Contacts of the helix formed by residues 78 - 91 (chain A) in PDB entry 4OQB
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 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A TYR* 3.0 25.0 + - - +
77A LEU* 1.3 75.4 - - - +
79A TRP* 1.3 66.6 + - - +
80A ASP* 3.3 14.7 + - - +
81A ASP* 3.0 12.1 + - - +
82A GLN* 2.9 20.2 + - - +
242A ASN* 3.7 1.6 - - - -
246A TRP* 3.1 67.1 + - + +
247A ASN* 5.7 1.6 + - - -
250A ASP* 2.8 27.0 + - - +
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Residues in contact with TRP 79 (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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78A ARG* 1.3 72.4 - - - +
80A ASP* 1.3 63.1 + - - +
82A GLN* 3.2 31.8 + - + +
83A GLN* 3.3 36.8 + - + +
86A LYS* 6.3 0.9 - - - -
235A GLU* 3.8 35.7 - - + -
238A LEU* 3.8 32.1 - - + -
239A LYS* 3.7 62.0 - - + +
242A ASN* 2.7 34.9 + - + +
243A ASP* 5.1 5.7 - - + +
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Residues in contact with ASP 80 (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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78A ARG* 3.5 20.1 + - - +
79A TRP* 1.3 77.9 + - + +
81A ASP* 1.3 73.6 + - - +
83A GLN* 3.5 16.5 + - - +
84A LYS* 3.4 17.8 + - - +
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Residues in contact with ASP 81 (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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13A TYR* 2.6 41.3 + - + +
33A LEU* 4.7 13.2 - - + +
77A LEU* 4.7 3.4 - - + -
78A ARG* 3.0 21.5 + - - +
80A ASP* 1.3 87.5 + - - +
82A GLN* 1.3 65.0 + - - +
84A LYS* 3.3 28.2 + - - +
85A VAL* 3.3 26.5 + - - +
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Residues in contact with GLN 82 (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 PHE* 3.3 59.7 - - + +
75A SER* 3.4 12.6 + - - +
77A LEU* 3.0 31.0 + - + -
78A ARG 2.9 14.5 + - - +
79A TRP* 3.4 26.4 - - + +
81A ASP* 1.3 76.2 - - - +
83A GLN* 1.3 57.1 + - + +
85A VAL 3.3 1.9 + - - -
86A LYS* 2.9 29.2 + - - +
242A ASN* 3.3 19.6 - - - +
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Residues in contact with GLN 83 (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 TRP* 3.3 37.9 + - + +
80A ASP* 3.7 13.8 - - - +
81A ASP 3.3 0.6 - - - -
82A GLN* 1.3 77.2 - - + +
84A LYS* 1.3 60.9 + - - +
86A LYS* 3.7 15.3 - - + +
87A LYS* 2.9 35.5 + - + +
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Residues in contact with LYS 84 (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* 3.7 30.0 - - - +
54A PHE* 4.0 22.3 - - + -
80A ASP 3.4 10.0 + - - +
81A ASP* 3.3 24.7 + - - +
82A GLN 3.3 0.4 - - - -
83A GLN* 1.3 78.3 - - - +
85A VAL* 1.3 57.4 + - - +
87A LYS* 4.2 2.6 - - - +
88A THR* 2.5 40.4 + - - +
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Residues in contact with VAL 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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11A VAL* 4.7 9.6 - - + -
33A LEU* 4.4 7.2 - - + -
35A MET* 4.8 9.0 - - + -
54A PHE* 3.9 22.9 - - + -
58A TRP* 4.4 14.6 - - + -
67A PRO* 3.8 24.9 - - + -
71A VAL* 5.5 2.0 - - + -
74A PHE* 4.1 8.5 - - + -
77A LEU* 4.3 18.2 - - + -
81A ASP 3.3 13.4 + - - +
82A GLN 3.3 7.5 + - - +
84A LYS* 1.3 75.5 - - - +
86A LYS* 1.3 58.7 + - - +
88A THR* 3.7 0.8 - - - -
89A ALA* 2.8 29.6 + - - +
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Residues in contact with LYS 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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67A PRO* 4.3 17.3 - - + +
68A ASP* 5.5 9.6 + - - +
74A PHE* 4.0 25.7 - - + -
79A TRP* 6.3 1.0 - - - -
82A GLN* 2.9 16.3 + - - +
83A GLN* 3.7 14.5 - - + +
85A VAL* 1.3 78.8 - - - +
87A LYS* 1.3 61.4 + - + +
89A ALA* 3.6 11.4 - - - +
90A GLU* 3.9 17.5 + - - +
235A GLU* 5.0 8.9 + - - -
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Residues in contact with LYS 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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83A GLN* 2.9 19.9 + - + +
84A LYS* 4.3 3.4 - - - +
86A LYS* 1.3 76.5 - - + +
88A THR* 1.3 65.5 + - - +
89A ALA 3.2 0.2 - - - -
90A GLU* 3.2 24.6 + - + +
91A ALA* 3.3 10.7 + - - +
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Residues in contact with THR 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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54A PHE* 4.0 16.8 - - + -
58A TRP* 3.5 41.0 - - + +
84A LYS* 2.5 29.3 + - - +
85A VAL 4.1 2.0 - - - -
87A LYS* 1.3 75.3 - - - +
89A ALA* 1.3 64.7 + - - +
90A GLU 3.3 0.2 - - - -
91A ALA 3.0 30.2 - - - +
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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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58A TRP* 3.8 19.6 - - + -
63A SER* 5.5 4.2 - - - -
64A ILE 3.6 22.3 + - - +
65A ARG 4.9 2.5 - - - +
67A PRO* 3.4 27.4 - - + -
85A VAL 2.8 18.6 + - - +
86A LYS 3.6 7.9 - - - +
87A LYS 3.2 0.2 - - - -
88A THR* 1.3 78.0 - - - +
90A GLU* 1.3 60.8 + - + +
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Residues in contact with GLU 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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65A ARG 5.5 5.8 - - - +
86A LYS* 4.0 17.4 - - - +
87A LYS* 3.2 16.0 + - + +
89A ALA* 1.3 78.6 - - + +
91A ALA* 1.3 63.2 + - + +
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Residues in contact with ALA 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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58A TRP* 5.2 6.9 - - - +
87A LYS 3.3 9.1 + - - +
88A THR* 3.0 34.1 + - - +
90A GLU* 1.3 82.7 - - + +
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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