Contacts of the strand formed by residues 699 - 706 (chain A) in PDB entry 2KFZ
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 699 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695A ALA* 3.5 11.4 - - + +
696A PRO* 3.0 35.5 + - + +
697A GLU 3.4 13.7 - - - -
698A ASP* 1.3 82.1 + - + +
700A VAL* 1.3 70.8 + - - +
873A ARG* 3.5 42.2 - - - +
874A VAL* 5.2 0.7 - - - -
875A ARG* 6.0 2.7 - - + -
887A GLU* 4.1 11.7 - - + -
888A VAL* 3.3 26.7 - - - +
889A HIS* 3.4 23.4 - + - -
890A LYS 4.0 0.2 - - - +
922A GLU* 4.3 8.5 - - - +
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Residues in contact with VAL 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A ALA* 3.6 7.4 - - - -
699A TYR* 1.3 80.5 - - - +
701A ILE* 1.3 59.8 + - - +
702A VAL* 3.7 15.0 + - + -
887A GLU* 3.4 3.6 - - - -
888A VAL 2.8 40.5 + - - +
890A LYS* 4.3 16.8 - - + -
893A VAL* 3.6 27.1 - - + -
920A SER* 4.5 4.7 - - - -
921A GLY* 3.5 17.7 - - - +
922A GLU* 4.5 13.2 - - - +
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Residues in contact with ILE 701 (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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545A VAL* 5.9 0.4 - - + -
693A PHE* 4.1 3.4 - - + +
694A ILE 4.1 6.7 - - - +
695A ALA* 3.7 31.1 - - + +
700A VAL* 1.3 71.9 - - - +
702A VAL* 1.3 60.4 + - - +
877A ILE* 3.9 13.0 - - + -
878A MET* 6.1 0.2 - - + -
885A VAL* 3.8 20.2 - - + -
886A PHE 3.4 9.6 - - - +
887A GLU* 3.9 16.4 - - + -
920A SER* 3.1 5.9 - - - -
921A GLY 2.9 31.6 + - - +
923A ASN* 3.9 22.9 - - - +
924A TRP* 3.7 24.7 - - + +
927A ALA* 3.2 10.3 - - + +
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Residues in contact with VAL 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700A VAL* 4.0 6.5 - - + -
701A ILE* 1.3 78.4 - - - +
703A SER* 1.3 64.6 + - - +
704A ALA* 5.6 0.9 - - + -
885A VAL* 3.4 5.7 - - - +
886A PHE* 2.8 49.0 + - + +
888A VAL* 3.4 38.8 - - + -
893A VAL* 4.5 8.1 - - + -
896A VAL* 6.1 0.9 - - + -
897A ALA* 5.5 5.8 - - + -
900A ILE* 5.6 7.2 - - + -
918A VAL* 3.8 21.5 - - + -
919A GLY 3.3 10.1 - - - +
920A SER* 3.9 14.4 - - - -
927A ALA* 4.3 0.4 - - - -
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Residues in contact with SER 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A VAL* 1.3 75.0 - - - +
704A ALA* 1.3 60.4 + - - +
705A ASP* 4.1 4.1 + - - +
883A GLU* 2.6 31.1 + - - +
884A LEU 3.8 3.1 - - - -
885A VAL* 4.7 1.6 - - - +
917A GLU 3.5 2.1 - - - +
918A VAL* 3.2 4.7 - - - +
919A GLY 2.8 37.3 + - - +
924A TRP* 5.1 5.6 - - - -
927A ALA* 3.5 31.7 + - - +
928A HIS* 4.2 5.6 + - - -
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Residues in contact with ALA 704 (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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702A VAL* 5.6 0.4 - - + -
703A SER* 1.3 72.7 + - - +
705A ASP* 1.3 59.9 + - - +
883A GLU* 3.2 2.6 - - - -
884A LEU 2.9 40.1 + - - +
886A PHE* 4.2 4.5 - - + -
900A ILE* 3.8 16.2 - - + -
904A MET* 3.4 35.7 - - + +
916A VAL* 4.2 0.9 - - + -
917A GLU 3.5 4.3 - - - -
918A VAL* 4.2 13.0 - - + -
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Residues in contact with ASP 705 (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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703A SER* 5.0 4.5 - - - +
704A ALA* 1.3 76.2 - - - +
706A TYR* 1.3 70.9 + - - +
707A SER* 3.4 11.1 + - - -
882A ASP* 3.3 28.7 + - - +
883A GLU* 3.7 13.2 - - + +
916A VAL* 3.1 7.0 - - - +
917A GLU* 2.7 48.6 + - + +
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Residues in contact with TYR 706 (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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705A ASP* 1.3 74.1 - - - +
707A SER* 1.3 67.3 + - - +
708A GLN 3.1 3.3 + - - -
709A ILE* 3.6 30.2 + - + -
855A ILE* 3.9 15.5 - - + +
856A ILE* 4.3 16.6 - - + -
859A ALA* 3.3 22.8 - - + +
882A ASP* 3.1 37.6 + - + +
884A LEU* 6.1 0.7 - - + -
904A MET* 2.4 53.8 + - + -
908A THR* 3.7 4.3 + - - -
914A LEU* 4.1 28.9 - - + -
915A LEU 3.4 7.0 - - - +
916A VAL* 3.4 19.3 - - + -
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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