Contacts of the strand formed by residues 4 - 10 (chain D) in PDB entry 2WY2
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 4 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D LYS* 1.3 81.5 - - - +
5D HIS* 1.3 57.1 + - - +
6D ILE* 4.9 0.2 - - - -
33D PRO* 2.9 10.0 + - + +
34D VAL* 3.2 16.7 - - + +
35D ILE 2.8 32.2 + - - +
52D ASP* 3.3 23.3 - - + +
100D ILE* 4.0 39.5 - - + +
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Residues in contact with HIS 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LYS* 3.4 18.7 + - - +
4D LYS* 1.3 73.4 - - - +
6D ILE* 1.3 61.3 + - - +
7D TYR* 3.0 33.7 + + + -
35D ILE* 3.4 35.5 - - + +
50D ASN* 3.8 22.6 + - + +
51D ALA* 3.7 2.1 - - - -
52D ASP* 2.7 42.8 + - - +
53D VAL 3.3 7.6 + - - +
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Residues in contact with ILE 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LYS 4.6 0.4 - - - +
5D HIS* 1.3 74.1 - - - +
7D TYR* 1.3 63.9 + - - +
8D LEU* 3.9 10.1 - - + -
23D MET* 4.3 5.8 - - + -
34D VAL* 4.0 31.0 - - + -
35D ILE 2.8 13.0 + - - +
36D ILE* 3.3 11.2 - - + +
37D GLU 3.1 23.9 + - - +
53D VAL* 3.8 21.5 - - + -
55D LEU* 3.9 28.7 - - + -
93D LEU* 4.2 17.3 - - + -
96D ALA* 3.8 18.4 - - + -
97D VAL* 5.3 2.2 - - + +
100D ILE* 4.7 7.6 - - + -
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Residues in contact with TYR 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D HIS* 3.0 38.2 + - + -
6D ILE* 1.3 83.7 - - - +
8D LEU* 1.3 62.2 + - - +
9D PHE* 4.0 17.0 - - + -
35D ILE* 4.8 2.7 - - + -
37D GLU* 3.3 41.5 + - + +
39D PHE* 4.2 15.0 - + + -
47D LYS* 3.4 34.1 - - + -
48D GLY 4.7 0.4 - - - -
50D ASN* 4.1 9.8 + - + +
51D ALA* 3.4 29.4 - - + -
53D VAL 3.3 6.9 + - - +
54D VAL* 3.7 2.8 - - - -
55D LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D ILE* 3.9 22.0 - - + -
7D TYR* 1.3 77.7 - - - +
9D PHE* 1.4 65.5 + - - +
16D THR* 3.5 32.3 - - + -
19D LEU* 3.7 15.7 - - + -
20D VAL* 4.0 9.4 - - + -
23D MET* 4.1 8.5 - - - -
36D ILE* 3.9 20.4 - - + -
37D GLU 2.9 11.9 + - - +
38D ALA* 3.4 3.4 - - - +
39D PHE* 2.9 26.9 + - - +
55D LEU* 3.4 13.0 - - + +
79D ILE* 3.6 26.9 - - + -
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Residues in contact with PHE 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D TYR* 4.0 25.1 - - + -
8D LEU* 1.4 75.1 - - - +
10D CYS* 1.4 62.1 + - - +
16D THR* 4.7 3.8 + - - +
39D PHE* 3.2 28.5 - + + -
40D PRO 3.4 18.6 - - - -
41D GLU* 4.2 6.3 - - - -
43D LEU 3.8 4.3 - - - -
44D ALA* 3.5 39.0 - - + -
47D LYS* 4.3 3.8 - - + -
48D GLY 4.1 15.3 - - - -
54D VAL* 3.5 34.8 - - + -
55D LEU 3.0 12.5 + - - +
56D LEU* 4.2 6.1 - - + -
57D GLY* 3.0 27.5 + - - -
60D ILE* 3.4 18.2 - - + +
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Residues in contact with CYS 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A MET* 4.9 10.1 - - + -
13A ILE* 4.7 4.0 - - + -
9D PHE* 1.4 69.9 - - - +
11D SER* 1.3 55.0 + - - +
13D GLY* 2.7 48.7 - - - -
14D MET 3.8 1.1 - - - -
16D THR* 3.3 28.0 - - - +
39D PHE 3.0 6.0 + - - -
40D PRO* 2.8 3.8 - - - +
41D GLU* 2.2 42.0 + - - +
57D GLY* 5.5 2.0 - - - -
60D ILE* 4.5 9.0 - - - -
200D PO3 3.4 13.5 - - - +
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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