Contacts of the strand formed by residues 69 - 76 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ASP* 5.4 5.2 + - - -
69F LYS* 5.4 14.4 - - - +
8G VAL* 3.5 29.9 + - + -
9G ILE* 3.1 20.9 - - - +
10G ASP* 3.2 25.2 + - - +
11G GLY* 4.0 1.3 - - - -
39G ASN* 2.8 31.0 + - - +
64G LYS 5.9 0.2 - - - +
65G VAL* 3.3 6.7 - - + +
66G ALA* 3.0 28.1 + - + +
67G HIS 4.6 2.7 - - - +
68G GLY* 1.3 82.3 - - - +
70G ALA* 1.3 59.7 + - - +
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Residues in contact with ALA 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ALA 4.0 0.3 - - - +
8G VAL* 3.4 5.4 - - - -
9G ILE* 2.6 53.2 + - + +
11G GLY* 3.8 8.0 - - - +
14G LEU* 3.9 22.7 - - + -
37G ILE 3.1 13.9 - - - +
38G ASP* 3.9 10.1 - - - -
65G VAL* 4.6 0.9 - - - -
69G LYS* 1.3 74.2 - - - +
71G LEU* 1.3 59.8 - - - +
72G LEU* 4.9 0.7 - - + -
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Residues in contact with LEU 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G ALA 3.8 4.0 - - - -
8G VAL* 4.6 1.6 - - + +
35G VAL* 5.2 1.3 - - + +
36G GLY* 3.2 6.1 - - - -
37G ILE* 3.0 64.0 + - + +
45G TRP* 4.5 6.3 - - + -
61G LEU* 4.8 2.5 - - + -
62G PRO* 3.8 18.2 - - + -
65G VAL* 3.9 20.3 - - + +
69G LYS 4.5 0.2 + - - -
70G ALA* 1.3 70.5 - - - +
72G LEU* 1.3 77.8 + - - +
73G TYR* 4.2 13.5 - - + -
90G ILE* 5.7 2.2 - - + -
92G TYR* 3.5 42.0 - - + +
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Residues in contact with LEU 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G ASP 3.9 7.4 - - - +
4G VAL 3.4 17.0 - - - +
5G ALA* 2.4 34.3 - - - +
6G GLY* 3.7 6.8 - - - -
7G ALA 3.1 9.2 + - - +
9G ILE* 4.0 32.1 - - + -
14G LEU* 4.0 25.1 - - + -
18G VAL* 3.5 30.1 - - + -
19G LEU* 4.7 2.9 - - + -
22G VAL* 4.4 9.6 - - + -
35G VAL 3.6 4.3 - - - +
36G GLY* 4.5 1.8 - - - -
62G PRO* 3.7 10.0 - - - +
70G ALA 4.7 0.9 - - - -
71G LEU* 1.3 83.5 - - - +
73G TYR* 1.3 61.2 + - - +
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Residues in contact with TYR 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G ALA* 4.3 4.0 - - - +
22G VAL* 3.9 6.6 - - - +
34G ALA* 3.6 2.1 - - - -
35G VAL* 2.9 44.1 + - + +
50G THR* 3.0 35.0 + - + -
52G PHE* 3.9 21.2 - + - -
57G SER* 3.9 8.7 - - - -
59G ILE* 3.5 44.5 + - + -
61G LEU* 3.8 27.2 - - + +
62G PRO* 4.5 0.4 - - + -
71G LEU* 4.2 10.8 - - + -
72G LEU* 1.3 76.5 - - - +
74G ASN* 1.3 82.7 + - - +
90G ILE* 3.9 19.3 - - + -
104G PHE* 5.2 4.3 - + - -
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Residues in contact with ASN 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G ALA* 3.5 22.8 - - - +
22G VAL* 4.1 17.8 + - + +
25G ALA* 6.2 0.2 - - - +
26G LEU* 3.8 34.0 - - + +
33G ILE* 3.3 15.7 - - - +
34G ALA* 4.4 0.4 - - - +
35G VAL* 4.6 0.9 - - - +
57G SER* 2.5 39.7 + - - -
58G ASP 5.0 0.7 + - - -
59G ILE* 3.4 13.1 - - - +
73G TYR* 1.3 93.5 - - - +
75G GLY* 1.3 60.0 + - - +
76G GLN* 5.9 0.2 - - - +
104G PHE* 6.4 0.4 - - - -
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Residues in contact with GLY 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G LEU* 3.7 5.3 - - - +
32G LYS* 3.4 1.6 - - - -
33G ILE* 2.9 40.6 + - - +
52G PHE* 4.6 4.9 - - - -
56G THR 3.4 11.4 - - - -
57G SER* 4.1 2.0 - - - -
74G ASN* 1.3 78.9 - - - +
76G GLN* 1.3 62.6 + - - +
86G VAL* 4.0 11.8 - - - +
104G PHE* 5.6 0.2 - - - -
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Residues in contact with GLN 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G LEU* 3.6 41.0 - - + +
29G VAL* 4.3 20.0 - - + +
31G ARG 3.6 11.2 - - - +
32G LYS* 4.2 3.4 - - + +
55G GLY* 3.3 3.1 - - - -
56G THR* 3.0 42.8 + - + +
57G SER* 5.6 2.2 - - - -
75G GLY* 1.3 75.5 - - - +
77G LYS* 1.3 74.1 + - - +
79G ARG* 5.3 9.7 - - - +
86G 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