Contacts of the helix formed by residues 93 - 100 (chain A) in PDB entry 2WJP
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 GLY 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A VAL* 4.1 9.2 - - - -
70A ALA 3.8 13.0 - - - -
72A PRO* 6.3 0.2 - - - -
92A VAL* 1.3 75.9 - - - +
94A ASP* 1.3 66.9 + - - -
95A ILE 3.3 2.9 - - - -
96A GLU* 3.2 5.0 + - - +
97A LEU* 3.2 21.7 + - - +
165A THR* 3.4 24.8 + - - -
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Residues in contact with ASP 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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16A THR* 3.3 26.6 - - + +
19A SER* 4.9 1.0 + - - +
20A CYS* 3.7 28.5 - - - -
69A VAL* 4.2 3.4 - - - +
70A ALA 4.9 1.6 + - - -
72A PRO* 4.7 7.5 - - - +
93A GLY* 1.3 71.8 - - - -
95A ILE* 1.3 81.2 + - - +
97A LEU* 3.2 8.6 + - - +
98A PHE* 2.9 28.5 + - - +
137A GLY 5.6 0.5 - - - +
142A PRO* 4.5 2.6 - - - +
143A ALA* 4.2 14.6 + - - +
144A LEU* 4.1 13.0 + - + +
162A GLN* 4.0 14.3 + - - +
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Residues in contact with ILE 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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93A GLY 3.3 1.2 - - - -
94A ASP* 1.3 87.2 + - - +
96A GLU* 1.3 57.6 + - - +
98A PHE* 3.2 4.6 + - + +
99A CYS* 2.9 38.9 + - - -
137A GLY* 4.6 4.7 - - - -
143A ALA* 3.6 28.5 - - + -
156A LEU* 4.6 7.0 - - + -
158A LEU* 3.8 38.4 - - + -
162A GLN* 3.7 32.3 - - + +
166A THR* 3.7 26.5 - - + +
169A LEU* 5.7 0.2 - - + -
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Residues in contact with GLU 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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92A VAL* 3.7 14.8 - - + -
93A GLY 3.2 11.1 + - - +
95A ILE* 1.3 74.8 - - - +
97A LEU* 1.3 66.0 + - - +
99A CYS* 3.2 2.3 + - - +
100A ARG* 2.9 50.5 + - - +
165A THR 3.6 17.3 - - - +
166A THR* 3.6 8.8 + - - +
167A SER* 2.8 36.0 + - - -
168A SER* 2.5 33.9 + - - -
1456A CL 3.6 10.3 - - + -
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Residues in contact with LEU 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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3A TYR* 3.4 32.0 + - + +
20A CYS* 4.4 4.7 - - + -
23A PHE* 4.3 10.6 - - + -
24A PHE* 3.8 33.7 - - + -
67A LEU* 4.7 0.7 - - + -
69A VAL* 4.0 19.5 - - + -
92A VAL* 4.1 17.3 - - + -
93A GLY 3.2 11.1 + - - +
94A ASP* 3.2 5.8 + - - +
96A GLU* 1.3 78.8 - - - +
98A PHE* 1.3 61.8 + - - +
100A ARG* 3.4 12.4 + - - +
101A GLU* 3.4 23.6 + - - +
144A LEU* 4.1 24.7 - - + -
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Residues in contact with PHE 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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94A ASP 2.9 12.9 + - - +
95A ILE 3.4 9.2 - - - +
96A GLU 3.2 0.2 - - - -
97A LEU* 1.3 74.4 - - - +
99A CYS* 1.3 67.1 + - - +
101A GLU* 2.9 4.7 + - - +
102A ALA* 2.9 38.6 + - + -
106A ILE* 3.9 13.0 - - + -
143A ALA* 3.3 40.6 - - + -
144A LEU* 3.7 12.2 - - + +
146A LEU* 4.6 0.4 - - + -
147A LEU* 3.6 30.1 - - + -
154A TYR* 3.6 40.6 - + + -
156A LEU* 3.8 32.5 - - + -
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Residues in contact with CYS 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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95A ILE* 2.9 32.0 + - - +
96A GLU* 3.2 6.5 + - - +
98A PHE* 1.3 82.4 - - - +
100A ARG* 1.3 61.0 + - - +
101A GLU 3.3 0.5 + - - -
102A ALA* 3.8 10.8 + - - +
106A ILE* 4.1 15.3 - - + +
156A LEU* 5.4 0.7 - - - -
166A THR* 4.5 1.6 - - - -
168A SER* 3.9 27.2 - - - +
169A LEU* 3.7 39.9 - - - -
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Residues in contact with ARG 100 (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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1A ALA* 4.3 18.3 + - + +
3A TYR* 3.0 38.3 + - - +
67A LEU* 5.3 1.8 - - - +
90A GLU* 2.8 31.9 + - - -
92A VAL* 3.9 11.7 - - - +
96A GLU* 2.9 47.4 + - - +
97A LEU* 3.6 11.2 - - - +
98A PHE 3.2 0.2 - - - -
99A CYS* 1.3 77.3 - - - +
101A GLU* 1.3 73.5 + - - +
102A ALA 5.4 0.2 - - - -
103A GLN* 5.3 2.1 + - - -
167A SER* 5.2 2.4 + - - -
168A SER* 4.3 9.5 + - - +
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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