Contacts of the helix formed by residues 67 - 89 (chain B) in PDB entry 3SSB
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 ASP 67 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LYS* 5.8 0.3 + - - -
55B TRP* 3.5 26.3 + - + -
57B ASP* 4.3 6.9 - - - +
61B GLN 4.1 2.9 - - - +
62B PHE* 3.3 41.8 - - + +
63B PHE 3.4 0.5 + - - -
64B ALA* 2.9 36.4 + - - +
66B TYR* 1.3 82.8 - - - +
68B ALA* 1.3 63.8 + - - +
69B PRO* 3.4 0.7 - - - -
70B ALA* 3.1 14.8 + - - +
71B VAL* 3.1 13.8 + - - +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG 3.4 13.9 - - - +
12B GLY 3.6 24.7 - - - +
13B VAL* 3.7 19.1 + - - +
64B ALA 3.5 3.6 + - - +
65B SER* 3.1 13.4 + - - +
67B ASP* 1.3 79.8 - - - +
69B PRO* 1.4 70.6 - - + +
70B ALA 3.3 0.2 + - - -
71B VAL* 3.4 3.3 + - - +
72B ASP 3.2 17.0 + - - -
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Residues in contact with PRO 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 3.7 5.4 - - + -
65B SER 3.7 6.3 - - - +
66B TYR 3.6 11.2 - - - +
67B ASP 3.5 3.8 - - - -
68B ALA* 1.4 94.9 - - + +
70B ALA* 1.3 56.1 + - - +
73B ALA* 3.0 21.0 + - - +
104B VAL* 3.8 19.7 - - + -
105B HIS* 3.7 18.2 - - + -
122B TYR* 6.2 0.4 - - + -
123B GLY 5.9 0.4 - - - +
124B ASP* 3.9 3.8 - - - +
132B PRO* 3.6 31.6 - - + -
134B SER* 2.8 29.5 + - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.5 24.0 - - + -
41B THR* 3.8 8.1 - - + +
55B TRP* 3.6 34.1 - - + -
62B PHE* 5.9 0.7 - - + -
67B ASP* 3.1 10.0 + - + +
69B PRO* 1.3 78.4 - - - +
71B VAL* 1.3 66.6 + - + +
74B HIS* 3.0 27.4 + - - +
104B VAL* 4.0 9.5 - - + +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLY* 4.1 8.3 - - - -
11B ARG 3.8 25.8 - - - +
12B GLY* 4.1 1.6 - - - +
18B LYS* 3.8 29.6 - - + -
20B ILE* 4.1 16.5 - - + +
30B LEU* 4.7 0.2 - - - +
62B PHE* 3.5 36.1 - - + +
67B ASP* 3.1 13.2 + - + +
68B ALA 3.5 7.6 - - - +
70B ALA* 1.3 76.9 - - - +
72B ASP* 1.3 57.3 + - - +
74B HIS* 3.6 4.7 - - - +
75B TYR* 2.9 31.4 + - - +
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Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY* 3.4 5.4 - - - -
13B VAL* 2.7 39.8 + - + +
14B LEU* 4.3 2.4 + - - +
16B ASP* 4.6 1.2 - - - +
18B LYS* 2.8 33.3 + - - -
68B ALA 3.2 7.2 + - - +
69B PRO 4.1 1.1 - - - +
71B VAL* 1.3 77.9 - - - +
73B ALA* 1.3 66.4 + - - +
75B TYR* 4.5 2.0 - - - +
76B TYR* 2.8 44.7 + - + +
134B SER* 3.4 22.2 - - - +
135B GLY* 3.5 6.4 - - - +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 4.3 4.3 - - + -
69B PRO 3.0 19.5 + - - +
70B ALA 3.4 2.7 + - - +
72B ASP* 1.3 74.4 - - - +
74B HIS* 1.3 58.0 + - - +
76B TYR* 4.6 0.2 - - - +
77B ALA* 3.0 31.5 + - - +
102B SER* 4.2 12.9 + - - -
104B VAL* 3.7 20.4 - - + -
122B TYR* 4.0 14.3 + - + -
134B SER* 3.7 13.8 - - - -
140B VAL* 4.6 8.3 - - - +
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Residues in contact with HIS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 4.2 14.8 - - + -
21B ASN 2.7 30.8 + - - -
30B LEU* 3.2 45.5 - - + -
31B GLN 3.5 0.7 - - - -
32B ASP* 3.6 13.8 - - + +
39B ILE* 3.2 30.1 + - + +
41B THR* 2.8 27.1 + - - +
70B ALA 3.0 18.1 + - - +
71B VAL* 3.6 4.7 - - - +
73B ALA* 1.3 79.2 - - - +
75B TYR* 1.3 60.7 + - - +
77B ALA* 3.5 5.8 + - - +
78B GLY* 3.2 17.2 + - - -
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Residues in contact with TYR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LYS* 3.5 36.9 - - + +
19B ASN 3.2 28.7 - - - -
20B ILE* 4.1 8.3 - - + -
35B ARG* 5.6 0.2 + - - -
71B VAL 2.9 18.1 + - - +
72B ASP* 4.1 1.8 - - - +
74B HIS* 1.3 77.2 - - - +
76B TYR* 1.3 79.3 + + + +
78B GLY* 3.1 5.6 + - - -
79B VAL* 3.0 41.8 + - + +
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Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 6.2 0.3 - - - +
16B ASP* 4.0 5.4 + - - -
18B LYS* 3.0 27.4 + - - -
72B ASP* 2.8 37.4 + - - +
75B TYR* 1.3 86.7 - + - +
77B ALA* 1.3 64.7 + - - +
79B VAL* 3.4 6.9 + - + +
80B THR* 2.9 30.0 + - - -
134B SER 3.2 26.7 - - - -
135B GLY 3.7 16.4 + - - -
137B ILE* 3.4 45.7 - - + +
140B VAL* 3.8 15.5 - - + -
180B ALA* 6.1 2.5 - - + -
182B LYS* 5.5 6.1 - - - +
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 3.6 23.0 - - + +
73B ALA 3.0 22.0 + - - +
74B HIS 3.6 5.8 - - - +
76B TYR* 1.3 75.8 - - - +
78B GLY* 1.3 58.6 + - - +
80B THR* 3.3 5.1 + - - -
81B TYR* 2.9 29.8 + - - +
100B ILE* 4.1 17.6 - - + +
102B SER* 4.6 2.2 - - - +
120B MET* 4.3 10.3 - - + -
140B VAL* 3.8 8.2 - - + +
144B LEU* 4.5 4.1 - - - +
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG* 3.2 32.9 + - - -
39B ILE* 3.4 17.8 - - - +
74B HIS 3.2 6.5 + - - -
75B TYR* 3.1 8.9 + - - -
77B ALA* 1.3 76.4 - - - +
79B VAL* 1.3 57.9 + - - +
81B TYR* 3.3 1.2 + - - +
82B ASP* 2.9 26.0 + - - -
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG* 4.7 1.5 - - - +
75B TYR* 3.0 42.1 + - + +
76B TYR* 3.4 13.2 + - + +
78B GLY* 1.3 73.3 - - - +
80B THR* 1.3 59.2 + - - +
82B ASP* 3.2 9.8 + - - +
83B TYR* 2.9 26.3 + - - +
137B ILE* 4.1 4.9 - - + -
176B VAL* 4.0 15.3 - - + -
179B TYR* 4.0 14.4 - - + -
180B ALA* 3.9 28.0 - - + -
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Residues in contact with THR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR 2.9 18.6 + - - -
77B ALA* 3.7 1.3 - - - -
78B GLY 3.3 0.2 - - - -
79B VAL* 1.3 71.6 - - - +
81B TYR* 1.3 65.9 + - - +
83B TYR* 3.2 2.9 + - - +
84B TYR* 3.1 44.6 + - + -
137B ILE* 4.3 1.0 - - - +
140B VAL* 4.3 1.3 - - - +
141B ALA* 3.5 35.2 + - + +
144B LEU* 3.3 36.3 - - + -
176B VAL* 3.8 12.3 - - + +
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Residues in contact with TYR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG* 3.7 33.0 - - + -
36B GLY* 3.2 21.0 + - - -
39B ILE* 4.2 1.6 - - + -
77B ALA 2.9 16.9 + - - +
78B GLY 3.5 4.5 - - - +
79B VAL 3.3 0.2 - - - -
80B THR* 1.3 77.0 - - - +
82B ASP* 1.3 72.9 + - - +
84B TYR* 3.4 4.9 + - - +
85B LYS* 3.0 54.6 + - + +
90B ARG 4.7 0.7 - - - +
91B LEU* 4.1 2.4 - - - +
92B SER* 3.6 26.0 + - - +
97B ASN* 2.7 32.4 + - - -
98B ALA 5.6 0.7 - - - -
100B ILE* 3.8 26.9 - - + -
144B LEU* 4.5 2.3 - - - +
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Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ARG* 2.7 43.6 + - - +
78B GLY 2.9 14.9 + - - +
79B VAL* 3.5 9.2 - - - +
81B TYR* 1.3 82.2 - - - +
83B TYR* 1.3 55.6 + - - +
85B LYS* 4.7 2.2 - - - +
86B ASN* 2.8 46.6 + - - +
179B TYR* 3.6 19.1 - - + +
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL 2.9 13.3 + - - +
80B THR 3.5 6.5 - - - +
81B TYR 3.2 0.2 - - - -
82B ASP* 1.3 75.2 - - - +
84B TYR* 1.3 73.3 + + - +
87B VAL* 2.8 61.7 + - + +
88B HIS* 2.8 37.9 + + - -
172B PHE* 3.4 24.7 - + - -
175B LEU* 3.6 33.4 - - + +
176B VAL* 3.5 27.1 - - + -
179B TYR* 3.7 34.0 - - + -
264B GLY* 4.6 1.0 - - - -
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Residues in contact with TYR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B THR* 3.1 39.5 + - + +
81B TYR* 4.1 4.0 - - - +
83B TYR* 1.3 94.4 - + - +
85B LYS* 1.3 61.9 + - - +
88B HIS* 3.1 25.0 + + - +
89B ASN 3.1 6.6 + - - -
90B ARG* 2.9 48.5 + - + +
92B SER* 5.1 6.5 - - - +
93B TYR* 6.4 0.2 - - - -
144B LEU* 5.3 3.4 - - + -
145B THR* 2.9 41.7 + - - +
148B VAL* 3.9 25.2 - - + +
172B PHE* 3.4 17.8 - + + +
176B VAL* 4.9 1.8 - - + -
268B TYR* 4.3 15.9 - + - -
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B TYR* 3.0 46.8 + - + +
82B ASP* 4.0 2.5 - - - +
84B TYR* 1.3 77.5 - - - +
86B ASN* 1.3 73.7 + - - +
89B ASN* 3.0 30.3 + - - -
90B ARG 3.2 13.8 + - - +
91B LEU* 3.7 26.7 - - + -
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Residues in contact with ASN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ASP* 2.8 31.2 + - - +
83B TYR 4.4 0.2 - - - +
85B LYS* 1.3 93.9 - - - +
87B VAL* 1.3 61.1 + - + +
89B ASN* 4.4 7.7 + - - +
179B TYR* 3.0 29.6 + - + +
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 2.8 52.4 + - + +
86B ASN* 1.3 76.2 - - + +
88B HIS* 1.3 82.2 + - + +
89B ASN* 3.6 4.6 - - - +
179B TYR* 4.0 19.7 - - + -
261B ASP* 6.1 5.2 - - - +
264B GLY* 6.3 0.2 - - - -
265B LYS* 4.6 17.1 + - + +
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Residues in contact with HIS 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 2.8 45.5 + + - -
84B TYR* 3.1 23.8 + + - +
87B VAL* 1.3 91.8 + - + +
89B ASN* 1.3 76.1 + - - +
90B ARG* 3.1 3.5 + - + +
172B PHE* 3.7 5.3 - - - -
264B GLY* 3.6 30.5 - - - -
265B LYS* 4.4 7.0 - - + +
268B TYR* 3.6 49.6 + + + +
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Residues in contact with ASN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LYS* 3.0 22.5 + - - -
86B ASN* 4.4 7.9 + - - +
87B VAL 4.6 3.6 - - - +
88B HIS* 1.3 81.3 - - - +
90B ARG* 1.3 58.2 + - - +
91B LEU* 4.2 7.7 + - - +
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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) + - + + + + + -
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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