Contacts of the helix formed by residues 82 - 92 (chain A) in PDB entry 6BJO
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 THR 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A GLY 3.4 15.7 - - - +
41A ALA* 5.8 1.1 - - - -
47A LEU* 4.8 0.9 - - - -
81A LYS* 1.3 77.8 - - - +
83A LYS* 1.3 65.5 + - - +
84A VAL* 3.6 9.7 + - - +
85A GLU* 3.2 20.0 + - - +
86A VAL* 3.0 23.3 + - - +
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Residues in contact with LYS 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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37A ILE* 3.8 38.9 + - + +
38A GLY* 4.2 1.8 - - - -
39A GLY 3.0 37.9 - - - +
40A GLY 3.7 3.6 + - - +
47A LEU* 4.3 7.7 - - + +
82A THR* 1.3 70.6 - - - +
84A VAL* 1.3 70.2 - - + +
86A VAL* 3.3 0.4 + - - -
87A ALA* 2.9 25.2 + - - +
201A DUY 4.2 19.0 - - + +
104B LEU* 4.9 19.1 - - - +
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Residues in contact with VAL 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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82A THR* 3.3 9.1 + - - +
83A LYS* 1.3 80.1 - - + +
85A GLU* 1.3 58.6 + - - +
87A ALA* 3.3 7.8 + - + +
88A LYS* 3.0 29.6 + - + +
201A DUY 4.9 6.3 - - + -
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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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81A LYS* 4.0 25.3 - - + +
82A THR* 3.2 19.8 + - - +
84A VAL* 1.3 78.4 - - - +
86A VAL* 1.3 50.9 - - - +
88A LYS* 3.3 6.5 + - - +
89A MET* 2.8 33.5 + - - +
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Residues in contact with VAL 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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37A ILE* 3.6 21.5 - - + -
47A LEU* 4.1 19.7 - - + -
70A ILE* 5.0 9.2 - - + -
73A VAL* 5.2 1.6 - - + -
78A ILE* 3.8 30.3 - - + -
81A LYS* 3.7 19.3 - - + -
82A THR 3.0 18.8 + - - +
83A LYS* 3.8 4.7 - - - +
85A GLU* 1.3 76.5 - - - +
87A ALA* 1.3 56.2 + - - +
89A MET* 3.0 24.0 + - - +
90A ILE* 3.0 32.4 + - + +
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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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37A ILE* 4.1 0.8 - - + +
83A LYS 2.9 13.5 + - - +
84A VAL* 3.4 10.8 - - + +
86A VAL* 1.3 74.6 - - - +
88A LYS* 1.3 57.1 + - - +
90A ILE* 3.2 2.6 + - - -
91A GLN* 2.8 38.7 + - - +
201A DUY 3.5 55.5 - - + +
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Residues in contact with LYS 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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84A VAL* 3.0 19.4 + - + +
85A GLU* 4.0 4.5 - - - +
87A ALA* 1.3 74.0 - - - +
89A MET* 1.3 61.8 + - - +
91A GLN* 3.8 13.7 + - + +
92A GLU* 3.0 36.0 + - - +
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Residues in contact with MET 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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73A VAL* 4.0 27.3 - - + +
76A ARG* 3.6 39.7 - - + +
77A SER 3.7 10.3 - - - +
78A ILE* 3.6 19.1 - - + -
81A LYS* 3.5 23.6 - - - +
85A GLU 2.8 16.5 + - - +
86A VAL* 3.0 12.3 + - - +
88A LYS* 1.3 72.4 - - - +
90A ILE* 1.3 60.2 + - - +
92A GLU* 3.9 9.7 + - - +
93A VAL* 3.1 28.3 + - + +
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Residues in contact with ILE 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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27A LYS* 2.9 19.6 + - - -
33A ILE* 4.1 15.7 - - + -
35A ILE* 5.0 5.8 - - + -
70A ILE* 5.0 7.2 - - + -
73A VAL* 3.9 27.8 - - + -
86A VAL* 3.0 29.1 + - + +
87A ALA 3.8 4.0 - - - +
89A MET* 1.3 77.4 - - - +
91A GLN* 1.4 64.0 + - - +
93A VAL* 3.2 12.5 + - - +
97A VAL* 4.2 14.3 - - + +
99A ILE* 4.4 10.5 - - + -
201A DUY 3.8 44.9 - - + +
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Residues in contact with GLN 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 LYS* 3.6 6.6 + - - +
31A ASN* 2.9 34.9 + - - +
32A LEU* 5.7 2.4 - - + +
87A ALA* 2.8 26.4 + - - +
88A LYS* 3.8 15.1 - - - +
90A ILE* 1.4 70.0 - - - +
92A GLU* 1.4 61.9 + - + +
93A VAL 3.2 1.6 + - - -
94A LYS* 3.6 5.4 + - - -
201A DUY 2.9 49.3 + - + +
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Residues in contact with GLU 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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88A LYS* 3.0 25.7 + - - +
89A MET* 4.1 9.7 - - - +
90A ILE 3.2 0.2 - - - -
91A GLN* 1.4 78.3 - - + +
93A VAL* 1.3 62.4 + - + +
94A LYS* 3.6 16.0 + - - +
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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