Contacts of the strand formed by residues 3 - 13 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ALA* 1.3 76.7 - - - +
4A VAL* 1.3 70.1 - - - +
49A GLU* 4.9 2.7 - - + -
50A GLY* 3.5 20.4 - - - +
51A ASP* 4.2 14.8 - - - +
81A PRO* 3.9 31.0 - - + +
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Residues in contact with VAL 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA* 4.4 5.4 - - + +
3A ILE* 1.3 80.7 - - - +
5A ARG* 1.3 60.3 + - - +
48A LEU 4.4 0.2 - - - -
49A GLU* 3.3 6.4 - - - +
50A GLY 2.9 37.8 + - - +
52A GLU* 3.7 39.5 - - + +
55A VAL* 3.9 12.3 - - + -
78A TRP* 3.7 25.1 - - + -
79A GLU 5.2 0.7 - - - -
81A PRO* 4.1 7.4 - - - -
64B GLN* 4.5 13.9 - - - +
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Residues in contact with ARG 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 1.3 77.0 - - - +
6A ALA* 1.3 61.5 + - - +
7A HIS* 5.8 0.2 + - - -
35A TRP* 4.7 4.6 - - - +
47A VAL* 3.5 35.8 - - + +
48A LEU 3.3 5.2 - - - +
49A GLU* 3.0 28.3 + - - +
78A TRP* 3.4 9.5 - - - -
79A GLU* 2.8 71.4 + - + +
80A GLN 3.2 21.4 + - - -
81A PRO* 4.0 5.2 - - + -
82A LYS* 3.7 25.6 - - - +
84A GLU* 2.8 32.3 + - - +
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Residues in contact with ALA 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ARG* 1.3 76.7 - - - +
7A HIS* 1.3 59.9 + - - +
8A LEU* 3.7 20.8 - - + +
47A VAL* 3.4 3.2 - - - -
48A LEU* 2.8 35.6 + - + +
55A VAL* 4.0 8.3 - - + +
59A ILE* 3.8 14.4 - - + -
76A VAL* 3.9 5.6 - - + -
77A LYS 3.7 3.6 - - - -
78A TRP* 3.7 22.4 - - + -
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Residues in contact with HIS 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA* 1.3 71.2 - - - +
8A LEU* 1.3 68.7 + - - +
9A LYS* 5.7 2.1 - - + +
35A TRP* 4.4 5.5 - + - -
45A GLU* 2.6 32.7 + - + +
46A ALA 3.4 13.0 - - - -
47A VAL* 4.1 12.1 - - + +
75A GLU 3.6 1.2 - - - +
76A VAL* 3.4 2.4 - - - -
77A LYS* 2.8 51.4 + - + +
79A GLU* 2.8 36.7 + - - +
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Residues in contact with LEU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA* 3.7 30.1 - - + +
7A HIS* 1.3 79.1 - - - +
9A LYS* 1.3 63.1 + - - +
10A ILE* 4.1 23.3 - - + -
23A MET* 5.5 0.7 - - + -
44A VAL 4.4 0.2 - - - -
45A GLU* 3.3 11.1 - - - +
46A ALA* 2.7 39.9 + - + +
48A LEU* 4.2 23.1 - - + -
59A ILE* 4.1 14.4 - - + -
62A ALA* 4.3 13.7 - - + -
74A VAL* 4.1 15.9 - - + -
75A GLU 3.2 3.1 - - - -
76A VAL* 3.9 19.5 - - + -
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Residues in contact with LYS 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A HIS* 5.7 2.0 - - + -
8A LEU* 1.3 77.7 - - - +
10A ILE* 1.3 62.1 + - - +
11A TYR* 2.8 42.2 + - + +
39A LEU* 3.5 19.7 - - + +
41A ASP* 3.3 16.0 + - - -
43A SER* 3.1 23.2 + - - +
44A VAL 3.4 6.5 - - - +
45A GLU* 4.5 12.8 - - + +
74A VAL* 3.4 4.3 - - - +
75A GLU* 2.9 42.6 + - + +
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Residues in contact with ILE 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.1 20.9 - - + -
9A LYS* 1.3 78.5 - - - +
11A TYR* 1.3 63.5 + - - +
14A VAL* 3.7 12.8 - - + +
19A PHE* 4.0 22.4 - - + -
23A MET* 3.7 29.6 - - + -
43A SER* 3.3 7.1 - - - -
44A VAL* 2.8 49.4 + - + +
46A ALA* 5.0 1.6 - - + -
62A ALA* 4.0 14.8 - - + +
71A VAL* 4.0 22.7 - - + -
73A ARG 3.7 3.1 - - - -
74A VAL* 4.3 11.4 - - + -
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Residues in contact with TYR 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LYS* 2.8 52.3 + - + +
10A ILE* 1.3 75.3 - - - +
12A GLY* 1.3 52.3 + - - +
14A VAL* 3.9 6.1 - - - -
41A ASP* 4.4 7.4 - - - -
43A SER* 3.7 16.6 - - - +
71A VAL* 3.5 7.4 - - - +
72A THR* 2.8 32.2 + - - +
73A ARG* 3.0 70.1 + - + +
75A GLU* 3.2 31.3 + - - -
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Residues in contact with GLY 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 1.3 75.8 - - - +
13A ARG* 1.3 62.2 + - - -
14A VAL* 3.1 12.7 + - - +
42A GLY 4.3 5.8 + - - +
70A ARG 3.3 9.9 - - - -
72A THR* 3.7 15.9 + - - -
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Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY* 1.3 67.6 - - - -
14A VAL* 1.3 59.4 + - - +
15A GLN 4.0 9.8 + - - -
16A GLY 5.8 0.9 + - - -
17A VAL* 3.4 28.0 - - - +
68A LEU* 4.1 9.4 + - - +
69A ALA* 3.3 9.5 - - - -
70A ARG* 2.9 71.8 + - + +
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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