Contacts of the strand formed by residues 734 - 738 (chain B) in PDB entry 1KT8
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 GLN 734 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728B LEU* 3.1 8.6 - - - -
729B TYR* 2.8 65.2 + - + +
730B GLY* 4.8 1.4 - - - -
732B ASP* 3.3 28.5 - - - +
733B HIS* 1.3 76.3 - - - +
735B LEU* 1.3 63.9 + - - +
736B THR* 3.6 6.3 + - + +
762B ASN* 4.7 12.1 - - - +
790B THR* 4.0 28.1 + - + +
791B ILE 3.1 15.0 - - - +
792B THR* 4.0 4.7 - - + +
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Residues in contact with LEU 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B LEU* 3.9 22.7 - - + -
727B TRP 4.0 3.8 - - - -
728B LEU* 4.1 2.9 - - + -
734B GLN* 1.3 75.5 - - - +
736B THR* 1.3 59.2 + - - +
743B ILE* 3.7 32.5 - - + -
745B VAL* 5.1 5.8 - - + -
759B PRO* 3.0 23.4 - - - +
791B ILE* 2.9 42.9 + - + +
792B THR 3.5 23.3 - - - +
793B MET* 3.5 17.3 - - - +
796B LEU* 4.3 19.5 - - + -
823B ILE* 5.4 0.9 - - + -
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Residues in contact with THR 736 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B ARG* 5.5 2.2 + - - +
726B LEU* 5.2 0.4 - - - +
727B TRP* 2.8 36.2 + - - +
728B LEU 4.5 0.4 - - - -
729B TYR* 3.5 33.0 - - + -
734B GLN* 3.9 9.2 - - + +
735B LEU* 1.3 74.8 - - - +
737B GLU* 1.3 70.9 + - - +
742B ASN* 5.1 0.7 - - - +
743B ILE* 3.4 16.1 + - - +
759B PRO* 3.6 10.4 - - - +
764B VAL* 4.9 11.7 - - + -
765B ILE* 3.7 29.8 - - + +
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Residues in contact with GLU 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B ARG* 2.2 54.6 + - - +
726B LEU* 3.8 5.4 - - - +
727B TRP* 2.9 31.5 + - + -
736B THR* 1.3 88.0 + - - +
738B VAL* 1.3 58.2 + - - +
739B GLY 5.2 0.9 - - - +
741B MET 3.0 17.3 - - - +
742B ASN* 3.6 11.0 - - - +
743B ILE* 4.1 7.4 - - - +
765B ILE* 3.6 6.4 - - + -
766B LEU 3.3 20.5 + - - -
900B ILP 2.8 33.1 + - + -
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Residues in contact with VAL 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B LEU* 3.0 45.8 - - + -
724B GLN* 4.1 8.1 - - - +
725B VAL 3.2 9.6 - - - +
726B LEU* 4.0 12.8 - - + +
737B GLU* 1.3 72.9 - - - +
739B GLY* 1.3 61.2 + - - +
740B THR 3.0 0.9 + - - -
741B MET* 2.9 54.8 + - + +
742B ASN 4.1 3.1 - - - +
743B ILE* 4.2 10.3 - - + -
809B PHE 5.3 0.4 - - - -
810B GLY* 4.1 14.4 - - - +
820B VAL* 5.5 2.7 - - + -
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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