Contacts of the strand formed by residues 792 - 800 (chain A) in PDB entry 3WAJ
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 GLU 792 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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759A MET* 3.1 32.7 - - + +
790A VAL* 3.5 4.9 - - - +
791A THR* 1.3 94.4 + - - +
793A VAL* 1.3 64.6 + - - +
794A SER 4.4 0.2 + - - -
812A THR* 4.0 20.8 - - + +
813A VAL 3.2 14.8 - - - +
814A GLU* 4.7 10.4 - - - +
815A VAL* 3.6 3.3 - - - +
843A LYS 4.2 4.7 - - - +
844A ALA* 4.5 5.9 - - - -
845A GLY 4.7 4.5 + - - -
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Residues in contact with VAL 793 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786A VAL* 3.8 22.7 - - + -
790A VAL* 6.0 0.2 - - + -
792A GLU* 1.3 78.1 - - - +
794A SER* 1.3 63.0 + - - +
795A VAL* 4.3 3.5 + - + +
811A GLN 4.1 0.5 - - - +
812A THR* 3.5 1.7 - - - -
813A VAL* 2.8 43.8 + - + +
815A VAL* 3.9 5.4 - - + -
820A TYR* 3.7 36.6 - - + -
822A VAL* 6.0 0.9 - - + -
842A ILE* 3.7 26.2 - - + -
843A LYS 3.5 12.1 - - - +
844A ALA* 4.0 6.1 - - + -
868A LEU* 3.8 11.9 - - + -
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Residues in contact with SER 794 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A GLU 4.3 0.4 + - - -
793A VAL* 1.3 73.7 - - - +
795A VAL* 1.3 62.0 + - - +
810A TRP* 3.7 21.7 - - - -
811A GLN 3.4 4.7 - - - -
812A THR* 3.4 21.8 - - - -
841A HIS 3.6 1.7 + - - +
842A ILE* 3.3 4.2 - - - +
843A LYS* 3.0 48.5 + - - +
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Residues in contact with VAL 795 (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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793A VAL* 5.1 3.8 - - + +
794A SER* 1.3 78.8 - - - +
796A ASN* 1.3 62.9 - - - +
809A TYR* 4.4 2.9 - - + -
810A TRP* 3.3 11.8 - - - -
811A GLN* 2.7 38.6 + - + +
822A VAL* 3.9 34.5 - - + -
824A LEU* 4.0 13.2 - - + -
840A TYR* 3.5 40.6 - - + -
841A HIS 3.7 6.7 - - - +
842A ILE* 3.9 17.5 - - + +
851A ILE* 5.3 0.7 - - + -
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Residues in contact with ASN 796 (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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795A VAL* 1.3 79.5 - - - +
797A ALA* 1.3 65.5 + - - +
808A GLU* 2.7 28.5 + - - +
809A TYR 3.3 8.9 + - - -
810A TRP* 3.2 47.2 - - + +
840A TYR* 3.3 3.6 - - - -
841A HIS* 2.7 59.7 + - + +
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Residues in contact with ALA 797 (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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796A ASN* 1.3 80.1 - - - +
798A THR* 1.3 61.1 + - - +
799A ILE* 4.6 11.9 - - + -
808A GLU* 3.1 9.8 - - - +
809A TYR* 2.9 33.8 + - + +
828A HIS* 6.1 0.2 - - + -
836A PRO* 5.0 2.9 - - + -
838A THR* 3.6 18.2 - - - +
839A PRO 4.1 4.5 - - - +
840A TYR* 3.8 25.8 - - + -
841A HIS* 4.8 0.7 - - - -
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Residues in contact with THR 798 (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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797A ALA* 1.3 74.8 - - - +
799A ILE* 1.3 59.2 + - - +
806A THR* 4.2 16.6 - - + -
807A PHE 3.8 5.2 - - - +
808A GLU* 2.5 28.6 + - - +
836A PRO* 3.2 5.7 - - - +
837A ILE* 2.8 50.6 + - + -
838A THR* 3.2 30.3 + - - +
841A HIS* 5.7 0.5 + - - -
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Residues in contact with ILE 799 (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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797A ALA* 4.5 5.2 - - + +
798A THR* 1.3 82.8 - - - +
800A LYS* 1.3 62.2 + - - +
801A THR 4.3 0.2 - - - -
805A ARG 3.7 0.5 - - - +
806A THR* 3.2 27.2 - - - -
807A PHE* 3.0 53.2 + - + +
809A TYR* 4.0 18.6 - - + -
826A TYR* 3.8 33.7 - - + -
834A VAL* 3.6 24.7 - - + -
835A LYS 3.6 7.4 - - - +
836A PRO* 3.8 18.6 - - + -
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Residues in contact with LYS 800 (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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798A THR 4.3 0.2 - - - -
799A ILE* 1.3 72.4 - - - +
801A THR* 1.3 69.5 + - - +
804A ASN* 3.1 41.4 + - - +
805A ARG 3.3 8.5 - - - +
806A THR* 4.1 15.0 - - + -
833A PRO 3.8 2.1 - - - +
834A VAL* 3.4 3.0 - - - -
835A LYS* 2.8 36.4 + - + +
837A ILE* 3.8 29.1 - - + +
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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