Contacts of the strand formed by residues 88 - 94 (chain A) in PDB entry 1WNA
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 ARG 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A SER 5.1 3.3 + - - +
28A GLU* 2.7 40.4 + - - +
29A ALA 3.5 13.2 + - - +
30A LYS* 3.5 33.2 - - - +
31A VAL* 2.9 30.0 + - - +
87A ARG* 1.3 84.6 - - + +
89A PHE* 1.3 60.5 + - - +
90A TYR* 3.8 24.0 - - + +
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Residues in contact with PHE 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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31A VAL* 3.4 34.3 - - + -
33A LEU* 4.9 10.8 - - + -
78A VAL* 4.3 16.4 - - + -
81A LEU* 4.4 10.3 - - + -
82A LEU* 3.7 37.9 - - + -
86A ALA* 4.0 16.6 - - + -
87A ARG 3.5 24.3 + - - -
88A ARG* 1.3 73.2 - - - +
90A TYR* 1.3 69.0 + - - +
120A PRO* 3.5 4.3 - - - +
121A THR* 2.9 43.0 + - + +
123A PRO* 3.7 26.5 - - + -
126A TYR* 5.3 0.2 - - + -
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Residues in contact with TYR 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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30A LYS* 3.7 44.9 + - + +
31A VAL 2.8 16.0 + - - +
32A TYR* 3.6 35.7 - + + -
33A LEU* 2.9 28.4 + - - +
88A ARG* 3.8 30.7 - - + +
89A PHE* 1.3 75.1 - - - +
91A GLU* 1.3 61.0 + - - +
118A ALA* 3.9 8.7 - - + -
119A ASN 3.2 9.6 - - - +
120A PRO* 3.7 36.1 - - + -
121A THR* 3.4 8.9 - - - +
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Residues in contact with GLU 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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33A LEU 3.2 10.1 - - - +
35A THR* 3.7 23.1 - - + +
41A ARG* 2.8 42.0 + - - -
46A TYR* 3.7 3.6 - - - -
90A TYR* 1.3 73.7 - - - +
92A ALA* 1.3 64.0 - - - +
93A VAL* 3.9 13.3 + - + +
117A ILE 4.2 1.0 - - - +
118A ALA* 3.2 3.4 - - - -
119A ASN* 2.9 33.2 + - + +
121A THR* 4.2 7.9 - - + -
125A ILE* 5.0 0.7 - - - -
126A TYR* 2.7 33.8 + - - +
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Residues in contact with ALA 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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32A TYR* 5.9 0.2 - - - +
33A LEU 2.9 8.6 + - - +
34A ILE* 3.4 12.7 - - + +
35A THR* 2.9 27.9 + - - +
91A GLU* 1.3 74.1 - - - +
93A VAL* 1.3 62.6 + - - +
94A VAL* 5.0 0.7 - - + -
114A VAL* 4.1 25.4 - - + -
117A ILE* 3.8 27.8 - - + -
118A ALA* 4.1 7.6 - - + +
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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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35A THR* 3.4 18.2 - - + +
36A ASP 4.3 1.8 - - - -
37A TRP* 3.9 35.4 - - + +
91A GLU* 3.9 15.5 + - + +
92A ALA* 1.3 74.9 - - - +
94A VAL* 1.3 70.4 + - - +
117A ILE* 3.9 13.0 + - - +
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Residues in contact with VAL 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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34A ILE* 4.5 5.2 - - + -
35A THR 2.9 16.8 + - - +
36A ASP* 3.2 5.6 - - - -
37A TRP* 3.0 25.2 + - - -
92A ALA* 5.0 0.4 - - + +
93A VAL* 1.3 82.4 - - - +
95A SER* 1.3 70.1 + - - +
98A GLU* 5.3 4.7 - - + -
99A MSE 4.1 32.1 - - + +
102A LEU* 3.4 32.5 - - + -
113A ARG* 5.8 4.3 - - - +
117A ILE* 4.0 15.9 - - + -
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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