Contacts of the helix formed by residues 95 - 124 (chain L) in PDB entry 5JKL
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 95 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L TYR* 3.8 4.0 + - - -
41L PHE* 3.6 9.0 - - - -
46L VAL* 6.3 0.4 - - - -
93L TRP 2.8 8.6 + - - +
94L GLU* 1.3 80.6 + - - +
96L GLY* 1.3 59.2 + - - +
97L LEU* 3.5 2.3 + - - +
98L ASN* 3.0 22.7 + - - +
99L ALA* 2.9 29.1 + - - +
161L PRO* 3.7 22.3 - - - +
167L GLU* 3.6 15.9 - - - -
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Residues in contact with GLY 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L PHE* 3.6 13.2 - - - -
51L PHE* 3.5 26.9 - - - -
95L SER* 1.3 69.5 - - - +
97L LEU* 1.3 62.2 + - - +
99L ALA* 3.4 1.4 + - - +
100L MET* 3.0 27.9 + - - +
155L LEU* 4.1 2.5 - - - -
167L GLU* 2.9 22.9 + - - -
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Residues in contact with LEU 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95L SER* 3.4 4.2 - - - +
96L GLY* 1.3 75.5 - - - +
98L ASN* 1.3 59.4 + - - +
100L MET* 3.2 2.3 + - - +
101L GLU* 2.9 54.7 + - - +
152L VAL* 3.9 31.2 - - + +
155L LEU* 4.0 17.1 - - + +
156L ARG* 4.0 13.5 - - + -
160L ALA* 3.7 31.6 - - + +
161L PRO* 3.8 13.7 - - + -
167L GLU* 2.9 14.0 + - - +
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Residues in contact with ASN 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90L GLU* 5.9 2.6 - - - +
92L ASP 5.4 0.2 + - - -
93L TRP* 2.9 32.7 + - - +
94L GLU* 3.8 27.6 + - + +
95L SER* 3.0 17.5 + - - +
97L LEU* 1.3 76.2 - - - +
99L ALA* 1.3 59.0 + - - +
101L GLU* 3.2 15.7 + - - +
102L GLU* 2.9 48.6 + - - +
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Residues in contact with ALA 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L MET* 3.5 18.5 - - - +
41L PHE* 3.6 29.2 - - + -
55L PHE* 4.0 11.9 - - + -
93L TRP* 3.9 12.7 + - + -
95L SER 2.9 16.8 + - - +
96L GLY 3.8 1.8 - - - +
98L ASN* 1.3 77.2 - - - +
100L MET* 1.3 56.6 + - - +
102L GLU* 3.4 1.6 + - - -
103L ALA* 2.9 29.5 + - - +
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Residues in contact with MET 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51L PHE* 3.9 19.1 - - + -
54L TYR* 3.7 28.7 - - + -
55L PHE* 3.8 14.8 - - + -
96L GLY 3.0 18.7 + - - +
97L LEU 3.6 6.7 - - - +
99L ALA* 1.3 74.4 - - - +
101L GLU* 1.4 57.7 + - - +
103L ALA* 3.3 3.6 + - - +
104L LEU* 2.9 29.1 + - - +
148L LEU* 3.7 25.4 - - + +
151L HIS* 3.9 24.5 - - + -
152L VAL* 3.8 19.8 - - + +
155L LEU* 3.9 16.4 - - + -
170L PHE* 4.5 1.6 - - + -
175L LEU* 4.1 9.2 - - + -
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Residues in contact with GLU 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97L LEU* 2.9 39.8 + - - +
98L ASN* 3.2 15.8 + - - +
100L MET* 1.4 76.6 - - - +
102L GLU* 1.3 56.9 + - + +
104L LEU* 3.3 9.2 + - + +
105L GLU* 3.1 25.8 + - - +
152L VAL* 4.0 19.1 - - + -
156L ARG* 2.9 36.2 + - - +
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Residues in contact with GLU 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L MET* 3.8 16.2 - - + -
89L ASP* 5.2 6.9 - - - +
90L GLU* 5.5 7.1 - - - +
93L TRP* 4.0 18.6 - - + -
98L ASN* 2.9 41.1 + - - +
99L ALA 3.8 3.8 - - - +
101L GLU* 1.3 73.5 - - + +
103L ALA* 1.3 60.8 + - - +
105L GLU* 3.3 24.3 + - - +
106L LEU* 2.9 28.4 + - - +
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Residues in contact with ALA 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L TYR* 3.9 25.8 - - + +
37L MET* 3.7 7.3 - - + +
55L PHE* 4.2 7.6 - - + -
99L ALA 2.9 18.3 + - - +
100L MET 3.6 4.5 - - - +
102L GLU* 1.3 72.1 - - - +
104L LEU* 1.3 66.2 + - - +
106L LEU* 3.2 7.1 + - - +
107L GLU* 2.9 28.9 + - - +
148L LEU* 3.7 21.5 - - + -
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Residues in contact with LEU 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100L MET 2.9 14.6 + - - +
101L GLU* 3.5 11.2 - - + +
102L GLU 3.3 0.2 - - - -
103L ALA* 1.3 76.8 - - - +
105L GLU* 1.3 64.4 + - - +
107L GLU* 3.3 1.2 + - - +
108L LYS* 3.0 39.7 + - + +
145L ILE* 3.8 41.1 - - + +
148L LEU* 3.8 13.4 - - + +
149L GLY* 4.2 14.4 - - - +
152L VAL* 4.4 20.9 - - + -
156L ARG* 6.3 0.2 - - - +
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Residues in contact with GLU 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101L GLU 3.1 12.2 + - - +
102L GLU* 3.5 29.1 - - - +
103L ALA 3.2 0.2 - - - -
104L LEU* 1.3 79.5 - - - +
106L LEU* 1.3 63.3 + - - +
108L LYS* 3.3 8.5 + - - +
109L ASN* 3.0 45.0 + - - +
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Residues in contact with LEU 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L LEU* 5.4 1.6 - - + -
29L TYR* 4.0 31.6 - - + -
30L ALA* 4.0 20.6 - - + -
33L VAL* 3.8 31.6 - - + -
34L TYR* 4.1 23.8 - - + -
102L GLU 2.9 14.6 + - - +
103L ALA* 3.5 8.5 - - - +
105L GLU* 1.3 75.9 - - - +
107L GLU* 1.3 61.2 + - + +
109L ASN* 3.1 14.0 + - + +
110L VAL* 2.8 43.4 + - + +
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Residues in contact with GLU 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L ALA* 6.1 0.4 - - - -
34L TYR* 2.5 42.8 + - - +
58L GLN* 5.2 2.8 - - - +
62L GLU* 3.4 14.6 - - - +
103L ALA 2.9 15.2 + - - +
104L LEU 3.9 2.0 - - - +
106L LEU* 1.3 81.2 - - + +
108L LYS* 1.3 57.6 + - - +
110L VAL* 4.4 5.4 - - - +
111L ASN* 3.0 25.6 + - - +
141L GLN* 2.8 43.8 + - - +
144L ALA* 4.1 16.6 - - + +
145L ILE* 3.8 20.8 - - + +
148L LEU* 3.6 13.9 - - + -
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Residues in contact with LYS 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L LEU* 3.0 37.7 + - + +
105L GLU* 3.8 6.1 - - - +
107L GLU* 1.3 78.0 - - - +
109L ASN* 1.3 58.6 + - - +
111L ASN* 3.4 3.1 + - - +
112L GLN* 2.9 29.1 + - - +
145L ILE* 3.9 31.6 - - + -
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Residues in contact with ASN 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L LEU* 4.7 5.1 - - + +
105L GLU* 3.0 39.1 + - - +
106L LEU* 3.5 13.2 - - + +
108L LYS* 1.3 78.3 - - - +
110L VAL* 1.4 62.5 + - + +
112L GLN* 3.3 8.8 + - - +
113L SER* 3.1 21.7 + - - -
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Residues in contact with VAL 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L GLN* 3.8 8.3 - - - +
26L LEU* 4.0 26.7 - - + +
27L GLU* 3.6 27.4 - - - +
30L ALA* 4.4 13.2 - - + -
62L GLU* 5.7 0.7 - - - +
106L LEU* 2.8 39.9 + - + +
107L GLU* 4.7 2.9 - - - +
109L ASN* 1.4 69.4 - - + +
111L ASN* 1.3 60.2 - - - +
113L SER* 3.2 3.1 + - - -
114L LEU* 2.9 32.6 + - + +
141L GLN* 3.8 21.5 - - - +
201L FE 4.4 2.7 - - - -
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Residues in contact with ASN 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107L GLU 3.0 18.3 + - - +
108L LYS* 3.6 5.6 - - - +
110L VAL* 1.3 73.4 - - - +
112L GLN* 1.3 61.5 + - - +
114L LEU* 3.2 2.6 + - - +
115L LEU* 2.8 56.0 + - - +
138L LEU* 4.4 13.3 - - - +
141L GLN* 3.4 30.7 - - + +
142L VAL* 5.1 9.5 - - - +
145L ILE* 3.9 17.9 - - + +
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Residues in contact with GLN 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108L LYS 2.9 14.6 + - - +
109L ASN* 3.3 11.4 + - - +
111L ASN* 1.3 76.4 - - - +
113L SER* 1.3 55.9 + - - +
115L LEU* 3.2 22.4 + - - +
116L GLU* 2.9 57.5 + - - +
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Residues in contact with SER 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L ARG 5.9 0.2 - - - -
23L GLN* 2.6 23.6 + - - -
26L LEU* 3.5 28.5 - - - +
109L ASN 3.1 9.6 + - - -
110L VAL 3.2 3.1 + - - -
112L GLN* 1.3 77.2 - - - +
114L LEU* 1.3 58.0 + - - +
116L GLU* 3.3 12.3 + - - +
117L LEU* 2.9 28.6 + - - +
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Residues in contact with LEU 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L GLN* 3.6 28.9 - - + +
27L GLU* 4.4 0.4 - - - +
69L LEU* 5.7 1.3 - - + -
110L VAL* 2.9 23.0 + - + +
111L ASN* 3.6 5.8 - - - +
113L SER* 1.3 75.7 - - - +
115L LEU* 1.3 56.5 + - - +
117L LEU* 3.3 14.7 + - + +
118L HIS* 2.9 29.3 + - - +
133L ILE* 4.1 10.1 - - + +
137L TYR* 3.9 39.9 - - + +
138L LEU* 4.0 15.0 - - + -
141L GLN* 3.4 37.0 - - + +
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Residues in contact with LEU 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L ASN* 2.8 46.7 + - - +
112L GLN* 3.2 22.2 + - - +
114L LEU* 1.3 68.3 - - - +
116L GLU* 1.3 66.1 + - - +
118L HIS* 3.3 7.7 + - + +
119L LYS* 3.0 23.4 + - - +
138L LEU* 4.1 26.9 - - + -
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Residues in contact with GLU 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112L GLN* 2.9 46.5 + - - +
113L SER* 3.6 9.7 - - - +
115L LEU* 1.3 75.8 - - - +
117L LEU* 1.3 62.7 + - - +
119L LYS* 3.3 11.3 + - + +
120L LEU* 3.0 22.7 + - - +
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Residues in contact with LEU 117 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L SER* 4.7 1.8 - - - +
19L ALA* 3.4 35.2 - - + +
20L ILE* 3.6 33.0 - - + -
23L GLN* 4.3 25.8 - - + +
69L LEU* 5.2 2.2 - - + -
113L SER 2.9 17.2 + - - +
114L LEU* 3.4 12.3 - - + +
116L GLU* 1.3 77.0 - - - +
118L HIS* 1.3 60.8 + - - +
120L LEU* 3.3 10.4 + - + +
121L ALA* 3.0 21.7 + - - +
129L LEU* 5.0 6.1 - - + -
133L ILE* 3.7 22.7 - - + -
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Residues in contact with HIS 118 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L LEU 2.9 16.7 + - - +
115L LEU* 3.6 10.5 - - + +
116L GLU 3.3 0.2 - - - -
117L LEU* 1.3 75.7 - - - +
119L LYS* 1.3 58.7 + - - +
121L ALA* 3.2 3.2 + - - +
122L THR* 2.8 50.5 + - - -
130L CYS* 3.6 31.1 - - + +
133L ILE* 3.9 19.7 - - + +
134L GLU* 2.7 37.4 + - + +
138L LEU* 4.4 8.7 - - + +
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Residues in contact with LYS 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115L LEU 3.0 16.1 + - - +
116L GLU* 3.7 10.3 - - + +
117L LEU 3.3 0.2 - - - -
118L HIS* 1.3 78.8 + - - +
120L LEU* 1.3 57.6 + - - +
122L THR* 3.2 8.6 + - + -
123L ASP* 2.8 62.4 + - - +
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Residues in contact with LEU 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L ASP* 3.5 44.4 - - + +
16L SER* 3.9 11.0 - - - +
19L ALA* 3.7 19.3 - - + -
22L ARG* 5.6 2.0 - - - +
116L GLU 3.0 13.8 + - - +
117L LEU* 3.5 10.5 - - + +
118L HIS 3.3 0.2 - - - -
119L LYS* 1.3 75.5 - - - +
121L ALA* 1.3 59.6 + - - +
123L ASP* 3.2 10.3 + - + +
124L LYS* 2.9 50.3 + - + +
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Residues in contact with ALA 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L SER* 4.8 4.0 - - - -
117L LEU 3.0 13.4 + - - +
118L HIS* 3.6 10.5 - - - +
120L LEU* 1.3 76.1 - - - +
122L THR* 1.3 60.3 + - - +
124L LYS* 3.4 2.1 + - - +
125L ASN 3.2 4.2 + - - -
126L ASP* 3.0 35.9 + - - +
129L LEU* 3.9 32.3 - - + +
130L CYS* 3.6 18.6 - - - +
133L ILE* 4.6 0.7 - - + -
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Residues in contact with THR 122 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118L HIS* 2.8 44.5 + - - -
119L LYS* 3.5 9.1 - - + +
120L LEU 3.2 0.2 - - - -
121L ALA* 1.3 75.9 - - - +
123L ASP* 1.3 64.1 + - - +
125L ASN* 3.0 26.3 + - - +
130L CYS* 3.6 8.6 - - - -
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Residues in contact with ASP 123 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119L LYS* 2.8 56.6 + - - +
120L LEU* 3.7 10.1 - - + +
122L THR* 1.3 79.6 - - - +
124L LYS* 1.3 67.1 + - + +
125L ASN* 3.3 10.1 + - - -
----------------------------------------------------------
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Residues in contact with LYS 124 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L ASN* 4.3 8.1 - - - +
13L HIS* 3.7 50.6 + - + -
15L ASP* 3.5 24.4 + - - -
16L SER* 4.3 7.2 - - - +
120L LEU* 2.9 37.9 + - + +
121L ALA* 4.2 2.7 - - - +
122L THR 3.3 0.2 - - - -
123L ASP* 1.3 79.4 - - + +
125L ASN* 1.3 72.7 + - - +
126L ASP* 3.4 6.6 + - + +
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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