Contacts of the helix formed by residues 932 - 937 (chain D) in PDB entry 3KKA
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 ALA 932 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908D THR* 6.5 0.2 - - - +
909D VAL* 3.6 8.3 - - - +
930D TYR 3.3 1.3 + - - -
931D THR* 1.3 83.4 + - - +
933D ILE* 1.3 60.1 + - - +
934D GLU* 4.2 20.0 - - + -
935D LYS* 3.0 38.2 + - - +
936D VAL* 3.4 10.0 + - - +
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Residues in contact with ILE 933 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903D GLY 5.7 3.8 - - - +
904D VAL* 3.5 27.1 - - + -
906D PHE* 4.3 19.5 - - + +
907D ARG 5.0 2.0 - - - +
908D THR* 3.7 33.6 - - - +
909D VAL* 3.8 8.5 - - - +
912D TRP* 3.9 22.9 - - + -
932D ALA* 1.3 66.8 - - - +
934D GLU* 1.3 65.1 + - - +
935D LYS 3.0 6.1 + - - -
936D VAL* 3.1 26.7 + - + +
937D VAL* 3.3 19.9 + - + +
965D LEU* 4.7 3.1 - - + -
969D VAL* 6.3 1.3 - - + -
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Residues in contact with GLU 934 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929A ARG* 2.9 46.2 + - - +
930A TYR* 5.1 3.7 + - - -
960A LEU* 4.0 28.3 - - + +
963A HIS* 3.4 10.7 - - - -
932D ALA* 4.2 14.8 - - + +
933D ILE* 1.3 80.6 - - - +
935D LYS* 1.3 72.3 + - + +
937D VAL* 4.1 11.6 - - - +
938D GLN* 4.3 6.4 + - - +
964E GLY* 5.0 6.4 - - - -
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Residues in contact with LYS 935 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929D GLY 3.5 19.5 + - - +
930D TYR* 3.4 20.0 - - + -
931D THR* 3.2 26.1 + - - +
932D ALA* 3.0 20.9 + - - +
933D ILE 3.0 0.8 - - - -
934D GLU* 1.3 94.7 - - + +
936D VAL* 1.3 64.0 + - - +
937D VAL 3.2 1.6 - - - -
938D GLN* 2.7 36.1 + - - +
960E TYR* 4.5 24.3 + - - +
961E SER* 5.2 2.2 - - - +
964E GLY* 6.1 2.0 - - - +
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Residues in contact with VAL 936 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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909D VAL* 3.9 22.4 - - + -
912D TRP* 3.8 26.5 - - + -
925D PHE* 4.2 16.8 - - + -
930D TYR* 4.1 6.7 - - + -
932D ALA 3.5 15.3 - - - +
933D ILE* 3.1 12.2 + - + +
935D LYS* 1.3 73.3 - - - +
937D VAL* 1.3 58.0 + - - +
938D GLN 3.0 4.7 - - - -
939D MET* 2.8 51.0 + - - +
962D LEU* 3.4 10.9 - - + +
965D LEU* 4.1 17.9 - - + -
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Residues in contact with VAL 937 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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959A THR* 5.9 0.7 - - - +
960A LEU* 3.5 20.6 - - + -
904D VAL* 5.4 1.8 - - + -
933D ILE* 3.6 23.6 - - + +
934D GLU* 4.1 9.2 - - - +
936D VAL* 1.3 82.8 - - + +
938D GLN* 1.3 57.8 + - + +
962D LEU* 4.2 6.7 - - - -
965D LEU* 4.3 24.2 - - + +
966D LYS* 3.1 27.5 - - - +
969D VAL* 3.4 42.0 - - + -
970D ASN* 4.4 4.6 + - - +
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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