8 26.9 + - - -
98Y SER* 3.0 40.1 + - - -
99Y LYS* 3.2 19.5 + - + +
101Y ILE* 1.3 78.8 - - + +
103Y GLU* 1.3 57.4 + - + +
105Y ALA* 3.4 3.7 + - - +
106Y ALA* 2.9 27.9 + - - +
124Y ILE* 4.5 13.0 - - + -
131Y GLU* 4.9 0.7 + - - -
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Residues in contact with GLU 103 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Y ARG* 5.9 0.5 + - - -
99Y LYS* 3.1 45.9 + - + +
100Y SER* 4.1 10.6 - - - +
102Y TYR* 1.3 75.1 - - + +
104Y LEU* 1.3 58.7 + - - +
106Y ALA* 3.2 7.4 + - - +
107Y LEU* 2.9 29.7 + - - +
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Residues in contact with LEU 104 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Y MET* 3.9 22.0 - - - +
9Y ALA* 3.7 36.8 - - + +
10Y LEU* 4.1 12.1 - - + -
13Y GLN* 3.6 36.6 - - + +
16Y ARG* 5.0 2.5 - - - +
57Y PHE* 4.6 2.9 - - + -
100Y SER 3.3 18.7 + - - +
101Y ILE* 3.3 6.4 + - + +
103Y GLU* 1.3 78.4 - - - +
105Y ALA* 1.3 57.1 + - - +
107Y LEU* 3.4 7.1 + - + +
108Y ALA* 3.1 27.4 + - - +
120Y LEU* 3.6 24.5 - - + +
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Residues in contact with ALA 105 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143 TYR* 4.4 9.9 - - + -
101Y ILE 3.0 17.7 + - - +
102Y TYR* 3.5 7.9 - - - +
103Y GLU 3.3 0.2 - - - -
104Y LEU* 1.3 75.6 - - - +
106Y ALA* 1.3 58.1 + - - +
108Y ALA* 3.5 0.8 + - - -
109Y GLU* 3.1 35.2 + - - +
117Y ARG* 3.6 28.1 - - - +
120Y LEU* 3.7 13.6 - - + +
124Y ILE* 4.4 11.4 - - + -
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Residues in contact with ALA 106 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143 TYR* 3.4 22.0 + - + +
102Y TYR 2.9 13.9 + - - +
103Y GLU* 3.2 9.6 + - - +
105Y ALA* 1.3 73.9 - - - +
107Y LEU* 1.3 64.5 - - - +
109Y GLU* 3.5 5.7 + - - +
110Y GLU* 3.2 23.4 + - - +
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Residues in contact with LEU 107 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Y ARG* 4.3 27.8 - - + +
6Y MET* 3.9 20.4 - - + -
9Y ALA* 3.9 27.1 - - + -
103Y GLU 2.9 17.0 + - - +
104Y LEU* 3.6 7.6 - - + +
105Y ALA 3.3 0.2 - - - -
106Y ALA* 1.3 77.2 - - - +
108Y ALA* 1.3 56.1 + - - +
110Y GLU* 3.6 16.6 + - - +
111Y GLU* 3.1 43.0 + - + +
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Residues in contact with ALA 108 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6Y MET* 3.6 17.2 - - + +
104Y LEU 3.1 16.6 + - - +
105Y ALA* 3.8 5.6 - - - +
106Y ALA 3.3 0.2 - - - -
107Y LEU* 1.3 76.3 - - - +
109Y GLU* 1.3 59.9 + - - +
111Y GLU* 3.6 0.4 + - - -
112Y LYS* 3.1 6.2 + - - -
113Y ASP* 2.8 48.1 + - + +
116Y THR* 4.3 6.1 - - + -
117Y ARG* 3.9 21.3 - - + +
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Residues in contact with GLU 109 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143 TYR* 2.9 34.4 + - - -
105Y ALA 3.1 18.7 + - - +
106Y ALA* 3.9 5.5 - - - +
107Y LEU 3.4 0.4 - - - -
108Y ALA* 1.3 76.5 - - - +
110Y GLU* 1.3 61.9 + - - +
112Y LYS* 3.5 15.1 + - - +
117Y ARG* 3.2 34.4 + - + -
----------------------------------------------------------
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Residues in contact with GLU 110 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106Y ALA 3.2 18.1 + - - +
107Y LEU* 3.8 19.2 - - - +
109Y GLU* 1.3 74.7 - - - +
111Y GLU* 1.3 60.4 + - + +
112Y LYS* 3.1 14.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 111 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Y SER* 2.7 32.2 + - - -
5Y ARG* 3.7 27.5 - - - +
6Y MET* 3.4 20.9 + - - +
107Y LEU* 3.1 28.1 + - + +
108Y ALA 4.3 2.5 - - - +
109Y GLU 3.5 0.2 - - - -
110Y GLU* 1.3 78.1 - - + +
112Y LYS* 1.3 68.3 + - - +
113Y ASP* 3.3 10.8 + - + +
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il