Contacts of the helix formed by residues 84 - 98 (chain B) in PDB entry 2KJB
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 ASP 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B HIS 4.8 8.8 - - - +
68B LEU 5.0 6.9 - - - +
82B LEU* 3.7 8.3 - - - +
83B ASP* 1.3 93.4 - - - +
85B ILE* 1.3 58.7 + - - +
86B HIS* 2.8 25.3 + - + +
87B VAL* 3.2 22.2 + - + +
88B ALA* 3.9 4.3 + - - +
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Residues in contact with ILE 85 (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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82B LEU* 6.1 1.8 - - - -
83B ASP 3.8 6.8 + - - +
84B ASP* 1.3 71.5 - - - +
86B HIS* 1.3 76.3 + - + +
88B ALA* 2.9 16.8 + - + +
89B THR* 2.9 31.3 + - + +
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Residues in contact with HIS 86 (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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97A HIS* 3.7 33.8 + + + +
84B ASP* 2.8 13.3 + - + +
85B ILE* 1.3 92.1 - - + +
87B VAL* 1.3 61.5 + - + +
89B THR* 2.6 23.8 + - - -
90B MET* 2.8 20.7 + - - +
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Residues in contact with VAL 87 (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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32B MET* 4.1 25.8 - - + -
68B LEU* 5.6 10.8 - - + -
82B LEU* 5.5 3.8 - - + -
84B ASP* 3.2 17.5 + - + +
86B HIS* 1.3 78.8 - - + +
88B ALA* 1.3 64.7 + - - +
90B MET* 3.9 11.4 - - + -
91B LEU* 2.8 33.7 + - + +
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Residues in contact with ALA 88 (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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36B SER* 4.5 17.0 - - - +
82B LEU* 5.6 9.5 - - + +
84B ASP 3.9 1.9 + - - +
85B ILE* 2.9 22.7 + - + +
87B VAL* 1.3 82.1 - - - +
89B THR* 1.3 64.3 + - + +
91B LEU* 3.5 6.0 + - - +
92B LYS* 3.3 18.8 + - - +
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Residues in contact with THR 89 (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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85B ILE* 2.9 20.0 + - + +
86B HIS* 2.6 24.1 + - - -
88B ALA* 1.3 73.2 - - + +
90B MET* 1.3 64.3 + - - +
92B LYS* 3.0 12.6 + - + +
93B GLN* 2.9 27.5 + - - +
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Residues in contact with MET 90 (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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90A MET* 5.5 20.6 - - + +
93A GLN* 5.3 9.0 - - + +
94A ALA* 5.3 17.7 - - + +
97A HIS* 6.4 1.8 - - - -
86B HIS* 2.8 23.7 + - - +
87B VAL* 3.2 13.9 + - + +
89B THR* 1.3 74.0 + - - +
91B LEU* 1.3 62.1 + - - +
93B GLN* 3.3 14.2 + - + +
94B ALA* 3.1 21.5 + - - +
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Residues in contact with LEU 91 (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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16A VAL* 5.3 9.0 - - + -
20A PHE* 5.1 16.4 - - + -
29B ILE* 5.5 17.0 - - + +
32B MET* 5.6 15.3 - - + -
33B GLU* 5.6 10.8 - - + +
87B VAL* 2.8 24.4 + - + +
88B ALA* 3.7 6.3 - - - +
90B MET* 1.3 75.8 - - - +
92B LYS* 1.3 64.3 + - - +
94B ALA* 3.1 11.4 + - + +
95B ILE* 3.0 46.1 + - + +
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Residues in contact with LYS 92 (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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88B ALA 3.3 10.7 + - - +
89B THR* 3.0 14.0 + - + +
91B LEU* 1.3 80.4 - - - +
93B GLN* 1.3 51.5 + - - +
95B ILE* 3.2 9.3 + - + +
96B HIS* 2.6 44.4 + - + +
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Residues in contact with GLN 93 (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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90A MET* 6.3 1.1 - - + -
89B THR* 2.9 13.9 + - - +
90B MET* 3.5 15.8 - - - +
91B LEU 3.2 0.2 - - - -
92B LYS* 1.3 77.1 - - - +
94B ALA* 1.3 62.6 + - - +
96B HIS* 3.4 8.7 + - + +
97B HIS* 3.2 23.6 + - - +
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Residues in contact with ALA 94 (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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16A VAL* 5.6 8.5 - - + -
19A ILE* 6.2 4.0 - - + -
90A MET* 5.1 17.9 - - + +
90B MET 3.1 12.0 + - - +
91B LEU* 3.1 16.2 + - + +
93B GLN* 1.3 77.4 - - - +
95B ILE* 1.3 59.6 + - + +
97B HIS* 3.5 4.9 + - - +
98B ALA* 3.1 21.5 + - - +
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Residues in contact with ILE 95 (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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12A THR* 5.7 10.1 - - + -
13A LEU* 6.1 2.7 - - + -
16A VAL* 4.6 28.3 - - + -
33B GLU* 5.3 10.1 - - - +
91B LEU* 3.0 39.5 + - + +
92B LYS* 3.7 8.5 - - + +
94B ALA* 1.3 73.7 - - - +
96B HIS* 1.3 66.8 + - - +
97B HIS 3.1 1.8 - - - -
98B ALA* 3.0 26.9 - - + +
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Residues in contact with HIS 96 (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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92B LYS* 2.6 26.9 + - + +
93B GLN* 3.6 11.0 - - + +
94B ALA 3.3 0.2 - - - -
95B ILE* 1.3 74.9 - - - +
97B HIS* 1.3 59.9 + - - +
99B ASN 4.6 6.4 + - - +
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Residues in contact with HIS 97 (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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86A HIS* 4.3 28.2 - + - -
93B GLN 3.2 15.4 + - - +
94B ALA* 3.9 4.0 - - - +
95B ILE 3.1 0.4 - - - -
96B HIS* 1.3 76.3 - - - +
98B ALA* 1.3 71.0 + - - +
99B ASN* 2.6 15.3 + - - -
100B HIS* 3.4 20.5 + - - +
101B PRO* 5.2 4.2 - - - +
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Residues in contact with ALA 98 (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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12A THR* 5.9 7.9 - - + +
15A ARG* 4.5 14.6 + - + +
16A VAL* 6.5 0.4 - - + -
94B ALA 3.1 10.1 + - - -
95B ILE* 3.0 27.8 + - + +
97B HIS* 1.3 79.0 - - - +
99B ASN* 1.3 69.8 + - + +
100B HIS 4.0 1.0 + - - -
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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