Contacts of the strand formed by residues 86 - 91 (chain A) in PDB entry 4HXG
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A MET* 3.6 6.6 - - - +
77A ARG* 2.9 49.1 + - + +
78A PHE 6.1 0.2 - - - -
84A THR 4.4 5.1 + - - -
85A ALA* 1.3 75.3 - - - +
87A ILE* 1.3 62.6 + - - +
88A TRP* 3.3 33.0 + - - +
99A LYS* 4.1 17.2 - - + +
101A LEU 3.5 8.5 - - - +
102A GLU* 2.7 36.3 + - - +
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Residues in contact with ILE 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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74A ALA* 5.1 0.4 - - + -
75A PHE 3.6 7.4 - - - +
76A MET* 4.1 16.6 - - - -
86A GLN* 1.3 73.7 - - - +
88A TRP* 1.3 66.8 + - - +
89A VAL* 5.3 0.2 - - + -
99A LYS* 3.8 2.1 - - - +
100A VAL* 2.7 39.1 + - + +
101A LEU* 2.6 31.3 + - + +
103A ALA* 5.7 1.8 - - + +
106A ILE* 5.0 10.5 - - + -
109A ILE* 3.9 31.0 - - + -
118A LEU* 4.1 22.2 - - + -
120A ALA* 4.9 3.4 - - + -
157A ILE* 4.1 25.1 - - + -
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Residues in contact with TRP 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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74A ALA* 3.2 6.4 - - - +
75A PHE* 2.8 63.8 + + + +
77A ARG* 3.4 29.0 - - + +
86A GLN* 3.3 46.0 + - + +
87A ILE* 1.3 78.8 - - - +
89A VAL* 1.3 66.0 + - - +
90A ALA 4.3 0.2 - - - -
97A ALA* 3.8 26.9 - - + -
98A LYS* 3.4 20.6 - - - -
99A LYS* 3.6 31.3 - - + +
100A VAL* 4.3 0.2 - - - -
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Residues in contact with VAL 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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72A LYS* 4.2 24.7 - - + +
73A ILE 3.5 6.7 - - - +
74A ALA* 4.3 11.4 - - + -
87A ILE* 5.3 0.4 - - + -
88A TRP* 1.3 80.9 - - - +
90A ALA* 1.3 71.6 + - - +
97A ALA* 3.4 2.8 - - - -
98A LYS* 3.1 39.8 + - + +
100A VAL* 3.5 22.6 - - + +
111A TRP* 4.4 7.6 - - + -
118A LEU* 5.1 2.2 - - + -
159A THR* 4.1 24.5 - - + -
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Residues in contact with ALA 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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58A ILE* 4.7 0.4 - - + -
72A LYS* 3.1 6.9 - - - +
73A ILE* 2.7 56.1 + - + -
75A PHE* 3.9 11.4 - - + -
88A TRP 4.3 0.2 - - - -
89A VAL* 1.3 76.9 - - - +
91A ASP* 1.3 60.3 + - - +
95A LEU* 3.7 17.9 - - + +
96A SER 3.3 7.6 - - - +
97A ALA* 3.5 18.6 - - + -
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Residues in contact with ASP 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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71A LYS 3.9 10.2 - - - +
72A LYS* 4.0 4.9 - - + -
90A ALA* 1.3 73.5 - - - +
92A LEU* 1.3 55.3 + - - +
93A LYS* 3.0 23.0 + - - +
94A THR* 2.6 36.7 + - - +
95A LEU* 2.6 36.6 + - - -
96A SER* 3.1 15.5 + - - +
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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