Contacts of the strand formed by residues 734 - 740 (chain A) in PDB entry 1KEK
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 TYR 734 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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708A LEU* 3.8 29.6 - - + -
709A ALA 3.4 18.8 - - - -
710A LYS* 3.4 42.5 + - + -
725A GLU* 3.7 4.2 - - - +
726A ALA* 2.8 35.0 + - + +
730A GLU 4.2 6.3 - - - -
731A LEU* 3.7 21.8 - - + -
732A LYS 3.0 6.8 - - - +
733A GLY* 1.3 82.5 - - - +
735A LYS* 1.3 56.9 + - - +
787A LYS* 4.2 15.9 - - + +
790A VAL* 3.9 28.0 - - + +
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Residues in contact with LYS 735 (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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707A VAL* 3.6 1.4 - - - +
708A LEU* 3.5 6.4 - - - +
709A ALA* 2.7 37.1 + - - +
711A GLU* 4.7 18.2 - - + +
714A LEU* 3.5 31.6 - - + -
723A ALA* 3.8 17.0 - - + -
724A LEU 3.1 13.7 - - - +
725A GLU* 4.3 19.8 + - + +
733A GLY 4.7 4.0 - - - +
734A TYR* 1.3 79.3 - - - +
736A PHE* 1.3 60.3 + - - +
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Residues in contact with PHE 736 (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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684A TRP* 4.0 7.2 - + - -
689A CYS* 3.8 4.9 - - - -
691A GLN* 3.4 61.5 - - + +
693A ASN* 3.3 30.7 - - - -
706A PRO* 4.4 3.4 - - + -
707A VAL 3.4 12.8 - - - -
708A LEU* 4.3 4.7 - - + -
723A ALA* 3.4 1.5 - - - -
724A LEU* 2.7 42.8 + - + +
726A ALA* 4.2 8.5 - - + +
735A LYS* 1.3 73.7 - - - +
737A ARG* 1.3 62.5 + - - +
738A ILE* 3.3 32.1 - - + -
797A LYS* 5.1 4.9 - - - -
801A PHE* 4.0 22.9 - + - -
2233A SF4 4.4 0.4 - - - -
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Residues in contact with ARG 737 (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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684A TRP* 3.8 18.8 - - + +
706A PRO* 3.6 1.0 - - - +
707A VAL* 2.7 50.2 + - + +
720A ASN 3.8 5.8 + - - -
721A PHE* 3.5 33.7 - - + -
722A THR* 2.6 54.8 + - - +
723A ALA* 4.3 6.1 - - + -
736A PHE* 1.3 78.4 - - - +
738A ILE* 1.3 77.2 + - - +
739A GLN* 2.9 33.2 + - + +
740A ILE 5.7 0.2 - - - +
774A GLN* 3.2 23.0 + - - +
777A ASN* 3.4 9.5 + - - -
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Residues in contact with ILE 738 (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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684A TRP* 3.4 58.7 - - + +
693A ASN* 3.8 13.0 - - - +
695A CYS* 4.0 14.1 - - - -
704A ILE* 3.8 20.2 - - + -
705A LEU 4.2 0.4 - - - -
706A PRO* 4.1 14.1 - - + -
736A PHE* 3.3 34.1 - - + -
737A ARG* 1.3 78.5 + - - +
739A GLN* 1.3 60.1 + - - +
740A ILE* 3.8 15.4 + - + -
762A LEU* 4.5 2.2 - - + -
2233A SF4 3.9 16.4 - - - -
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Residues in contact with GLN 739 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704A ILE* 3.8 0.3 - - - -
705A LEU* 2.9 46.8 + - + +
707A VAL* 4.1 13.9 - - + -
721A PHE* 3.5 6.1 - - - -
737A ARG* 2.9 40.7 + - - +
738A ILE* 1.3 72.9 - - - +
740A ILE* 1.3 85.5 + - - +
741A ASN 3.6 1.0 + - - -
774A GLN* 2.9 23.2 + - - +
777A ASN* 3.2 19.7 - - - +
778A LEU* 3.7 23.4 + - + +
781A ALA* 3.8 11.2 - - + -
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Residues in contact with ILE 740 (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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681A VAL* 4.7 0.7 - - + -
682A PRO* 3.4 51.4 - - + +
683A GLN* 4.8 0.2 - - - -
684A TRP* 4.5 13.0 - - + +
703A ALA 3.9 4.3 - - - +
704A ILE* 3.8 23.6 - - + -
737A ARG* 5.7 0.2 - - - +
738A ILE* 3.8 18.7 + - + -
739A GLN* 1.3 98.9 + - - +
741A ASN* 1.3 67.3 + - - +
742A THR* 3.4 25.7 + - + -
745A CYS* 5.1 0.2 - - + -
762A LEU* 4.0 9.9 - - + -
774A GLN* 4.0 14.8 - - + +
778A LEU* 4.3 2.9 - - - +
2234A SF4 5.0 1.8 - - - -
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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