Contacts of the helix formed by residues 114 - 138 (chain I) in PDB entry 2GD4
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 LYS 114 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F ZDO 2.9 49.6 + - - +
2F IDS 2.6 53.6 + - - +
3F SUS 3.3 23.2 + - - -
12I PRO* 5.7 2.7 - - - -
13I ARG* 5.5 3.4 - - - -
47I ARG* 3.1 32.3 - - - +
113I GLU* 1.3 74.9 - - - +
115I THR* 1.3 67.8 + - - +
117I ASP* 2.6 28.6 + - - +
118I GLN* 3.0 18.3 + - + -
122I PHE* 4.8 4.7 - - + -
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Residues in contact with THR 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I ARG* 3.0 45.5 + - + +
50I GLU* 3.3 12.7 + - + +
51I LEU* 5.2 6.1 - - + -
111I ILE* 4.1 12.3 - - + -
112I SER* 2.6 31.7 + - - -
113I GLU 2.9 1.0 + - - -
114I LYS* 1.3 74.0 - - - +
116I SER* 1.3 52.0 + - - -
117I ASP 2.3 14.7 + - - -
119I ILE* 2.6 28.0 + - - +
122I PHE* 4.1 18.8 - - + -
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Residues in contact with SER 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I ILE* 5.8 0.3 - - - -
23I TYR* 4.9 7.9 + - - +
24I ARG* 4.4 9.2 - - - -
91I LYS* 4.7 5.4 - - - +
103I MET* 4.4 16.9 - - - +
108I PHE 4.3 5.2 - - - -
109I ASP* 6.1 0.4 - - - -
111I ILE* 3.4 29.1 - - - +
112I SER 3.0 16.5 + - - -
113I GLU 2.7 10.4 + - - -
115I THR* 1.3 71.6 - - - +
117I ASP* 1.3 64.4 + - - +
119I ILE* 3.5 9.8 - - - +
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Residues in contact with ASP 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ASN* 4.6 13.2 - - - +
19I PRO* 5.2 11.4 - - + +
22I ILE* 3.2 39.4 - - + +
23I TYR 4.8 0.2 - - - +
24I ARG* 3.0 25.8 + - - -
91I LYS* 5.2 2.4 - - - +
92I LEU* 6.2 0.2 - - - -
113I GLU 3.1 15.8 - - - +
114I LYS* 2.6 11.0 + - - +
115I THR 2.3 16.2 + - - -
116I SER* 1.3 75.7 - - - +
118I GLN* 1.3 64.0 + - + +
119I ILE* 2.8 18.5 + - - +
120I HIS* 3.7 12.2 - - - -
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Residues in contact with GLN 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F ZDO 4.0 2.4 + - - +
12I PRO* 4.0 25.0 - - + +
13I ARG* 3.4 10.7 - - + +
15I ILE* 4.9 3.2 - - - +
17I MET* 2.8 39.5 - - - +
18I ASN* 3.1 23.4 + - - +
19I PRO* 5.6 1.0 - - - +
114I LYS* 3.0 23.1 + - + +
117I ASP* 1.3 77.6 - - + +
119I ILE* 1.3 52.0 + - - +
120I HIS* 3.1 18.6 + - - -
121I PHE* 2.5 42.6 + - + +
122I PHE* 3.4 22.7 + - + -
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Residues in contact with ILE 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I LEU* 3.6 21.3 - - + +
88I ALA* 4.4 5.8 - - + -
91I LYS* 4.1 19.5 - - + -
103I MET* 6.3 0.2 - - - -
108I PHE* 3.9 33.0 - - + -
111I ILE* 4.7 1.6 - - + -
115I THR* 2.6 29.0 + - - +
116I SER* 3.5 8.1 - - - +
117I ASP* 2.9 23.1 - - - +
118I GLN* 1.3 70.6 - - - +
120I HIS* 1.3 68.3 + - + +
121I PHE 2.9 0.5 + - - -
122I PHE* 3.0 9.4 + - - -
123I PHE* 2.8 48.3 + - + +
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Residues in contact with HIS 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ILE* 6.0 4.9 - - + -
16I PRO 5.7 3.4 - - - -
17I MET* 6.0 1.4 - - - -
19I PRO* 4.9 7.2 - - + +
88I ALA* 3.9 14.6 - - - +
89I MET* 3.4 31.0 - - + +
91I LYS* 6.4 0.2 - - + -
92I LEU* 3.5 35.2 - - + +
117I ASP 3.7 15.0 + - - -
118I GLN* 2.8 18.1 + - - -
119I ILE* 1.3 85.0 - - + +
121I PHE* 1.3 89.1 + + + +
123I PHE* 3.8 5.0 - - - +
124I ALA 3.6 8.3 + - - -
161I ILE* 4.0 21.4 - - + +
165I VAL* 3.1 29.2 - - + +
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Residues in contact with PHE 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I ILE* 4.4 19.5 - - + -
10I ALA 2.8 31.0 - - - -
11I LYS* 3.6 2.2 - - - -
12I PRO* 3.2 51.6 - - + -
15I ILE* 4.4 14.8 - - + -
118I GLN* 2.5 20.5 + - + +
120I HIS* 1.3 87.1 + + + +
122I PHE* 1.3 67.9 + + - +
124I ALA* 2.6 36.0 + - + +
125I LYS* 3.0 30.3 + - + -
164I LEU 5.9 0.4 - - - -
165I VAL* 4.1 15.7 - - + -
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Residues in contact with PHE 122 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F SUS 3.7 33.9 - - - -
12I PRO* 4.1 7.6 - - + -
45I ASN* 4.2 4.7 - - - -
47I ARG* 3.1 47.3 - - + -
48I VAL* 4.6 16.3 - - + +
51I LEU* 3.5 19.7 - - + -
114I LYS* 4.8 3.4 - - + -
115I THR* 4.1 17.3 - - + -
118I GLN* 3.4 35.6 + - + -
119I ILE* 3.0 2.6 + - - +
121I PHE* 1.3 90.7 - + - +
123I PHE* 1.3 59.0 + - - +
125I LYS* 2.5 29.4 + - + -
126I LEU* 2.6 12.6 + - - +
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Residues in contact with PHE 123 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I LEU* 3.0 35.7 - - + +
55I ASN* 5.1 4.0 - - + -
81I LEU* 5.0 3.8 - - + -
84I SER* 3.8 15.7 - - - -
85I THR* 3.1 33.2 - - + +
88I ALA* 3.4 23.8 - - + -
108I PHE* 3.3 43.5 - + - -
119I ILE* 2.8 33.0 + - + +
120I HIS* 3.8 7.2 - - - +
122I PHE* 1.3 68.8 - - - +
124I ALA* 1.3 52.8 + - - +
126I LEU* 3.3 20.9 - - + +
127I ASN* 2.5 40.0 + - - -
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Residues in contact with ALA 124 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I ILE* 4.6 18.6 - - + +
85I THR* 5.3 0.6 - - - +
120I HIS 3.6 4.6 + - - +
121I PHE* 2.6 20.0 + - + +
122I PHE 2.6 3.2 + - - -
123I PHE* 1.3 70.2 - - - +
125I LYS* 1.3 52.5 + - - +
126I LEU 2.6 15.3 + - - -
127I ASN* 2.8 21.2 + - - +
128I CYS* 3.0 13.6 + - - +
165I VAL* 3.3 33.7 - - + +
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Residues in contact with LYS 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F SUS 4.0 8.8 + - - +
4F BDP 3.2 35.6 + - - +
5F SGN 3.4 27.1 + - - +
7I ILE* 4.1 23.9 - - - +
8I CYS* 4.5 13.5 + - - +
9I THR* 5.2 1.2 - - - +
10I ALA 4.6 3.6 - - - +
11I LYS* 4.4 18.0 - - - +
48I VAL* 4.2 9.9 - - + -
121I PHE* 3.0 30.2 + - + -
122I PHE* 2.5 18.2 + - + +
124I ALA* 1.3 75.4 - - - +
126I LEU* 1.3 57.9 + - - +
128I CYS* 4.2 8.4 - - - +
129I ARG* 3.8 10.9 + - - +
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Residues in contact with LEU 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I VAL* 3.3 32.1 - - + +
51I LEU* 5.1 3.4 - - + -
52I SER* 4.5 18.6 - - - +
55I ASN* 6.2 0.2 - - + -
81I LEU* 3.2 32.3 - - + -
122I PHE 2.6 12.6 + - - +
123I PHE* 3.3 31.6 - - + +
124I ALA 2.6 4.0 + - - -
125I LYS* 1.3 68.1 - - - +
127I ASN* 1.3 67.3 + - - +
128I CYS 3.1 1.6 - - - -
129I ARG* 2.9 17.7 + - - +
130I LEU* 3.0 22.1 + - + +
417I LEU* 3.6 19.5 - - + -
419I THR* 4.4 2.2 - - - +
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Residues in contact with ASN 127 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I LEU* 2.8 32.7 - - - +
85I THR* 3.6 23.6 + - - +
123I PHE 2.5 25.4 + - - -
124I ALA* 2.8 12.9 + - - +
126I LEU* 1.3 76.9 - - - +
128I CYS* 1.3 52.1 + - - +
130I LEU* 3.1 8.7 + - - +
131I TYR* 2.5 39.0 + - + +
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Residues in contact with CYS 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I ILE* 5.0 1.1 - - + -
8I CYS* 2.0 55.4 - - + -
124I ALA 3.0 14.7 + - - +
125I LYS* 4.2 6.5 - - - +
127I ASN* 1.3 76.2 - - - +
129I ARG* 1.3 55.7 + - - +
131I TYR* 2.5 33.1 + - - +
132I ARG* 2.9 27.5 + - - +
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Residues in contact with ARG 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F SGN 3.5 35.7 + - - +
43I ALA* 3.3 21.5 + - - +
44I THR* 3.5 18.0 + - - -
48I VAL* 4.8 2.9 - - - -
125I LYS 3.8 7.2 + - - +
126I LEU 2.9 12.2 + - - +
128I CYS* 1.3 78.7 - - - +
130I LEU* 1.3 65.0 + - + +
131I TYR 3.0 0.2 + - - -
132I ARG* 3.4 27.7 + - - +
133I LYS* 3.0 48.9 + - + +
414I GLU* 2.7 31.5 + - - +
416I PRO* 3.7 13.9 - - - +
417I LEU* 3.6 22.7 - - - +
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Residues in contact with LEU 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I LEU* 3.8 19.7 - - + -
126I LEU* 3.0 23.7 + - + +
127I ASN* 3.2 9.0 - - - +
129I ARG* 1.3 77.8 - - + +
131I TYR* 1.3 60.5 + - - +
133I LYS* 5.2 3.1 - - - +
134I ALA* 3.2 22.3 + - - +
140I LEU* 4.2 6.7 - - + +
279I ILE* 5.2 2.1 - - + +
414I GLU* 3.4 44.4 - - + +
417I LEU* 4.8 2.7 - - + -
419I THR* 3.6 32.5 - - + +
421I ILE* 4.0 25.4 - - + +
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Residues in contact with TYR 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I ASN 2.5 13.0 + - - +
128I CYS* 2.5 29.6 + - - +
130I LEU* 1.3 71.6 - - - +
132I ARG* 1.3 72.6 + - + +
134I ALA* 3.4 3.6 - - - +
135I ASN* 2.9 54.7 + - + +
140I LEU* 3.5 26.0 + - + -
141I VAL* 5.5 1.1 - - - -
142I SER* 5.0 12.6 - - - -
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Residues in contact with ARG 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F SGN 5.1 5.1 + - - -
8I CYS* 4.6 12.5 + - - +
9I THR* 6.1 1.0 - - - +
128I CYS* 2.9 30.5 + - - +
129I ARG* 3.4 27.3 + - - +
131I TYR* 1.3 77.9 - - + +
133I LYS* 1.3 68.2 + - + +
134I ALA 2.7 3.3 + - - -
135I ASN* 2.8 4.5 + - - -
136I LYS* 2.6 37.1 + - + +
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Residues in contact with LYS 133 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I ARG* 3.0 65.2 + - + +
130I LEU* 5.2 1.3 - - - +
132I ARG* 1.3 87.3 - - + +
134I ALA* 1.3 63.7 + - - +
136I LYS* 3.5 16.9 - - - +
137I ALA* 4.1 4.3 + - - +
275I LYS 5.4 2.6 - - - +
278I ASP* 4.0 40.5 + - + +
279I ILE* 4.3 13.4 - - + +
414I GLU* 3.1 21.6 + - + -
416I PRO* 4.2 11.1 - - - +
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Residues in contact with ALA 134 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I LEU 3.2 22.9 + - - +
131I TYR 3.4 4.0 + - - +
132I ARG 2.7 3.8 + - - -
133I LYS* 1.3 80.0 - - - +
135I ASN* 1.3 58.1 + - - +
138I SER* 2.9 34.9 + - - +
139I LYS 5.6 0.2 - - - -
140I LEU* 3.8 25.4 - - + -
221I PHE* 4.8 9.0 - - + -
279I ILE* 4.2 17.4 - - + +
421I ILE* 5.6 2.0 - - + -
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Residues in contact with ASN 135 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131I TYR* 2.9 64.1 + - + +
132I ARG* 2.8 6.2 + - - +
134I ALA* 1.3 73.2 - - - +
136I LYS* 1.3 67.4 + - - +
137I ALA 3.8 0.7 - - - -
138I SER 2.7 20.3 + - - +
139I LYS* 3.4 4.7 - - - -
140I LEU* 2.6 37.9 + - - +
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Residues in contact with LYS 136 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I ARG* 2.6 22.9 + - + +
133I LYS* 3.5 15.9 - - - +
134I ALA 3.2 0.2 - - - -
135I ASN* 1.3 72.5 - - - +
137I ALA* 1.3 59.2 + - + +
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Residues in contact with ALA 137 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133I LYS 4.1 2.2 + - - +
134I ALA 3.6 2.6 + - - +
135I ASN 3.8 0.7 - - - -
136I LYS* 1.3 82.1 - - + +
138I SER* 1.3 64.2 + - - +
224I LEU* 3.6 20.6 - - + +
275I LYS* 3.4 40.6 - - + +
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Residues in contact with SER 138 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I ALA* 2.9 15.0 + - - -
135I ASN* 2.7 26.2 - - - +
137I ALA* 1.3 83.7 - - - +
139I LYS* 1.3 63.4 + - - +
221I PHE* 4.8 7.9 - - - -
222I LYS 3.9 12.6 - - - -
223I GLY* 4.0 5.0 - - - -
224I LEU* 3.5 25.2 + - - +
274I PHE* 4.2 11.4 - - - +
275I LYS 5.4 0.3 + - - -
----------------------------------------------------------
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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