Contacts of the strand formed by residues 778 - 783 (chain A) in PDB entry 2WAC
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 ASN 778 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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774A VAL* 3.8 5.2 - - - +
775A GLN* 2.9 36.7 + - + +
776A GLY 3.2 0.2 - - - -
777A SER* 1.3 91.4 - - - +
779A ALA* 1.3 61.7 + - - +
791A THR* 4.3 15.7 - - + -
792A LEU 3.2 9.8 - - - +
793A PRO* 3.4 27.0 - - - +
794A THR* 3.7 3.6 - - - -
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Residues in contact with ALA 779 (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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771A VAL* 4.3 7.0 - - + -
773A ARG 3.3 12.1 - - - +
774A VAL* 4.2 11.4 - - + -
775A GLN 4.8 0.4 - - - +
778A ASN* 1.3 75.5 - - - +
780A THR* 1.3 61.1 + - - +
781A VAL* 3.9 4.8 + - + +
790A GLU 3.7 1.2 - - - +
791A THR* 3.3 4.2 - - - -
792A LEU* 2.7 39.8 + - + +
794A THR* 4.0 5.6 - - + +
797A LEU* 3.9 27.6 - - + -
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Residues in contact with THR 780 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A VAL* 3.8 0.9 - - - -
772A GLU* 2.8 37.7 + - + +
773A ARG* 2.8 33.9 + - + +
779A ALA* 1.3 72.5 - - - +
781A VAL* 1.3 68.3 + - - +
789A LYS* 5.1 10.8 - - + -
790A GLU 3.5 9.4 - - - +
791A THR* 3.0 24.4 + - - +
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Residues in contact with VAL 781 (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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758A ALA* 4.5 3.8 - - + -
769A ALA* 4.1 15.7 - - + -
770A LYS 3.2 11.7 - - - +
771A VAL* 4.2 15.7 - - + -
772A GLU* 5.1 2.0 - - - -
779A ALA* 4.5 10.5 - - + +
780A THR* 1.3 80.8 - - - +
782A LEU* 1.3 59.4 + - - +
783A TYR* 3.9 31.4 + - + +
789A LYS* 3.2 9.4 - - - +
790A GLU* 3.0 41.0 + - + +
792A LEU* 4.8 6.3 - - + -
797A LEU* 4.0 23.8 - - + -
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Residues in contact with LEU 782 (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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717A PHE* 4.0 18.2 - - + -
769A ALA* 3.2 3.6 - - - -
770A LYS* 2.9 42.0 + - + +
772A GLU* 3.7 27.3 - - + +
781A VAL* 1.3 72.0 - - - +
783A TYR* 1.3 66.0 + - - +
784A ILE* 3.1 22.4 + - + +
787A GLY* 3.5 32.3 - - - +
788A ASN 3.7 5.8 - - - +
789A LYS* 3.8 20.6 - - + +
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Residues in contact with TYR 783 (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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758A ALA* 3.8 23.3 - - + +
760A PHE* 3.5 28.5 + + + -
767A TYR* 3.6 30.1 - + + -
768A ARG 3.7 7.4 - - - +
769A ALA* 4.2 3.6 - - + -
781A VAL* 3.9 10.3 - - + -
782A LEU* 1.3 69.1 - - - +
784A ILE* 1.3 58.5 + - - +
785A ASP 3.2 2.5 - - - -
786A TYR* 3.1 14.8 + - + -
787A GLY* 2.8 32.2 + - - -
788A ASN* 2.9 47.7 + - - +
789A LYS* 4.6 0.7 - - - -
790A GLU* 2.6 44.6 + - + +
792A LEU* 3.7 13.0 - - - +
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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