Contacts of the helix formed by residues 757 - 771 (chain A) in PDB entry 1WKB
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 PHE 757 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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675A LEU* 4.1 12.6 - - + -
697A LEU* 3.7 20.2 - - + -
700A GLN* 3.9 34.1 - - + -
701A ILE* 4.1 6.7 - - + -
704A PHE* 3.9 23.8 - + + -
753A VAL* 2.9 22.9 + - + +
756A ALA* 1.3 80.8 - - - +
758A TYR* 1.3 91.8 + + - +
759A SER 3.5 1.1 + - - -
760A ILE 3.6 1.6 + - - -
761A MET* 3.1 33.2 + - + +
790A TRP* 3.9 14.4 - + - +
794A MET* 3.5 32.5 - - + -
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Residues in contact with TYR 758 (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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676A TYR* 6.0 0.5 - - - -
679A SER* 4.4 10.8 + - - -
697A LEU* 3.7 22.0 - - + +
700A GLN* 4.0 27.1 + - - -
753A VAL* 3.2 31.1 + - + -
754A GLN* 3.6 41.1 - - - +
757A PHE* 1.3 96.8 - + - +
759A SER* 1.3 57.3 + - - +
761A MET* 3.3 5.8 + - + +
762A ASN* 2.8 32.5 + - - +
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Residues in contact with SER 759 (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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732A ARG* 3.8 5.2 + - - -
736A ALA* 5.1 2.8 - - - +
754A GLN 2.8 20.5 + - - -
755A TRP* 3.5 39.0 + - - -
757A PHE 3.5 0.2 - - - -
758A TYR* 1.3 73.0 - - - +
760A ILE* 1.3 59.1 + - - +
762A ASN* 3.3 5.1 + - - +
763A ASP* 2.8 43.7 + - - -
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Residues in contact with ILE 760 (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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729A MET* 5.6 1.3 - - + -
732A ARG 6.2 0.4 - - - -
733A LEU* 4.4 14.8 - - + -
736A ALA* 3.9 15.9 - - + -
755A TRP 3.7 10.0 + - - +
756A ALA 3.6 16.6 - - - +
757A PHE 3.6 2.8 + - - +
758A TYR 3.4 0.2 - - - -
759A SER* 1.3 74.6 - - - +
761A MET* 1.3 60.8 + - - +
763A ASP* 3.9 5.7 - - - +
764A LEU* 2.8 32.7 + - - +
786A LEU* 4.3 19.9 - - + +
789A VAL* 4.8 1.1 - - + -
790A TRP* 3.5 48.9 - - + +
793A LEU* 3.8 26.0 - - + -
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Residues in contact with MET 761 (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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700A GLN* 3.5 35.9 - - + +
703A ARG* 4.2 9.0 - - + -
704A PHE* 3.9 15.7 - - + +
707A LEU* 4.2 13.9 - - + -
757A PHE* 3.1 32.5 + - + +
758A TYR* 3.7 7.6 - - + +
760A ILE* 1.3 77.5 - - - +
762A ASN* 1.3 58.0 + - - +
764A LEU* 3.7 4.1 - - - +
765A ARG* 3.0 64.2 + - - +
790A TRP* 3.8 27.3 - - + -
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Residues in contact with ASN 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A TYR 2.8 18.6 + - - +
759A SER* 3.7 5.6 - - - +
761A MET* 1.3 74.9 - - - +
763A ASP* 1.3 73.4 + - - +
765A ARG* 3.2 10.9 + - - +
766A TRP* 3.2 22.0 + - - +
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Residues in contact with ASP 763 (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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728A TRP* 3.4 31.5 - - + -
729A MET* 3.9 15.0 - - + -
732A ARG* 2.9 44.2 + - - +
759A SER* 2.8 27.9 + - - +
760A ILE* 3.9 3.4 - - - +
762A ASN* 1.3 78.9 - - - +
764A LEU* 1.3 58.1 + - - +
766A TRP* 3.3 2.4 + - - +
767A TYR* 2.9 28.8 + - - +
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Residues in contact with LEU 764 (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 LEU* 3.9 21.3 - - + -
711A PHE* 4.0 15.5 - - + -
729A MET* 4.1 4.2 - - - -
760A ILE 2.8 23.2 + - - +
761A MET* 3.7 4.9 - - - +
763A ASP* 1.3 74.2 - - - +
765A ARG* 1.3 60.0 + - + +
767A TYR* 3.2 8.7 + - + +
768A LEU* 2.8 43.3 + - + +
783A LEU* 3.7 30.1 - - + -
786A LEU* 4.0 17.0 - - + -
790A TRP* 3.7 27.4 - - + -
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Residues in contact with ARG 765 (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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700A GLN* 5.3 11.9 - - - +
703A ARG* 3.6 42.5 - - - +
707A LEU* 6.2 0.7 - - + -
761A MET* 3.0 53.2 + - - +
762A ASN* 3.2 9.2 + - - +
764A LEU* 1.3 78.8 - - + +
766A TRP* 1.3 63.8 + - - +
768A LEU* 3.4 8.9 + - + +
769A ARG* 3.0 31.8 + - + +
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Residues in contact with TRP 766 (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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725A ILE* 3.7 25.6 - - + -
728A TRP* 3.3 46.2 - + + -
762A ASN* 3.2 10.8 + - - +
763A ASP* 3.7 6.3 - - - +
765A ARG* 1.3 77.0 - - - +
767A TYR* 1.3 64.9 + - - +
769A ARG* 3.0 17.6 + - + +
770A ARG* 2.8 56.1 + - + +
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Residues in contact with TYR 767 (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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725A ILE* 3.6 28.9 - - + -
726A ASP* 2.6 29.5 + - - -
728A TRP* 4.0 6.7 - + + -
729A MET* 3.7 34.1 - - + -
763A ASP 2.9 15.3 + - - +
764A LEU* 3.2 9.6 + - + +
766A TRP* 1.3 77.6 - - - +
768A LEU* 1.3 62.2 + - + +
770A ARG* 3.4 4.9 + - - +
771A THR* 2.8 48.2 + - + +
774A ARG* 4.2 0.7 + - - -
779A LYS* 3.6 18.9 - - + +
782A VAL* 3.6 18.1 - - + +
783A LEU* 3.7 34.5 - - + -
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Residues in contact with LEU 768 (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 ARG* 4.9 9.2 - - - +
707A LEU* 4.4 21.1 - - + -
711A PHE* 4.7 4.7 - - + -
764A LEU* 2.8 49.7 + - + +
765A ARG* 3.8 8.1 - - + +
766A TRP 3.2 0.2 - - - -
767A TYR* 1.3 80.2 - - + +
769A ARG* 1.3 62.1 + - + +
771A THR* 3.4 3.1 + - - -
772A GLU* 3.0 28.9 + - - +
779A LYS* 4.4 11.6 + - - +
783A LEU* 4.1 19.5 - - + -
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Residues in contact with ARG 769 (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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765A ARG* 3.0 21.4 + - + +
766A TRP* 3.0 19.1 + - + +
768A LEU* 1.3 75.5 - - + +
770A ARG* 1.3 66.5 + - + +
771A THR 3.2 1.2 + - - -
772A GLU* 3.2 21.3 + - - +
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Residues in contact with ARG 770 (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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725A ILE* 4.1 24.3 - - + +
766A TRP* 2.8 61.3 + - + +
767A TYR 3.8 4.7 - - - +
769A ARG* 1.3 77.4 - - - +
771A THR* 1.3 60.0 + - - +
772A GLU 3.5 1.1 + - - +
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Residues in contact with THR 771 (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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725A ILE* 3.9 17.5 - - + -
767A TYR* 2.8 34.6 + - + +
768A LEU* 3.6 5.8 - - - -
769A ARG 3.1 0.2 - - - -
770A ARG* 1.3 79.3 - - - +
772A GLU* 1.3 68.0 + - - +
774A ARG* 3.0 47.0 + - - +
779A LYS* 3.0 37.7 + - - -
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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