Contacts of the strand formed by residues 764 - 771 (chain A) in PDB entry 4WGK
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 VAL 764 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754A ASN 3.8 0.3 - - - +
755A ARG* 3.6 5.7 - - - +
756A LYS* 3.1 40.2 + - + +
762A PRO 4.3 15.5 - - - +
763A ALA* 1.3 79.7 - - - +
765A ILE* 1.3 67.8 + - - +
766A LEU* 3.6 32.8 + - + +
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Residues in contact with ILE 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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683A ASN* 3.5 38.1 - - + +
753A HIS* 3.7 23.5 - - + -
754A ASN 3.6 3.1 - - - +
755A ARG* 3.9 37.7 - - + +
763A ALA 5.6 2.2 - - - +
764A VAL* 1.3 81.1 - - - +
766A LEU* 1.3 68.7 + - - +
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Residues in contact with LEU 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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753A HIS* 3.2 10.2 - - - -
754A ASN* 3.0 48.2 + - - +
756A LYS* 3.9 35.0 - - + +
764A VAL* 3.6 27.6 - - + +
765A ILE* 1.3 78.4 - - - +
767A SER* 1.3 63.8 + - - +
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Residues in contact with SER 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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752A GLY 3.7 1.1 - - - -
753A HIS* 3.5 26.4 - - - -
754A ASN* 4.6 0.7 - - - +
766A LEU* 1.3 79.8 - - - +
768A PHE* 1.3 65.5 + - - +
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Residues in contact with PHE 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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655A PHE* 3.6 44.6 - - + +
656A GLY* 3.8 7.4 - - - -
677A VAL 4.4 0.4 - - - -
678A GLY 4.6 0.2 - - - -
679A ALA* 3.9 15.3 - - + -
750A TYR* 3.4 40.6 - + - -
751A PHE* 3.9 1.6 - - - +
752A GLY 3.2 38.6 + - - +
753A HIS 3.4 28.3 - - - -
754A ASN* 3.6 21.1 - - + +
767A SER* 1.3 76.2 - - - +
769A GLU* 1.3 73.4 + - - +
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Residues in contact with GLU 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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655A PHE 4.0 3.8 - - - +
656A GLY* 3.7 14.5 - - - -
749A ARG* 2.6 36.7 + - - +
750A TYR 3.3 8.1 - - - +
751A PHE* 3.6 27.2 - - + -
767A SER* 6.4 0.4 - - - -
768A PHE* 1.3 82.4 - - - +
770A GLY* 1.3 58.9 - - - +
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Residues in contact with GLY 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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656A GLY* 3.2 24.1 - - - -
676A PHE* 3.9 9.6 - - - -
749A ARG* 3.2 7.3 + - - +
750A TYR* 2.8 34.6 + - - +
769A GLU* 1.3 74.7 - - - +
771A THR* 1.3 65.3 + - - -
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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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656A GLY 4.2 2.0 + - - -
658A VAL* 3.8 11.6 - - - +
676A PHE* 4.0 1.0 - - - -
747A ARG* 3.9 32.8 - - - +
748A ILE 3.8 2.5 - - - +
749A ARG* 2.8 36.2 + - + -
770A GLY* 1.3 74.0 - - - -
772A SER* 1.3 73.4 + - - +
773A PRO* 3.8 1.7 - - - +
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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