Contacts of the strand formed by residues 69 - 76 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E VAL* 3.5 30.4 + - + -
9E ILE* 3.1 20.3 - - - +
10E ASP* 3.2 25.8 + - - +
11E GLY* 4.0 1.3 - - - -
39E ASN* 2.8 23.6 + - - +
64E LYS 5.9 0.2 - - - +
65E VAL* 3.2 15.1 - - + +
66E ALA* 3.1 28.0 + - + +
67E HIS 4.5 2.7 - - - +
68E GLY* 1.3 83.1 - - - +
70E ALA* 1.3 59.4 + - - +
10H ASP* 5.5 6.1 + - - -
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Residues in contact with ALA 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ALA 3.9 0.3 - - - +
8E VAL* 3.4 5.9 - - - -
9E ILE* 2.6 56.7 + - + +
11E GLY* 3.9 13.0 - - - +
14E LEU* 3.9 17.0 - - + -
37E ILE 3.1 14.6 - - - +
38E ASP* 3.9 11.0 - - - -
65E VAL* 4.6 0.4 - - - -
69E LYS* 1.3 74.5 - - - +
71E LEU* 1.3 60.4 + - - +
72E LEU* 4.9 0.9 - - + -
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Residues in contact with LEU 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ALA 3.8 4.3 - - - -
8E VAL* 4.6 1.6 - - - +
35E VAL* 5.2 0.9 - - + +
36E GLY* 3.2 4.7 - - - -
37E ILE* 3.0 62.3 + - + +
45E TRP* 4.5 6.5 - - + -
61E LEU* 4.9 2.5 - - + -
62E PRO* 3.9 15.0 - - + -
65E VAL* 3.8 23.4 - - + +
70E ALA* 1.3 70.6 - - - +
72E LEU* 1.3 74.7 + - - +
73E TYR* 4.3 13.0 - - + -
90E ILE* 5.7 1.8 - - + -
92E TYR* 3.5 40.4 - - + +
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Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ASP 3.9 8.1 - - - +
4E VAL 3.4 17.7 - - - +
5E ALA* 2.4 34.2 - - - +
6E GLY* 3.7 1.2 - - - -
7E ALA 3.1 9.3 + - - +
9E ILE* 4.0 37.7 - - + -
14E LEU* 4.0 20.2 - - + -
18E VAL* 3.4 28.9 - - + -
19E LEU* 4.7 2.7 - - + -
22E VAL* 4.4 9.4 - - + -
35E VAL 3.6 4.7 - - - +
36E GLY* 4.5 2.0 - - - -
62E PRO* 3.7 15.9 - - - +
70E ALA 4.4 1.6 - - - +
71E LEU* 1.3 82.4 - - - +
73E TYR* 1.3 61.1 + - - +
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Residues in contact with TYR 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ASN* 4.5 6.4 + - - +
163D PHE* 5.0 0.5 - - - -
5E ALA* 4.3 4.9 - - - -
22E VAL* 3.9 7.0 - - - +
34E ALA* 3.7 2.1 - - - -
35E VAL* 2.8 43.1 + - + +
50E THR* 3.1 34.2 + - + -
52E PHE* 3.9 21.2 - + - -
57E SER* 3.9 10.0 - - - -
59E ILE* 3.5 43.8 + - + -
61E LEU* 3.7 27.0 - - + +
62E PRO* 4.5 1.1 - - + -
71E LEU* 4.3 11.0 - - + -
72E LEU* 1.3 76.7 - - - +
74E ASN* 1.3 82.7 + - - +
90E ILE* 3.9 19.5 - - + -
104E PHE* 5.2 4.5 - + - -
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Residues in contact with ASN 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ALA* 3.6 22.2 - - - +
22E VAL* 4.0 17.6 + - + +
25E ALA* 6.2 0.4 - - - +
26E LEU* 3.8 34.6 - - + +
33E ILE* 3.2 15.9 - - - +
35E VAL* 4.6 1.1 - - - +
57E SER* 2.6 40.2 + - - -
58E ASP 5.0 1.2 + - - -
59E ILE* 3.4 13.7 - - - +
73E TYR* 1.3 93.4 - - - +
75E GLY* 1.3 59.3 + - - +
76E GLN* 5.9 0.2 - - - +
104E PHE* 6.4 0.4 - - - -
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Residues in contact with GLY 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LEU* 3.7 5.9 - - - +
32E LYS* 3.5 1.7 - - - -
33E ILE* 2.9 40.0 + - - +
52E PHE* 4.5 4.9 - - - -
56E THR 3.5 12.1 - - - -
57E SER* 4.1 1.8 - - - -
74E ASN* 1.3 78.2 - - - +
76E GLN* 1.3 61.7 + - - +
86E VAL* 4.0 11.4 - - - +
104E PHE* 5.7 0.4 - - - -
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Residues in contact with GLN 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LEU* 3.6 35.8 - - + +
29E VAL* 4.3 19.4 - - + +
31E ARG 3.6 11.2 - - - +
32E LYS* 4.2 8.5 - - + +
55E GLY* 3.4 2.6 - - - -
56E THR* 3.0 42.5 + - + +
57E SER* 5.6 1.8 - - - -
74E ASN* 5.9 0.2 - - - +
75E GLY* 1.3 76.5 - - - +
77E LYS* 1.3 75.9 + - - +
79E ARG* 5.3 9.3 - - - +
86E VAL* 3.9 7.7 - - - +
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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