Contacts of the helix formed by residues 98 - 103 (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 LEU 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B MET 3.3 19.7 - - - +
84B PHE 4.7 1.8 - - - +
86B GLY* 3.6 15.0 - - - +
96B ALA* 4.2 6.3 - - + -
97B VAL* 1.3 89.2 - - - +
99B HIS* 1.3 66.5 + - - +
100B VAL* 3.0 8.5 - - + +
101B ALA* 3.0 25.5 + - + +
102B LEU 3.6 1.4 + - - -
110B ILE* 3.9 15.3 - - + -
112B VAL* 3.5 32.5 - - + -
117B VAL* 4.4 4.9 - - + -
268B TRP* 3.0 52.1 + - + -
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Residues in contact with HIS 99 (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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83B MET* 4.2 15.2 - - - -
97B VAL* 3.5 30.5 - - + +
98B LEU* 1.3 73.4 - - - +
100B VAL* 1.3 68.7 + - + +
102B LEU* 3.2 29.5 + - + +
103B ARG* 3.3 28.4 + - - +
268B TRP 4.2 3.9 + - - +
269B VAL* 5.6 2.2 - - - +
270B GLY 5.5 1.6 + - - -
273B TYR* 3.5 56.5 - + + +
276B TRP* 4.4 0.6 - - + +
494B GLU* 3.7 26.7 + - - +
495B HIS* 4.8 4.2 + - - -
509B PHE* 4.1 9.9 - + - -
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B MET* 4.4 7.0 - - + +
84B PHE* 3.9 49.8 - - + +
97B VAL 4.9 2.0 - - - +
98B LEU* 4.4 15.0 - - + -
99B HIS* 1.3 83.7 - - + +
101B ALA* 1.3 63.0 + - + +
103B ARG* 3.5 22.0 + - - +
104B ASN* 3.3 20.1 + - - +
110B ILE* 5.1 4.3 - - + -
300B HIS* 5.2 0.9 + - - -
303B ASP* 3.7 28.1 - - - +
495B HIS* 3.9 9.2 - - + -
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Residues in contact with ALA 101 (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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98B LEU* 3.0 26.9 + - + +
100B VAL* 1.3 80.7 - - - +
102B LEU* 1.3 65.0 + - - +
104B ASN* 3.1 16.9 + - - +
110B ILE* 3.7 27.6 - - + -
117B VAL* 4.1 17.0 - - + -
118B MET* 3.5 16.6 - - - +
121B VAL* 3.9 2.8 - - + +
268B TRP* 4.4 5.4 - - + -
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Residues in contact with LEU 102 (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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98B LEU 3.9 6.1 - - - +
99B HIS* 3.2 24.2 + - - +
101B ALA* 1.3 78.8 - - - +
103B ARG* 1.3 57.2 + - - +
104B ASN 3.5 0.4 + - - -
105B ARG* 5.4 1.0 + - - -
118B MET* 5.6 0.2 - - - +
121B VAL* 3.9 20.6 - - + +
125B LEU* 4.2 11.3 - - - +
266B TRP* 4.1 14.4 - - + -
268B TRP* 3.9 11.2 - - + -
269B VAL* 3.9 33.2 - - + -
273B TYR 4.1 4.9 - - - +
276B TRP* 3.8 33.3 - - + +
277B SER* 3.8 30.5 - - - +
296B LEU* 4.3 4.5 - - - +
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Residues in contact with ARG 103 (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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99B HIS* 3.3 28.9 + - - -
100B VAL* 3.7 11.7 - - - +
102B LEU* 1.3 77.4 - - - +
104B ASN* 1.3 59.3 + - - +
105B ARG* 2.8 17.1 + - - +
276B TRP* 3.1 33.9 - - - +
296B LEU* 3.5 35.0 - - + +
299B ALA* 3.6 20.0 - - + +
300B HIS* 3.2 20.4 - - - +
303B ASP* 2.7 44.8 + - - +
491B ALA* 3.8 6.2 - - - +
494B GLU* 2.7 29.9 + - - -
495B HIS* 3.7 10.7 + - - -
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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