Contacts of the strand formed by residues 704 - 709 (chain B) 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 ILE 704 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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695B CYS* 3.6 25.6 - - + +
696B ALA* 3.9 26.8 - - + +
699B CYS* 4.5 4.1 - - + +
702B SER* 3.3 6.2 + - - +
703B ALA* 1.3 83.2 - - - +
705B LEU* 1.3 64.0 + - - +
706B PRO* 3.7 7.3 - - - +
738B ILE* 3.6 31.2 - - + -
739B GLN 3.7 3.6 - - - +
740B ILE* 3.8 12.8 - - + -
751B CYS* 3.5 33.9 - - + -
762B LEU* 4.6 1.1 - - + -
822B ARG* 4.0 11.6 + - - -
3234B SF4 3.5 18.6 - - - -
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Residues in contact with LEU 705 (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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702B SER 5.8 0.9 - - - +
703B ALA 4.2 0.4 - - - -
704B ILE* 1.3 75.4 - - - +
706B PRO* 1.3 80.6 - - + +
707B VAL* 3.5 3.4 + - + +
739B GLN* 2.9 41.1 + - + +
741B ASN* 6.2 0.4 - - + -
778B LEU* 4.3 15.7 - - + -
781B ALA* 3.7 41.1 - - + +
782B ALA* 4.0 9.6 - - + +
786B VAL* 4.9 17.5 - - + -
804B PRO* 5.9 7.6 - - + -
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Residues in contact with PRO 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693B ASN* 3.5 27.8 - - - +
696B ALA* 3.5 23.8 - - + -
704B ILE 3.7 8.3 - - - +
705B LEU* 1.3 98.4 - - + +
707B VAL* 1.3 59.8 + - - +
708B LEU 4.2 0.7 + - - -
736B PHE* 4.5 1.3 - - + -
737B ARG 3.5 7.0 - - - +
738B ILE* 4.0 9.9 - - + -
786B VAL* 6.0 1.0 - - - +
800B GLN* 3.6 22.0 - - + +
801B PHE* 4.0 19.9 - - + -
822B ARG* 5.4 2.7 - - - +
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Residues in contact with VAL 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B LEU* 3.7 14.6 - - + +
706B PRO* 1.3 77.8 - - - +
708B LEU* 1.3 62.6 + - - +
709B ALA* 4.0 13.7 - - + -
714B LEU* 5.1 0.2 - - + -
721B PHE* 4.3 13.7 - - + -
735B LYS 5.2 0.7 - - - +
736B PHE* 3.4 11.7 - - - -
737B ARG* 2.7 45.2 + - + +
739B GLN* 4.1 5.8 - - + -
781B ALA* 3.7 29.6 - - + +
784B ILE* 3.5 31.9 - - + -
801B PHE* 4.8 0.4 - - - -
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Residues in contact with LEU 708 (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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706B PRO 4.1 1.0 + - - -
707B VAL* 1.3 73.0 - - - +
709B ALA* 1.3 59.9 + - - +
726B ALA* 4.2 14.1 - - + -
731B LEU* 4.0 16.4 - - + -
734B TYR* 3.6 36.6 - - + -
735B LYS 3.5 3.8 - - - +
736B PHE* 4.5 7.2 - - + -
784B ILE* 4.1 3.9 - - - +
785B PRO 4.2 0.9 - - - +
787B LYS* 2.8 46.6 + - + +
790B VAL* 3.6 31.0 - - + -
801B PHE* 3.8 31.6 - - + -
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Residues in contact with ALA 709 (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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707B VAL* 4.2 6.7 - - + -
708B LEU* 1.3 74.8 - - - +
710B LYS* 1.3 65.0 + - - +
713B GLU* 3.4 10.5 - - + +
714B LEU* 3.4 34.5 - - + -
734B TYR* 3.4 8.6 - - - -
735B LYS* 2.7 41.7 + - + +
784B ILE* 4.2 11.9 - - + -
787B LYS* 4.1 0.4 - - - +
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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