Contacts of the strand formed by residues 85 - 93 (chain B) in PDB entry 6S6A
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 VAL 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LYS* 3.9 12.6 - - + +
11B LEU* 3.8 17.5 - - + -
81B ILE 3.5 20.6 - - - +
82B PHE* 3.5 16.2 - - - +
83B ARG 3.3 14.4 - - - +
84B ASN* 1.3 73.8 - - - +
86B GLU* 1.3 57.9 + - - +
87B VAL 3.4 29.8 - - - +
113B ILE* 4.0 16.8 - - + -
117B SER* 3.0 24.3 + - - +
119B ASP 5.0 0.3 - - - -
120B ALA* 3.5 12.4 + - + +
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Residues in contact with GLU 86 (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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8B LYS* 3.6 46.9 + - + +
9B LYS 3.1 19.5 + - - +
10B VAL* 5.5 0.2 - - + -
84B ASN 3.6 5.4 + - - +
85B VAL* 1.3 73.1 - - - +
87B VAL* 1.3 71.0 + - + +
119B ASP 4.6 1.4 - - - +
120B ALA* 3.4 2.6 - - - +
121B LYS* 2.8 50.4 + - - -
180B LEU* 4.7 1.3 - - + -
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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
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9B LYS 3.4 1.6 + - - -
10B VAL* 3.5 12.7 - - + -
11B LEU 3.0 24.8 + - - +
85B VAL* 3.4 9.2 - - - +
86B GLU* 1.3 89.3 - - + +
88B LEU* 1.3 61.6 + - - +
89B ILE* 3.8 18.2 - - + -
120B ALA* 4.6 0.2 - - - -
121B LYS* 3.1 15.7 - - + +
123B PHE* 3.7 30.5 - - + -
176B ILE* 4.1 8.7 - - + +
180B LEU* 3.5 36.3 - - + -
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Residues in contact with LEU 88 (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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11B LEU* 3.6 24.5 - - + +
13B MET* 3.9 23.8 - - + -
85B VAL* 4.3 0.4 - - - +
87B VAL* 1.3 72.2 - - - +
89B ILE* 1.3 68.8 + - - +
90B TYR* 4.5 12.3 - - + +
106B TYR* 5.1 0.2 - - + -
109B CYS* 4.6 13.0 - - + -
110B LEU* 4.1 22.4 - - + -
113B ILE* 4.0 30.3 - - + -
120B ALA* 4.6 0.8 - - + +
121B LYS 2.7 13.2 + - - +
122B ILE* 3.2 14.8 - - + -
123B PHE* 2.6 35.9 + - - +
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Residues in contact with ILE 89 (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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10B VAL* 3.4 26.9 - - + -
11B LEU 2.8 12.6 + - - +
12B LEU* 3.3 16.9 - - + +
13B MET 3.0 24.8 + - - +
87B VAL* 3.8 12.8 - - + -
88B LEU* 1.3 77.0 - - - +
90B TYR* 1.3 59.9 + - - +
91B VAL* 4.6 0.2 - - + -
123B PHE* 3.5 5.8 - - + +
125B LEU* 3.5 34.3 - - + -
173B TRP* 3.6 30.3 - - + -
176B ILE* 4.2 27.4 - - + -
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Residues in contact with TYR 90 (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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13B MET* 3.2 15.0 - - + -
14B GLY* 3.7 20.5 - - - -
15B LYS* 4.6 2.4 + - - +
70B MET* 3.9 5.9 - - + +
88B LEU* 3.9 12.1 - - + -
89B ILE* 1.3 72.4 - - - +
91B VAL* 1.3 87.5 + - - +
92B PHE* 3.7 34.6 + + - -
102B ASP* 4.1 3.2 + - + -
105B TYR* 3.6 14.0 - - - +
106B TYR* 3.4 47.8 + + + -
109B CYS* 3.7 29.2 - - + -
123B PHE 2.7 15.5 + - - +
124B CYS* 3.4 5.8 - - - +
125B LEU* 2.9 27.2 + - - +
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Residues in contact with VAL 91 (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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12B LEU* 3.7 29.6 - - + -
13B MET 2.8 11.4 + - - +
14B GLY* 3.3 18.9 - - - -
15B LYS* 4.3 1.4 + - - +
18B SER* 3.4 39.9 + - - +
19B GLY 4.7 0.4 - - - +
20B LYS* 3.9 8.1 - - + +
23B MET* 4.1 12.8 - - + -
89B ILE* 4.6 0.2 - - + -
90B TYR* 1.3 84.2 - - - +
92B PHE* 1.3 63.5 + - - +
93B ASP 4.2 0.2 - - - -
125B LEU* 3.7 20.4 - - + +
127B HIS* 4.0 17.0 - - + -
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Residues in contact with PHE 92 (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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15B LYS* 6.5 0.2 - - - -
90B TYR* 3.7 26.7 - + - -
91B VAL* 1.3 75.8 - - - +
93B ASP* 1.3 61.6 + - - +
94B VAL* 5.7 0.7 - - - -
102B ASP* 4.4 16.6 - - + -
103B MET* 4.1 20.4 - - + -
106B TYR* 3.5 30.1 - + + -
124B CYS* 3.9 15.9 - - + -
125B LEU 3.0 14.8 + - - +
126B VAL* 4.7 9.0 - - + -
127B HIS* 2.9 33.4 + - - +
148B LEU* 3.3 47.3 - - + -
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Residues in contact with ASP 93 (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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15B LYS* 4.9 10.4 - - + +
16B SER 5.5 0.5 - - - +
17B GLY 4.0 4.7 - - - +
18B SER* 4.1 23.9 - - - +
92B PHE* 1.3 72.0 - - - +
94B VAL* 1.3 64.7 + - - +
95B GLU* 3.3 22.2 + - - +
96B SER* 3.2 30.7 + - - +
99B LEU* 5.5 1.6 - - - +
102B ASP* 5.1 1.5 + - - +
127B HIS 4.1 2.7 - - - -
128B LYS* 2.7 44.6 + - - +
144B ARG* 5.0 1.0 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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