Contacts of the strand formed by residues 69 - 76 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C VAL* 3.5 31.0 + - + -
9C ILE* 3.1 19.9 - - - +
10C ASP* 3.2 25.0 + - - +
11C GLY* 4.1 1.8 - - - -
39C ASN* 2.8 35.5 + - - +
64C LYS 5.9 0.2 - - - +
65C VAL* 3.3 7.2 - - + +
66C ALA* 3.0 27.5 + - + +
67C HIS 4.6 2.5 - - - +
68C GLY* 1.3 81.0 - - - +
70C ALA* 1.3 56.2 + - - +
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ALA 3.9 0.2 - - - +
8C VAL* 3.4 5.5 - - - -
9C ILE* 2.6 52.4 + - + +
11C GLY* 3.9 7.7 - - - +
14C LEU* 3.9 22.4 - - + -
37C ILE 3.1 13.7 - - - +
38C ASP* 3.9 10.5 - - - -
65C VAL* 4.6 0.7 - - - -
69C LYS* 1.3 73.7 - - - +
71C LEU* 1.3 62.4 + - - +
72C LEU* 4.9 0.4 - - + -
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ALA 3.8 3.8 - - - -
8C VAL* 4.6 1.6 - - - +
35C VAL 5.2 0.7 - - - +
36C GLY* 3.3 3.1 - - - -
37C ILE* 3.0 60.3 + - + +
45C TRP* 4.5 7.9 - - + -
61C LEU* 4.9 2.2 - - + -
62C PRO* 3.9 15.3 - - + -
65C VAL* 3.9 22.9 - - + +
69C LYS 4.5 0.2 + - - -
70C ALA* 1.3 70.3 - - - +
72C LEU* 1.3 81.0 + - - +
73C TYR* 4.2 14.1 - - + +
90C ILE* 5.7 2.0 - - + -
92C TYR* 3.4 43.1 - - + +
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C ASP 4.0 6.3 - - - +
4C VAL 3.5 17.3 - - - +
5C ALA* 2.4 33.6 - - - +
6C GLY* 3.7 6.8 - - - -
7C ALA 3.1 9.3 + - - +
9C ILE* 4.0 37.5 - - + -
14C LEU* 4.0 20.6 - - + -
18C VAL* 3.5 28.3 - - + -
19C LEU* 4.8 3.1 - - + -
22C VAL* 4.4 9.0 - - + -
35C VAL 3.6 4.7 - - - +
36C GLY* 4.5 1.8 - - - -
62C PRO* 3.7 10.2 - - - +
70C ALA 4.4 1.6 - - - +
71C LEU* 1.3 84.8 - - - +
73C TYR* 1.3 61.4 + - - +
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Residues in contact with TYR 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ASN* 4.6 6.1 + - - +
163B PHE* 5.2 0.5 - - - -
5C ALA* 4.3 4.9 - - - -
22C VAL* 3.9 6.3 - - - +
34C ALA* 3.7 1.7 - - - -
35C VAL* 2.9 42.8 + - + +
50C THR* 3.1 34.5 + - + -
52C PHE* 3.9 15.0 - + - -
57C SER* 3.9 16.4 - - - -
59C ILE* 3.6 42.9 + - + -
61C LEU* 3.7 27.5 - - + +
62C PRO* 4.5 0.7 - - + -
71C LEU* 4.2 11.2 - - + -
72C LEU* 1.3 76.7 - - - +
74C ASN* 1.3 84.5 + - - +
90C ILE* 4.0 18.2 - - + -
104C PHE* 5.2 4.5 - + - -
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Residues in contact with ASN 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C ALA* 3.5 22.8 - - - +
22C VAL* 4.1 17.6 + - + -
25C ALA* 6.2 0.2 - - - +
26C LEU* 4.0 33.5 - - + +
33C ILE* 3.2 16.2 - - - +
34C ALA* 4.4 0.4 - - - +
35C VAL* 4.6 1.1 - - - +
57C SER* 2.5 39.8 + - - -
58C ASP 5.0 0.9 + - - -
59C ILE* 3.4 12.6 - - - +
73C TYR* 1.3 94.7 - - - +
75C GLY* 1.3 59.3 + - - +
76C GLN* 6.0 0.2 - - - +
104C PHE* 6.4 0.4 - - - -
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Residues in contact with GLY 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 3.7 5.2 - - - +
32C LYS* 3.4 1.9 - - - -
33C ILE* 2.8 40.3 + - - +
52C PHE* 4.6 4.7 - - - -
56C THR 3.5 11.4 - - - -
57C SER* 4.1 1.8 - - - -
74C ASN* 1.3 79.9 - - - +
76C GLN* 1.3 62.9 + - - +
86C VAL* 4.0 11.6 - - - +
104C PHE* 5.7 0.4 - - - -
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Residues in contact with GLN 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LEU* 3.5 40.9 - - + +
29C VAL* 4.2 19.1 - - + +
31C ARG 3.6 11.2 - - - +
32C LYS* 4.2 2.9 - - + +
55C GLY* 3.4 2.9 - - - -
56C THR* 3.0 42.6 + - + +
57C SER* 5.7 1.6 - - - -
74C ASN* 6.0 0.2 - - - +
75C GLY* 1.3 77.2 - - - +
77C LYS* 1.3 75.3 + - - +
79C ARG* 5.3 9.3 - - - +
86C VAL* 3.9 7.1 - - - +
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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