Contacts of the helix formed by residues 83 - 92 (chain A) in PDB entry 1WH1
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 ASN 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A TYR* 3.6 9.4 + - - -
50A ILE* 4.0 8.8 - - - +
81A VAL* 3.8 1.3 - - - +
82A GLN* 1.3 100.1 + - - +
84A ARG* 1.3 66.1 + - - +
85A GLU* 4.5 4.3 - - + +
86A GLU* 3.5 33.7 + - + +
87A ALA* 3.0 21.5 + - - +
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Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A THR* 5.9 1.4 - - - +
38A VAL* 3.1 36.4 + - + +
39A CYS* 3.8 27.7 - - - +
40A TYR* 3.3 34.0 + - + +
50A ILE* 3.8 7.9 - - + -
83A ASN* 1.3 70.3 - - - +
85A GLU* 1.3 82.7 + - + +
87A ALA* 2.7 20.1 + - - +
88A VAL* 3.1 9.7 + - + +
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Residues in contact with GLU 85 (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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83A ASN* 3.5 4.4 - - + +
84A ARG* 1.3 90.1 + - + +
86A GLU* 1.3 54.1 + - - +
88A VAL* 2.7 11.7 + - - +
89A ALA* 2.4 37.6 + - + +
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Residues in contact with GLU 86 (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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81A VAL* 4.6 8.3 - - + -
82A GLN 5.2 0.7 - - - +
83A ASN* 3.5 34.4 + - + +
84A ARG 3.1 0.6 - - - -
85A GLU* 1.3 79.4 - - - +
87A ALA* 1.3 59.4 + - - +
89A ALA* 3.3 21.9 - - - +
90A LEU* 2.7 52.5 + - + +
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Residues in contact with ALA 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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38A VAL* 4.5 7.2 - - + +
50A ILE* 3.7 31.2 - - + -
73A ILE* 5.3 0.4 - - + -
76A ILE* 3.1 16.9 - - + +
81A VAL* 4.0 8.5 - - + +
83A ASN 3.0 13.4 + - - +
84A ARG 2.7 18.6 + - - +
86A GLU* 1.3 71.8 - - - +
88A VAL* 1.3 56.8 + - - +
91A LEU* 2.9 30.8 - - - +
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Residues in contact with VAL 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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36A LEU 5.5 2.7 - - - +
37A THR* 5.9 0.4 - - - -
38A VAL* 2.8 38.6 - - + -
84A ARG* 3.1 12.9 + - + +
85A GLU* 2.7 11.1 + - - +
87A ALA* 1.3 77.0 - - - +
89A ALA* 1.3 61.7 + - - +
90A LEU 3.1 1.3 - - - -
91A LEU* 2.7 13.8 + - + +
92A THR* 2.6 40.5 + - + +
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Residues in contact with ALA 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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85A GLU* 2.4 21.6 + - + +
86A GLU* 3.3 25.1 - - - +
88A VAL* 1.3 72.6 - - - +
90A LEU* 1.3 55.8 + - - +
92A THR* 2.5 44.0 + - - +
93A SER* 3.3 3.2 + - - -
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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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76A ILE* 4.0 32.8 - - + +
77A ASN* 5.3 2.9 - - + +
79A ILE* 3.9 38.1 - - + -
81A VAL* 4.0 20.0 - - + -
86A GLU* 2.7 30.3 + - + +
89A ALA* 1.3 72.1 - - - +
91A LEU* 1.3 66.7 + - + +
92A THR 3.0 1.2 + - - -
93A SER* 3.2 25.5 + - - +
96A ASN* 4.0 19.9 + - - +
99A PHE* 3.4 8.8 - - + -
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Residues in contact with LEU 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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27A ARG* 4.8 1.7 + - - -
34A LEU* 3.4 50.6 - - + +
36A LEU* 4.0 15.9 - - + -
76A ILE* 3.0 37.5 - - + -
87A ALA 2.9 21.1 - - - +
88A VAL* 2.7 16.4 + - + +
90A LEU* 1.3 70.6 - - - +
92A THR* 1.3 59.8 + - + +
93A SER 3.4 1.3 - - - -
99A PHE* 3.5 22.7 - - + -
101A LEU* 3.7 22.9 - - + -
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Residues in contact with THR 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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27A ARG* 5.3 2.5 - - - +
88A VAL* 2.6 40.8 - - + +
89A ALA* 2.5 27.6 + - - +
91A LEU* 1.3 83.5 - - + +
93A SER* 1.3 57.8 + - - +
94A GLU* 3.9 1.7 + - - +
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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