Contacts of the strand formed by residues 93 - 99 (chain A) in PDB entry 1WBP
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 THR 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A LYS* 3.9 21.1 - - + -
87A GLY 4.0 8.1 - - - +
88A TRP* 4.2 9.4 - - + +
92A SER* 1.3 83.8 + - - +
94A VAL* 1.3 64.7 + - - +
95A TRP* 3.5 31.0 - - + +
108A MET 3.6 0.9 - - - +
109A LYS* 3.5 0.7 - - - -
110A VAL* 2.7 39.5 + - - +
112A LYS* 4.1 12.8 + - - +
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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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85A LYS* 3.6 10.0 - - - +
86A LEU* 2.8 35.7 + - + -
87A GLY 3.1 7.7 + - - +
93A THR* 1.3 79.3 - - - +
95A TRP* 1.3 67.3 + - - +
107A ALA* 3.9 27.4 - - + -
108A MET 3.4 9.2 - - - +
109A LYS* 4.1 20.4 - - + +
950A ADP 3.6 53.2 - - + +
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Residues in contact with TRP 95 (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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70A VAL* 3.5 50.8 - - + +
71A LYS* 4.8 3.1 - - - -
72A ILE* 3.7 25.6 - - + -
82A VAL* 4.5 10.8 - - + -
84A ARG* 3.3 19.5 - - - +
85A LYS* 3.7 29.4 - - + -
86A LEU* 4.1 4.7 - - - -
93A THR* 3.5 30.3 - - + +
94A VAL* 1.3 78.7 - - - +
96A LEU* 1.3 62.2 + - - +
97A SER 3.5 1.3 + - - -
107A ALA* 3.3 5.4 - - - -
108A MET* 2.7 59.6 + - + +
110A VAL* 3.9 18.5 - - + +
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Residues in contact with LEU 96 (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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82A VAL* 4.0 0.2 - - - -
83A ILE* 2.6 38.9 + - + +
84A ARG* 2.6 47.0 + - + +
86A LEU* 3.7 20.7 - - + +
95A TRP* 1.3 68.8 - - - +
97A SER* 1.3 51.8 + - - +
105A PHE* 3.9 26.0 - - + -
106A VAL 3.6 15.3 - - - +
167A VAL* 4.5 13.5 - - + -
228A ILE* 4.6 5.6 - - + +
231A LEU* 4.3 11.2 - - + -
232A ALA* 3.7 29.2 - - + +
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Residues in contact with SER 97 (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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80A TYR* 4.0 8.7 - - - +
81A HIS 3.3 21.5 - - - -
82A VAL* 3.5 20.0 - - - -
83A ILE* 3.7 3.4 - - - -
96A LEU* 1.3 75.0 - - - +
98A TRP* 1.3 61.3 + - - +
105A PHE* 3.8 4.6 - - - -
106A VAL* 3.0 39.9 + - - +
108A MET* 3.6 25.6 - - - +
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Residues in contact with TRP 98 (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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79A ARG 3.1 4.7 - - - +
80A TYR* 3.5 3.5 - - - -
81A HIS* 2.9 43.8 + + + +
83A ILE* 3.8 8.1 - - + +
97A SER* 1.3 72.1 - - - +
99A ASP* 1.3 71.6 + - - +
100A ILE* 3.4 28.3 + - + +
103A LYS* 3.0 44.8 - - + +
104A LYS* 3.8 15.3 - - - -
105A PHE* 3.7 46.4 - + + -
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Residues in contact with ASP 99 (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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79A ARG* 2.5 52.8 + - - +
80A TYR* 3.7 18.3 + - + -
97A SER 3.9 1.2 + - - -
98A TRP* 1.3 74.3 + - - +
100A ILE* 1.3 57.4 + - - +
101A GLN 2.9 10.0 + - - -
102A GLY* 3.3 10.3 + - - -
103A LYS* 3.0 28.8 + - - -
104A LYS* 2.8 32.9 + - + +
106A VAL* 4.1 10.7 - - + +
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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