Contacts of the helix formed by residues 75 - 85 (chain B) in PDB entry 1KOJ
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 GLY 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B LYS 2.8 15.0 + - - -
73B SER 3.1 2.8 + - - -
74B ARG* 1.3 80.3 - - - +
76B VAL* 1.3 64.8 + - - +
77B GLU 3.3 3.0 + - - -
78B ALA* 3.4 11.6 + - - +
79B ALA* 3.0 23.4 + - - +
502B VAL* 4.2 0.8 - - - +
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Residues in contact with VAL 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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71B ALA* 3.1 36.4 + - + +
72B LYS* 4.4 0.4 + - - +
74B ARG* 3.5 1.3 - - + -
75B GLY* 1.3 75.1 - - - +
77B GLU* 1.3 61.4 + - + +
79B ALA* 3.2 3.1 + - - +
80B ARG* 2.8 29.0 + - + +
306B PHE* 4.8 9.0 - - + -
311B LEU* 4.9 5.6 - - + -
317B VAL* 4.7 10.8 - - + -
498B PHE* 4.6 2.8 - - + -
499B VAL* 3.9 44.0 - - + +
502B VAL* 4.0 15.9 - - + -
503B VAL* 4.2 11.7 - - + -
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS* 4.1 17.5 - - - +
75B GLY 3.3 0.6 - - - -
76B VAL* 1.3 76.4 - - - +
78B ALA* 1.3 63.1 + - - +
80B ARG* 3.0 33.9 + - - +
81B GLU* 2.9 28.4 + - + +
310B PRO* 6.0 1.0 - - - +
311B LEU* 3.9 43.0 + - + +
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Residues in contact with ALA 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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75B GLY* 3.4 13.2 + - - +
77B GLU* 1.3 78.0 - - - +
79B ALA* 1.3 62.2 + - - +
81B GLU* 3.3 8.6 + - - +
82B SER* 3.0 26.4 + - - -
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Residues in contact with ALA 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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75B GLY 3.0 18.1 + - - +
76B VAL 3.5 4.0 - - - +
78B ALA* 1.3 74.4 - - - +
80B ARG* 1.3 67.2 + - - +
82B SER* 3.2 9.1 + - - -
83B MET* 3.1 18.2 + - - +
89B ILE* 4.9 3.3 - - + +
365B LYS* 6.3 0.7 - - - +
498B PHE* 3.6 11.0 - - + -
502B VAL* 3.7 31.6 - - + -
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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
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76B VAL* 2.8 16.3 + - - +
77B GLU* 3.2 43.2 + - - +
79B ALA* 1.3 77.3 - - - +
81B GLU* 1.3 84.0 + - - +
83B MET* 3.1 4.0 + - - +
84B PHE* 3.1 37.8 + - + -
306B PHE* 3.0 57.6 + - + -
307B ARG* 3.4 27.4 + - - +
309B THR 4.6 5.3 + - - -
311B LEU* 4.9 5.3 - - - +
314B ASN* 4.3 5.9 - - - +
498B PHE* 3.7 15.4 - - + -
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU* 2.9 17.2 + - + +
78B ALA* 3.7 9.6 - - - +
79B ALA 3.3 0.2 - - - -
80B ARG* 1.3 106.5 + - - +
82B SER* 1.3 60.8 + - - +
84B PHE* 3.3 2.1 + - - +
85B ASN* 2.8 45.8 + - - +
307B ARG* 2.9 46.3 + - - +
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Residues in contact with SER 82 (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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78B ALA 3.0 14.5 + - - -
79B ALA* 3.2 11.8 + - - -
81B GLU* 1.3 76.3 - - - +
83B MET* 1.3 60.2 + - - +
85B ASN 3.6 0.3 + - - -
86B GLY 3.5 1.4 + - - -
87B GLU* 3.0 62.8 + - - +
89B ILE* 3.7 20.0 - - - -
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Residues in contact with MET 83 (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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79B ALA 3.1 11.0 + - - +
80B ARG 3.5 5.4 - - - +
81B GLU 3.1 0.2 - - - -
82B SER* 1.3 76.5 - - - +
84B PHE* 1.3 89.9 + - + +
86B GLY* 3.2 11.1 + - - -
87B GLU 5.0 1.4 - - - +
89B ILE* 3.7 22.8 - - + +
97B VAL* 3.3 24.2 - - - +
98B LEU* 3.3 17.5 - - - +
99B HIS* 4.2 19.7 - - - +
100B VAL* 4.4 7.6 - - + +
306B PHE* 4.5 0.4 - - + -
495B HIS* 3.8 24.5 - - + +
498B PHE* 4.0 34.5 - - + -
509B PHE* 4.4 0.9 - - - -
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Residues in contact with PHE 84 (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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80B ARG* 3.1 41.7 + - + +
81B GLU 4.0 1.1 - - - +
83B MET* 1.3 104.3 - - + +
85B ASN* 1.3 61.7 + - - +
86B GLY 3.2 1.5 + - - -
98B LEU* 4.7 0.9 - - - +
100B VAL* 3.9 32.0 - - + +
110B ILE* 4.0 25.7 - - + +
303B ASP* 3.7 39.0 - - + -
304B GLN* 5.7 0.2 - - - -
306B PHE* 4.0 9.4 - + - -
307B ARG* 3.5 47.9 + - + +
495B HIS* 4.3 0.9 - + - -
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Residues in contact with ASN 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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81B GLU* 2.8 34.9 + - - +
82B SER 4.2 3.1 - - - +
83B MET 3.2 0.4 - - - -
84B PHE* 1.3 76.5 - - - +
86B GLY* 1.3 61.3 + - - +
87B GLU* 3.4 19.1 + - + +
110B ILE* 4.5 5.4 - - - +
111B VAL* 3.6 15.8 + - - +
307B ARG* 3.4 19.7 + - - +
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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