Contacts of the strand formed by residues 69 - 76 (chain D) in PDB entry 3ZWG
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 69 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D VAL* 3.5 30.7 + - + -
9D ILE* 3.1 20.3 - - - +
10D ASP* 3.2 25.3 + - - +
11D GLY* 4.1 1.6 - - - -
39D ASN* 2.8 35.8 + - - +
65D VAL* 3.3 6.9 - - + +
66D ALA* 3.0 27.7 + - + +
67D HIS 4.5 2.7 - - - +
68D GLY* 1.3 82.8 - - - +
70D ALA* 1.3 56.2 + - - +
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Residues in contact with ALA 70 (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 ALA 3.9 0.2 - - - +
8D VAL* 3.4 5.5 - - - -
9D ILE* 2.6 53.5 + - + +
11D GLY* 3.9 7.4 - - - +
14D LEU* 3.9 22.7 - - + -
37D ILE 3.1 12.6 - - - +
38D ASP* 3.9 11.2 - - - -
65D VAL* 4.6 0.4 - - - -
69D LYS* 1.3 74.8 - - - +
71D LEU* 1.3 61.6 + - - +
72D LEU* 4.9 0.9 - - + -
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Residues in contact with LEU 71 (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 ALA 3.8 4.0 - - - -
8D VAL* 4.6 1.1 - - - +
35D VAL* 5.2 1.6 - - + +
36D GLY* 3.2 6.2 - - - -
37D ILE* 2.9 59.7 + - + +
45D TRP* 4.4 9.0 - - + -
61D LEU* 5.0 2.2 - - + -
62D PRO* 3.8 15.7 - - + -
65D VAL* 3.8 24.1 - - + +
70D ALA* 1.3 70.8 - - - +
72D LEU* 1.3 77.0 + - - +
73D TYR* 4.2 12.3 - - + +
90D ILE* 5.6 2.7 - - + -
92D TYR* 3.5 40.6 - - + +
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Residues in contact with LEU 72 (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 ASP 3.9 7.9 - - - +
4D VAL 3.4 17.7 - - - +
5D ALA* 2.4 34.4 - - - +
6D GLY* 3.8 1.2 - - - -
7D ALA 3.1 8.3 + - - +
9D ILE* 4.1 30.7 - - + -
14D LEU* 4.0 25.4 - - + -
18D VAL* 3.5 29.2 - - + -
19D LEU* 4.7 2.9 - - + -
22D VAL* 4.4 9.2 - - + -
35D VAL 3.6 4.9 - - - +
36D GLY* 4.5 2.2 - - - -
62D PRO* 3.7 16.1 - - - +
70D ALA 4.5 1.6 - - - +
71D LEU* 1.3 84.2 - - - +
73D TYR* 1.3 60.8 + - - +
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Residues in contact with TYR 73 (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 ALA* 4.3 4.3 - - - -
22D VAL* 3.9 6.7 - - - +
34D ALA* 3.7 2.1 - - - -
35D VAL* 2.9 43.7 + - + +
50D THR* 3.2 34.7 + - + -
52D PHE* 3.9 14.9 - + - -
57D SER* 3.8 17.6 - - - -
59D ILE* 3.5 43.4 + - + -
61D LEU* 3.7 27.0 - - + +
62D PRO* 4.5 0.4 - - + -
71D LEU* 4.2 11.9 - - + -
72D LEU* 1.3 76.2 - - - +
74D ASN* 1.3 83.0 + - - +
90D ILE* 3.9 18.4 - - + -
104D PHE* 5.2 4.5 - + - -
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Residues in contact with ASN 74 (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 ALA* 3.5 23.0 - - - +
22D VAL* 4.1 17.4 + - + +
25D ALA* 6.2 0.6 - - - +
26D LEU* 3.8 34.3 - - + +
33D ILE* 3.2 16.2 - - - +
35D VAL* 4.6 0.9 - - - +
57D SER* 2.6 40.7 + - - -
58D ASP 5.0 1.0 + - - -
59D ILE* 3.4 11.8 - - - +
73D TYR* 1.3 94.0 - - - +
75D GLY* 1.3 57.4 + - - +
76D GLN* 6.0 0.2 - - - +
104D PHE* 6.4 0.4 - - - -
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Residues in contact with GLY 75 (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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26D LEU* 3.7 5.3 - - - +
32D LYS* 3.5 1.6 - - - -
33D ILE* 2.9 40.3 + - - +
52D PHE* 4.5 4.9 - - - -
56D THR 3.5 11.9 - - - -
57D SER* 4.1 1.8 - - - -
74D ASN* 1.3 78.7 - - - +
76D GLN* 1.3 61.3 + - - +
86D VAL* 3.9 11.7 - - - -
104D PHE* 5.6 0.4 - - - -
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Residues in contact with GLN 76 (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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26D LEU* 3.6 36.5 - - + +
29D VAL* 4.3 20.2 - - + +
31D ARG 3.6 11.2 - - - +
32D LYS* 4.2 8.1 - - + +
55D GLY* 3.4 3.1 - - - -
56D THR* 3.0 41.3 + - + +
57D SER* 5.6 2.0 - - - -
74D ASN* 6.0 0.2 - - - +
75D GLY* 1.3 76.0 - - - +
77D LYS* 1.3 76.4 + - - +
79D ARG* 5.3 9.1 - - - +
86D VAL* 3.8 7.0 - - - +
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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