Contacts of the strand formed by residues 3 - 13 (chain B) in PDB entry 1W2I
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 ILE 3 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ALA* 1.3 77.1 - - - +
4B VAL* 1.3 70.4 + - - +
49B GLU* 4.3 5.8 - - + +
50B GLY* 3.4 14.6 - - - +
51B ASP* 3.3 37.5 - - - +
81B PRO* 3.7 33.3 - - + +
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Residues in contact with VAL 4 (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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64A GLN* 4.5 13.5 - - - +
2B ALA* 4.1 6.3 - - + +
3B ILE* 1.3 79.7 - - - +
5B ARG* 1.3 62.3 + - - +
48B LEU 3.9 0.6 - - - +
49B GLU* 3.3 5.9 - - - +
50B GLY 3.0 31.7 + - - +
52B GLU* 3.7 42.6 - - + +
55B VAL* 4.0 12.1 - - + -
56B GLU* 6.2 0.2 - - + -
78B TRP* 3.7 25.6 - - + -
79B GLU 5.3 0.2 - - - -
81B PRO* 4.1 6.3 - - - -
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Residues in contact with ARG 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 1.3 77.4 - - - +
6B ALA* 1.3 61.6 + - - +
7B HIS* 5.8 0.4 + - - -
35B TRP* 4.9 3.2 - - - +
47B VAL* 3.5 33.6 - - + +
48B LEU 3.3 8.3 - - - +
49B GLU* 2.9 29.4 + - + +
78B TRP* 3.4 9.3 - - - -
79B GLU* 2.8 70.2 + - + +
80B GLN 3.2 20.9 - - - -
81B PRO* 3.9 5.2 - - + -
82B LYS* 3.6 35.6 - - - +
84B GLU* 2.9 29.1 + - - +
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Residues in contact with ALA 6 (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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5B ARG* 1.3 75.3 - - - +
7B HIS* 1.3 60.8 + - - +
8B LEU* 4.0 10.4 + - + -
46B ALA 3.8 0.9 - - - +
47B VAL* 3.4 3.9 - - - +
48B LEU* 2.8 40.5 + - + +
55B VAL* 4.3 4.3 - - + -
59B ILE* 4.0 17.9 - - + -
76B VAL* 4.3 4.5 - - + -
77B LYS 3.7 4.0 - - - -
78B TRP* 3.6 27.7 - - + -
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Residues in contact with HIS 7 (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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5B ARG* 4.2 0.4 + - - -
6B ALA* 1.3 72.5 - - - +
8B LEU* 1.3 68.6 + - - +
9B LYS* 4.4 18.0 + - - -
35B TRP* 4.5 3.5 - + - -
45B GLU* 2.6 32.9 + - + +
46B ALA 3.4 14.1 - - - -
47B VAL* 4.1 14.7 - - + +
75B GLU 3.7 0.5 - - - +
76B VAL* 3.5 3.3 - - - -
77B LYS* 2.9 45.4 + - + +
79B GLU* 2.9 36.5 + - - +
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Residues in contact with LEU 8 (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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6B ALA* 4.3 11.2 - - + +
7B HIS* 1.3 75.8 - - - +
9B LYS* 1.3 64.8 + - - +
10B ILE* 4.2 26.2 - - + -
23B MET* 4.8 5.2 - - + -
44B VAL 4.5 0.2 - - - -
45B GLU* 3.4 8.0 - - - +
46B ALA* 2.8 38.7 + - + +
48B LEU* 3.6 30.7 - - + -
59B ILE* 4.2 19.3 - - + -
62B ALA* 5.0 2.2 - - + -
74B VAL* 3.8 24.0 - - + -
75B GLU 3.2 2.5 - - - +
76B VAL* 3.7 28.9 - - + -
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Residues in contact with LYS 9 (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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7B HIS* 4.4 21.6 + - - -
8B LEU* 1.3 76.7 - - - +
10B ILE* 1.3 61.3 + - - +
11B TYR* 3.6 33.4 - - + +
39B LEU* 5.0 11.7 - - + -
43B SER* 5.3 2.5 - - - +
44B VAL 3.4 5.4 - - - +
45B GLU* 4.6 20.6 - - + -
74B VAL* 3.4 3.1 - - - -
75B GLU* 2.8 46.2 + - + +
77B LYS* 6.2 1.8 - - - +
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Residues in contact with ILE 10 (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 LEU* 4.2 22.7 - - + -
9B LYS* 1.3 77.2 - - - +
11B TYR* 1.3 64.5 + - - +
14B VAL* 3.7 19.0 - - + +
19B PHE* 3.9 22.7 - - + -
23B MET* 3.8 28.5 - - + -
43B SER* 3.4 5.9 - - - -
44B VAL* 2.8 49.2 + - + +
46B ALA* 4.8 2.9 - - + -
62B ALA* 4.4 5.2 - - + +
71B VAL* 3.9 23.3 - - + -
73B ARG 3.7 2.7 - - - -
74B VAL* 4.2 11.0 - - + -
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Residues in contact with TYR 11 (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* 3.6 37.5 - - + +
10B ILE* 1.3 75.1 - - - +
12B GLY* 1.3 59.7 + - - +
14B VAL* 3.7 7.1 - - - +
41B ASP* 4.5 9.9 + - - -
43B SER* 3.7 26.0 + - - +
71B VAL* 3.4 8.0 - - - +
72B THR* 2.8 32.7 + - - +
73B ARG* 3.0 44.4 + - + +
75B GLU* 3.1 36.4 + - - -
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Residues in contact with GLY 12 (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 TYR* 1.3 76.9 - - - +
13B ARG* 1.3 61.8 + - - -
14B VAL* 3.2 12.1 + - - +
42B GLY 4.4 5.2 + - - +
70B ARG* 3.2 10.5 - - - -
72B THR* 3.7 16.8 - - - -
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Residues in contact with ARG 13 (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 GLY* 1.3 66.7 - - - -
14B VAL* 1.3 59.8 + - - +
15B GLN 3.8 6.3 + - - +
16B GLY 4.8 4.4 + - - -
17B VAL* 3.5 27.7 - - + +
68B LEU* 3.6 39.6 + - - +
69B ALA* 3.3 10.0 - - - -
70B ARG* 2.8 50.5 + - + +
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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