Contacts of the strand formed by residues 86 - 94 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ARG 4.6 2.2 - - - -
32A LYS* 4.5 17.7 - - - +
33A ILE* 4.4 10.1 - - + -
52A PHE* 4.1 8.7 - - + -
54A SER 3.2 8.7 - - - +
75A GLY 4.0 14.8 - - - -
76A GLN 3.8 24.5 - - - +
77A LYS 4.1 0.2 - - - +
85A GLY* 1.3 74.5 - - - +
87A VAL* 1.3 60.4 + - - +
104A PHE* 3.9 20.7 - - + -
105A SER* 3.8 0.7 - - - -
106A VAL* 2.8 53.2 + - + +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A PHE* 3.6 2.2 - - - -
53A ARG* 2.8 39.4 + - + -
54A SER* 2.9 22.4 + - - +
85A GLY* 4.8 1.8 - - - -
86A VAL* 1.3 81.9 - - - +
88A GLY* 1.3 60.4 + - - +
104A PHE* 3.2 9.9 - - - +
105A SER* 3.2 26.9 - - - +
106A VAL 3.9 9.4 - - - +
107A PRO* 5.1 2.0 - - + -
133A TYR* 3.4 36.6 - - + +
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Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TYR* 3.1 13.2 - - - -
52A PHE* 4.4 0.7 - - - -
53A ARG* 4.4 1.6 - - - -
87A VAL* 1.3 77.8 - - - +
89A VAL* 1.3 69.5 + - - +
103A LEU* 3.3 3.9 - - - +
104A PHE* 2.7 55.9 + - - -
133A TYR* 5.4 0.9 - - - -
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A THR* 3.2 4.8 - - - +
51A TYR* 2.8 38.9 + - + +
88A GLY* 1.3 80.8 - - - +
90A ILE* 1.3 72.9 + - - +
101A ALA* 4.4 0.7 - - + -
102A VAL 3.0 10.5 - - - +
103A LEU* 4.3 6.7 - - + -
104A PHE* 4.0 0.8 - - - -
128A ALA* 3.7 12.9 - - + +
132A MET* 3.8 20.0 - - - -
133A TYR* 3.8 35.9 - - + +
136A LEU* 3.8 24.9 - - + -
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Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 4.5 18.4 - - + -
37A ILE* 4.9 10.8 - - + -
49A ASN 3.6 4.5 - - - +
50A THR* 3.9 15.0 - - + +
61A LEU* 4.0 11.0 - - + -
71A LEU* 5.7 1.1 - - + -
73A TYR* 3.9 24.2 - - + -
89A VAL* 1.3 77.5 - - - +
91A ALA* 1.3 64.1 + - - +
92A TYR* 3.7 32.5 - - + -
100A LEU 3.6 0.7 - - - +
101A ALA* 3.2 5.5 - - - -
102A VAL* 2.7 46.5 + - + +
104A PHE* 4.0 23.6 - - + -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ALA* 4.2 0.2 - - - -
48A MET* 2.9 40.6 + - + +
49A ASN* 2.9 21.8 + - - +
61A LEU* 4.5 1.0 - - - +
90A ILE* 1.3 76.7 - - - +
92A TYR* 1.3 63.6 + - - +
99A THR* 4.4 3.1 - - + -
100A LEU 3.4 5.4 - - - +
126A LYS 3.9 5.4 - - - +
128A ALA* 3.9 27.4 - - + +
132A MET* 5.1 3.6 - - - -
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Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 5.4 2.7 - - + -
45A TRP* 3.9 26.5 - + + -
46A THR 3.4 12.6 - - - -
47A ALA* 3.2 26.5 - - + -
48A MET* 3.6 3.6 - - - -
61A LEU* 3.6 12.7 - - + +
62A PRO* 2.9 50.8 + - - +
63A HIS 4.2 1.6 - - - -
65A VAL* 4.0 11.7 - - + -
71A LEU* 3.6 30.6 - - + +
90A ILE* 3.7 27.4 - - + -
91A ALA* 1.3 74.9 - - - +
93A SER* 1.3 60.2 + - - +
99A THR* 3.5 3.6 - - - +
100A LEU* 2.9 43.7 + - + +
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A THR 3.9 0.2 - - - +
45A TRP* 3.3 4.5 - - - +
46A THR* 2.7 53.2 + - - -
48A MET* 3.5 24.6 - - - +
92A TYR* 1.3 73.7 - - - +
94A MET* 1.3 65.5 + - - +
98A ASN 3.5 7.2 - - - -
125A GLN* 4.3 22.6 + - - -
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Residues in contact with MET 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LYS* 4.4 9.6 - - + -
44A THR 3.7 4.7 - - - -
45A TRP* 3.7 27.1 - - + +
93A SER* 1.3 82.2 + - - +
95A SER* 1.3 58.0 + - - +
96A ASP* 2.9 40.5 + - - +
97A GLY* 3.0 15.9 + - - -
98A ASN* 2.8 27.5 + - + +
99A THR 4.6 0.4 - - - +
100A LEU* 4.1 28.0 - - + +
121A VAL* 4.1 14.1 - - + -
125A GLN* 5.9 0.5 + - - -
156A TYR* 5.4 0.7 - - + -
158A LEU* 3.8 31.2 - - + -
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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