Contacts of the helix formed by residues 904 - 907 (chain A) in PDB entry 1KQG
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 TRP 904 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A THR* 3.6 34.5 - - + -
52A TYR* 3.6 15.8 - + - -
101A TYR* 3.2 54.1 - + - -
168A GLY* 5.0 4.3 - - - -
448A HIS* 4.0 13.9 - + - -
585A LEU* 3.5 16.1 - - + +
901A PHE* 2.9 39.2 + + - +
903A THR* 1.3 75.5 - - - +
905A THR* 1.3 63.9 + - - +
906A LYS 3.2 3.3 + - - -
907A HIS* 3.2 26.7 + - - +
908A ALA 4.6 0.2 + - - -
1017A MGD 3.6 60.3 - + - +
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Residues in contact with THR 905 (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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52A TYR* 3.3 44.6 - - + +
94A LYS* 4.9 2.2 - - + -
900A HIS* 2.8 29.6 + - - +
901A PHE* 2.8 30.6 + - + +
902A HIS 4.8 0.2 + - - -
903A THR 3.8 0.2 - - - -
904A TRP* 1.3 72.6 - - - +
906A LYS* 1.3 58.8 + - - +
907A HIS 3.1 2.2 - - - -
908A ALA* 2.8 31.6 + - - +
911A ASN* 3.7 23.6 - - - +
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Residues in contact with LYS 906 (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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588A GLU* 2.6 29.5 + - - -
900A HIS* 3.8 13.4 + - + -
902A HIS 5.6 0.2 + - - -
903A THR* 3.0 37.0 + - - +
904A TRP 4.5 0.2 - - - +
905A THR* 1.3 79.5 + - - +
907A HIS* 1.3 61.4 + - + +
908A ALA 3.2 1.7 + - - -
912A ALA* 4.3 1.5 - - - +
975A HIS 3.4 23.1 + - - +
976A TRP* 4.2 3.8 - - + -
977A GLY 3.4 24.2 - - - +
979A GLU 2.6 30.7 + - - +
980A GLY* 4.7 1.3 - - - -
981A VAL* 2.9 25.9 + - - +
982A ALA* 3.4 26.7 + - + +
983A ARG 6.1 0.4 - - - +
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Residues in contact with HIS 907 (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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100A ASP 4.1 0.2 - - - +
101A TYR* 5.6 0.9 - - + -
104A SER* 2.6 37.3 + - - +
105A GLU 4.8 0.5 + - - -
106A ASN* 2.8 34.0 + - + +
585A LEU* 3.8 24.9 - - + -
586A VAL* 3.0 28.6 + - + -
587A THR* 5.0 2.4 - - - +
588A GLU* 5.2 0.6 + - - -
903A THR 3.8 15.3 + - - -
904A TRP* 3.2 21.7 + - - +
905A THR 3.1 1.8 + - - -
906A LYS* 1.3 78.3 + - - +
908A ALA* 1.3 57.3 - - - +
909A LEU 4.1 0.5 + - - -
979A GLU* 3.7 13.8 + - + +
980A GLY* 3.5 16.2 - - - -
981A VAL* 4.1 16.5 - - - +
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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