Contacts of the strand formed by residues 89 - 94 (chain A) in PDB entry 2PWA
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 GLN 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLY 5.8 0.2 - - - +
33A SER 3.2 14.5 + - - +
34A CYS* 3.3 7.3 - - - +
35A VAL* 2.8 27.7 + - - +
51A GLY 5.2 1.5 + - - +
52A ARG* 2.9 31.6 + - - +
53A ALA 4.2 0.2 - - - -
54A GLN* 3.4 26.4 + - - +
88A THR* 1.3 76.8 + - - +
90A LEU* 1.3 72.6 + - - +
91A PHE* 3.3 33.2 - - + -
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Residues in contact with LEU 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* 3.4 10.5 - - + +
37A VAL* 4.3 8.1 - - + -
42A ILE* 4.3 8.5 - - + -
49A PHE* 3.5 38.8 - - + -
52A ARG* 2.8 15.7 + - - +
53A ALA* 3.3 12.1 - - + +
54A GLN 3.0 25.1 + - - -
74A ALA* 3.8 10.5 - - + +
77A VAL* 3.6 36.1 - - + -
78A GLY 4.2 12.6 - - - +
88A THR* 3.9 12.8 - - + +
89A GLN* 1.3 82.4 + - - +
91A PHE* 1.3 62.7 + - - +
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Residues in contact with PHE 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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34A CYS* 3.6 29.4 - - + -
35A VAL 2.9 8.2 + - - -
36A TYR* 3.2 46.1 - + + +
37A VAL 2.8 27.9 + - - -
42A ILE* 3.9 2.7 - - - -
54A GLN* 3.3 17.5 - - + -
56A VAL* 3.7 21.8 - - + -
89A GLN* 3.3 33.7 - - + -
90A LEU* 1.3 81.6 - - - +
92A GLY* 1.3 62.6 + - - +
93A VAL 3.9 0.3 + - - -
121A ARG* 3.7 38.4 - - + -
122A ASN 5.9 0.4 - - - -
123A CYS* 4.1 0.2 - - - -
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Residues in contact with GLY 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 VAL 3.7 3.4 - - - -
41A GLY 5.2 0.4 - - - -
42A ILE* 3.5 20.0 - - - +
54A GLN 2.8 13.7 + - - -
55A MET* 3.5 20.9 - - - +
56A VAL* 2.9 28.6 + - - +
57A LYS 3.4 3.5 + - - -
91A PHE* 1.3 72.5 - - - +
93A VAL* 1.3 62.3 + - - -
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Residues in contact with VAL 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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36A TYR* 3.9 20.0 - - + -
37A VAL 3.1 10.5 + - - +
38A ILE* 3.4 11.1 - - + +
39A ASP 2.9 26.0 + - - -
41A GLY* 5.0 1.5 - - - -
55A MET* 4.2 0.6 - - - +
56A VAL* 3.8 17.5 - - + -
57A LYS* 3.4 17.0 - - + -
59A TYR* 4.2 3.8 - - + -
91A PHE 4.6 0.9 - - - +
92A GLY* 1.3 77.4 - - - +
94A LYS* 1.3 59.4 + - - +
95A VAL* 3.2 21.4 + - + -
110A GLY* 4.1 19.5 - - - +
113A PHE* 4.2 5.4 - - + -
114A VAL* 3.9 10.3 - - + -
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Residues in contact with LYS 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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39A ASP 3.2 4.3 - - - -
40A THR* 2.8 23.9 + - - +
41A GLY 4.0 4.3 - - - +
55A MET* 3.8 14.5 - - + +
57A LYS 2.9 10.0 + - - +
58A THR* 3.6 11.2 - - - +
59A TYR* 3.0 26.8 + - - -
60A TYR* 3.6 9.5 - - + -
62A SER* 3.6 21.3 - - - +
63A SER 4.1 4.0 - - - +
64A ARG 3.3 18.8 - - - +
93A VAL* 1.3 68.0 - - - +
95A VAL* 1.3 58.7 + - - +
96A LEU 2.8 29.6 + - - +
97A ASP 3.7 2.6 - - - -
98A ASP* 2.7 24.1 + - - -
3004A NO3 3.1 22.5 + - - -
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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