Contacts of the strand formed by residues 86 - 94 (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 VAL 86 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31G ARG 4.6 1.8 - - - -
32G LYS* 4.5 17.0 - - - +
33G ILE* 4.4 10.5 - - + -
52G PHE* 4.1 8.5 - - + -
54G SER 3.2 9.4 - - - +
75G GLY* 4.0 14.6 - - - -
76G GLN 3.9 24.0 - - - +
77G LYS 4.2 0.2 - - - +
85G GLY* 1.3 75.1 - - - +
87G VAL* 1.3 62.5 + - - +
104G PHE* 3.9 20.5 - - + -
105G SER* 3.8 0.9 - - - -
106G VAL* 2.8 57.1 + - + +
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Residues in contact with VAL 87 (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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52G PHE* 3.6 1.7 - - - -
53G ARG* 2.8 40.0 + - + -
54G SER* 2.8 23.8 + - - +
85G GLY* 4.8 1.8 - - - +
86G VAL* 1.3 86.3 - - - +
88G GLY* 1.3 60.7 + - - +
104G PHE* 3.2 10.5 - - - +
105G SER* 3.2 26.9 - - - +
106G VAL 3.9 6.5 - - - +
107G PRO* 5.0 2.2 - - + -
133G TYR* 3.4 36.3 - - + +
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Residues in contact with GLY 88 (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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51G TYR* 3.1 11.4 - - - -
52G PHE* 4.4 1.6 - - - -
53G ARG* 4.4 2.0 - - - -
87G VAL* 1.3 78.2 - - - +
89G VAL* 1.3 69.4 + - - +
103G LEU* 3.3 3.5 - - - +
104G PHE* 2.7 57.2 + - - +
133G TYR* 5.5 0.9 - - - -
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Residues in contact with VAL 89 (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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50G THR* 3.2 4.7 - - - -
51G TYR* 2.8 39.4 + - + +
88G GLY* 1.3 80.7 - - - +
90G ILE* 1.3 72.3 + - - +
102G VAL 3.2 9.2 - - - +
103G LEU* 4.4 8.5 - - + -
104G PHE* 4.1 0.6 - - - -
128G ALA* 3.6 14.0 - - + +
132G MET* 3.7 29.6 - - + -
133G TYR* 3.8 35.9 - - + +
136G LEU* 3.7 17.7 - - + -
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Residues in contact with ILE 90 (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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35G VAL* 4.5 18.2 - - + -
37G ILE* 5.0 8.3 - - + -
49G ASN 3.6 3.1 - - - -
50G THR* 4.0 14.1 - - + +
61G LEU* 4.0 13.0 - - + -
71G LEU* 5.7 1.3 - - + -
73G TYR* 3.9 25.4 - - + -
89G VAL* 1.3 78.8 - - - +
91G ALA* 1.3 63.9 + - - +
92G TYR* 3.8 31.9 - - + -
100G LEU 3.6 0.7 - - - +
101G ALA* 3.2 6.1 - - - -
102G VAL* 2.8 45.1 + - + +
104G PHE* 4.0 24.2 - - + -
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Residues in contact with ALA 91 (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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48G MET* 2.9 41.8 + - + +
49G ASN* 2.9 21.0 + - - +
61G LEU* 4.5 1.0 - - - +
90G ILE* 1.3 76.9 - - - +
92G TYR* 1.3 63.8 + - - +
99G THR* 4.3 3.1 - - + -
100G LEU 3.4 5.6 - - - +
126G LYS 3.9 5.2 - - - +
128G ALA* 3.9 26.7 - - + +
132G MET* 5.1 3.4 - - - -
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Residues in contact with TYR 92 (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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37G ILE* 5.4 2.0 - - + -
45G TRP* 3.9 25.6 - + + -
46G THR 3.3 11.7 - - - +
47G ALA* 3.2 27.6 - - + -
48G MET* 3.6 2.9 - - - -
61G LEU* 3.6 12.5 - - + +
62G PRO* 2.8 50.6 + - - +
63G HIS 4.3 1.3 - - - -
65G VAL* 4.0 11.4 - - + -
71G LEU* 3.5 31.0 - - + +
90G ILE* 3.8 27.1 - - + -
91G ALA* 1.3 73.9 - - - +
93G SER* 1.3 60.0 + - - +
99G THR* 3.5 3.6 - - - +
100G LEU* 2.9 45.3 + - + +
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Residues in contact with SER 93 (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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44G THR 3.8 0.3 - - - +
45G TRP* 3.3 4.2 - - - +
46G THR* 2.7 54.5 + - - -
48G MET* 3.5 25.5 - - - +
92G TYR* 1.3 72.6 - - - +
94G MET* 1.3 66.1 + - - +
98G ASN 3.5 9.0 - - - -
125G GLN* 4.3 21.9 + - - -
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Residues in contact with MET 94 (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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43G LYS* 4.4 9.6 - - + -
44G THR 3.6 4.0 - - - -
45G TRP* 3.8 27.1 - - + -
92G TYR 4.5 0.2 - - - +
93G SER* 1.3 82.6 + - - +
95G SER* 1.3 58.7 + - - +
96G ASP* 2.9 41.2 + - - +
97G GLY* 2.9 15.9 + - - -
98G ASN* 2.8 26.8 + - + +
99G THR 4.6 0.7 - - - +
100G LEU* 4.2 26.5 - - + +
121G VAL* 4.0 14.6 - - + -
125G GLN* 5.9 0.7 + - - +
156G TYR* 5.3 0.9 - - + -
158G LEU* 3.7 31.6 - - + -
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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