Contacts of the helix formed by residues 748 - 757 (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 ARG 748 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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682A GLU* 2.8 53.1 + - - +
683A HIS* 3.8 27.1 + - - +
743A ALA* 3.0 23.4 + - + +
744A LEU* 4.5 0.9 - - - +
746A GLU* 3.1 27.8 + - + +
747A PHE* 1.3 73.2 - - - +
749A THR* 1.3 57.2 + - - +
751A THR* 4.0 11.6 + - - -
752A ALA* 2.9 29.8 + - - +
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Residues in contact with THR 749 (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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55A ARG* 5.7 0.5 + - - -
59A ILE* 4.3 22.0 - - + +
62A VAL* 5.1 6.1 - - + -
63A ILE* 5.6 1.1 - - + -
678A MET* 3.0 46.7 + - + +
681A ALA 3.0 14.4 + - - -
682A GLU* 3.4 4.4 + - - +
744A LEU* 4.7 10.1 - - + -
747A PHE* 3.1 15.9 + - - +
748A ARG* 1.3 72.5 - - - +
750A ARG* 1.3 65.6 + - - +
752A ALA* 3.4 6.0 + - - +
753A VAL* 3.0 30.3 + - - +
797A PHE* 4.8 2.2 - - - -
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Residues in contact with ARG 750 (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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678A MET 3.4 7.4 - - - -
679A SER* 2.9 40.5 + - - +
680A LEU* 3.5 26.5 + - - +
681A ALA* 3.8 18.4 - - - +
682A GLU* 2.8 20.1 + - - +
749A THR* 1.3 74.7 + - - +
751A THR* 1.3 65.9 + - - +
753A VAL* 3.2 3.5 + - - +
754A GLN* 3.0 46.3 + - + +
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Residues in contact with THR 751 (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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682A GLU* 2.7 35.4 + - - -
739A GLU* 5.4 0.7 - - - +
743A ALA* 4.0 12.8 - - + -
748A ARG* 4.0 15.9 + - + -
750A ARG* 1.3 75.4 - - - +
752A ALA* 1.3 63.1 + - - +
754A GLN* 3.2 10.6 + - + +
755A TRP* 3.2 37.8 + - + +
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Residues in contact with ALA 752 (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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740A THR* 3.8 10.5 + - + +
743A ALA* 3.6 12.7 - - + +
744A LEU* 3.6 32.5 - - + -
748A ARG 2.9 20.3 + - - +
749A THR 3.7 4.5 - - - +
750A ARG 3.2 0.2 - - - -
751A THR* 1.3 77.2 - - - +
753A VAL* 1.3 51.0 + - - +
755A TRP* 3.3 1.7 + - - +
756A ALA* 2.7 40.1 + - - +
797A PHE* 3.7 7.6 - - + -
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Residues in contact with VAL 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A LEU* 3.8 25.4 - - + -
678A MET* 4.2 1.6 - - + -
679A SER* 3.6 38.1 - - - +
749A THR 3.0 20.3 + - - +
750A ARG 3.2 4.0 + - - +
752A ALA* 1.3 73.2 - - - +
754A GLN* 1.3 67.3 + - - +
756A ALA* 4.6 2.0 - - - -
757A PHE* 2.9 27.5 + - + +
758A TYR* 3.2 18.4 + - + -
797A PHE* 3.5 30.1 - - + -
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Residues in contact with GLN 754 (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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679A SER* 4.7 2.8 + - - -
750A ARG* 3.0 51.2 + - + +
751A THR* 3.2 13.0 + - + +
753A VAL* 1.3 78.8 - - - +
755A TRP* 1.3 60.7 + - + +
758A TYR* 3.6 37.1 - - - +
759A SER* 2.8 30.1 + - - -
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Residues in contact with TRP 755 (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 13.2 - - - -
735A LYS* 3.7 38.4 - - + -
736A ALA* 4.0 20.7 - - + +
739A GLU* 3.4 40.9 + - + +
740A THR* 3.4 18.2 - - - +
751A THR* 3.2 37.2 + - + +
752A ALA 3.8 2.7 - - - +
753A VAL 3.1 0.2 - - - -
754A GLN* 1.3 82.2 - - + +
756A ALA* 1.3 65.4 + - - +
757A PHE 3.5 0.5 + - - -
759A SER* 3.5 41.4 - - - -
760A ILE* 3.7 13.5 + - - +
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Residues in contact with ALA 756 (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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740A THR* 3.2 24.4 + - + +
752A ALA 2.7 21.2 + - - +
753A VAL* 4.6 0.9 - - - -
755A TRP* 1.3 74.9 - - - +
757A PHE* 1.3 56.6 + - - +
760A ILE* 3.6 5.5 - - - +
790A TRP* 2.9 27.7 + - - -
793A LEU* 3.9 28.7 - - + +
794A MET* 3.8 6.7 - - - +
797A PHE* 4.0 10.8 - - + -
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Residues in contact with PHE 757 (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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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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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