Contacts of the helix formed by residues 71 - 81 (chain B) in PDB entry 2BXJ
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 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ASN* 4.0 17.2 + - - +
33B TYR* 3.2 59.6 - - + +
34B GLY* 5.6 0.4 - - - -
67B MET* 3.9 3.8 - - + +
68B PRO* 3.2 21.1 + - + +
69B GLU 3.1 0.8 - - - -
70B ASP* 1.3 83.5 - - + +
72B VAL* 1.3 64.7 + - - +
73B ASN 3.5 2.5 - - - -
74B ASP* 3.4 15.9 + - - +
75B ALA* 3.3 20.8 + - - +
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR* 3.8 25.1 - - + +
67B MET* 3.9 20.2 - - + -
68B PRO 3.5 12.1 - - - +
69B GLU* 3.4 24.5 + - - +
71B ARG* 1.3 76.9 - - - +
73B ASN* 1.3 65.9 + - - +
75B ALA* 3.1 5.4 + - + +
76B ALA* 2.9 21.2 + - + +
90B VAL* 3.9 35.6 - - + +
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Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLU 4.9 0.8 + - - -
70B ASP 5.1 3.3 + - - +
71B ARG 3.5 0.4 - - - -
72B VAL* 1.3 79.4 - - - +
74B ASP* 1.3 60.1 + - - +
76B ALA* 3.3 6.0 + - - +
77B ARG* 2.9 41.1 + - - +
80B ARG* 4.3 16.6 - - - +
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Residues in contact with ASP 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TYR* 3.6 26.6 + - + +
70B ASP 4.3 12.9 - - - +
71B ARG* 3.4 14.3 + - - +
72B VAL 3.2 0.8 - - - -
73B ASN* 1.3 78.7 - - - +
75B ALA* 1.3 63.7 + - - +
77B ARG* 3.0 37.2 + - - +
78B GLU* 3.0 23.7 + - - +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ALA 5.8 0.4 - - - -
30B ALA* 5.2 7.6 - - + -
33B TYR* 3.6 32.6 - - + -
67B MET* 4.2 14.1 - - + -
71B ARG 3.3 8.7 + - - +
72B VAL 3.1 9.5 + - - +
74B ASP* 1.3 79.0 - - - +
76B ALA* 1.3 57.6 + - - +
78B GLU* 3.4 2.8 + - - +
79B LEU* 3.0 38.8 + - + +
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B VAL* 2.9 13.3 + - + +
73B ASN* 3.6 13.0 - - - +
74B ASP 3.2 0.2 - - - -
75B ALA* 1.3 74.9 - - - +
77B ARG* 1.3 64.6 + - - +
79B LEU* 3.2 6.9 + - - +
80B ARG* 3.0 53.5 + - - +
88B VAL* 4.7 11.7 - - + -
90B VAL* 4.8 13.0 - - + -
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Residues in contact with ARG 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASN* 2.9 28.4 + - - +
74B ASP* 3.0 36.7 + - - +
76B ALA* 1.3 75.6 - - - +
78B GLU* 1.3 64.8 + - - +
80B ARG* 3.3 22.4 + - - +
81B ILE* 3.6 19.5 + - + +
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ALA* 4.3 18.9 - - + +
32B ASN* 5.3 5.4 + - - -
33B TYR* 2.4 44.0 + - - +
74B ASP 3.0 15.7 + - - +
75B ALA* 3.6 5.6 - - - +
77B ARG* 1.3 77.7 - - - +
79B LEU* 1.3 60.3 + - + +
81B ILE* 3.1 34.2 - - + +
82B ARG* 4.3 4.7 + - - +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL* 5.2 5.4 - - + -
8B ILE* 4.2 12.3 - - + -
25B ILE* 5.0 2.2 - - + +
26B ILE* 4.1 41.1 - - + +
29B ALA* 3.9 27.4 - - + -
30B ALA* 5.6 6.5 - - + +
75B ALA* 3.0 26.4 + - + +
76B ALA* 3.2 5.4 + - - +
78B GLU* 1.3 79.3 - - + +
80B ARG* 1.3 62.6 + - - +
81B ILE 3.3 0.9 + - - -
82B ARG* 3.4 28.7 + - + +
85B VAL* 3.6 13.3 - - + +
88B VAL* 4.4 16.2 - - + -
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Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASN* 4.3 14.3 - - - +
76B ALA* 3.0 37.5 + - - +
77B ARG* 3.3 16.6 + - - +
79B LEU* 1.3 77.3 - - - +
81B ILE* 1.3 61.8 + - + +
82B ARG 3.3 6.4 + - - +
85B VAL* 4.2 13.2 - - + +
87B ARG* 5.7 0.7 - - - +
88B VAL* 3.4 48.0 + - + +
89B MET* 5.6 0.6 - - - +
90B VAL* 6.2 0.4 - - - +
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ARG* 3.6 15.3 - - + +
78B GLU* 3.1 24.2 - - + +
80B ARG* 1.3 75.6 - - + +
82B ARG* 1.3 72.2 + - + +
83B ASP* 3.5 5.0 + - - +
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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