Contacts of the strand formed by residues 793 - 798 (chain A) in PDB entry 3ZNS
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 LEU 793 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649A ALA* 3.7 24.7 - - - +
652A VAL* 4.5 6.1 - - + -
653A ALA* 3.8 24.7 - - + +
692A LEU* 4.2 14.4 - - + -
698A ALA* 4.4 14.8 - - + -
700A LYS 3.5 2.4 + - - -
701A ILE* 3.4 11.1 - - + +
702A LEU 3.1 23.0 + - - -
791A PRO* 3.4 2.2 - - - +
792A ASP* 1.3 81.7 - - - +
794A VAL* 1.3 82.0 + - - +
795A LEU* 3.6 25.6 - - + -
831A ALA* 3.7 1.3 - - - -
834A ALA* 3.6 17.5 - - + +
836A VAL* 4.9 2.2 - - + -
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Residues in contact with VAL 794 (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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702A LEU* 3.4 36.3 - - + +
704A VAL* 4.5 0.9 - - + -
791A PRO* 4.1 7.2 - - + -
793A LEU* 1.3 84.1 - - - +
795A LEU* 1.3 68.3 + - - +
796A VAL* 4.0 15.3 - - + -
827A LEU* 4.4 19.3 - - + +
830A LEU* 4.0 24.7 - - + -
831A ALA* 4.1 6.1 - - + -
834A ALA 2.8 14.4 + - - +
835A VAL* 3.4 9.0 - - + -
836A VAL 2.9 25.3 + - - -
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Residues in contact with LEU 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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645A VAL* 5.2 3.8 - - + -
649A ALA* 4.2 12.1 - - + -
685A VAL* 3.7 39.9 - - + +
688A ALA* 4.5 6.1 - - + -
689A CYS* 3.7 27.1 - - + +
692A LEU* 4.7 2.0 - - + -
701A ILE* 4.1 9.0 - - + -
702A LEU 2.7 12.5 + - - +
703A ILE* 3.3 6.3 - - + -
704A VAL 2.8 25.6 + - - +
793A LEU* 3.6 19.7 - - + +
794A VAL* 1.3 73.4 - - - +
796A VAL* 1.3 63.6 + - - +
797A SER 4.2 0.4 - - - -
836A VAL* 3.5 31.9 - - + +
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Residues in contact with VAL 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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685A VAL* 4.8 3.6 - - - -
704A VAL* 3.2 11.4 - - + +
706A TRP* 3.8 41.3 - - + -
794A VAL* 4.0 8.5 - - + -
795A LEU* 1.3 78.5 - - - +
797A SER* 1.3 60.6 + - - +
798A ALA* 3.1 9.2 + - + +
827A LEU* 3.6 25.1 - - + -
835A VAL* 4.4 2.2 - - + -
836A VAL 2.7 10.6 + - - +
837A LEU* 3.3 28.0 - - + -
838A ALA* 2.8 32.6 + - - +
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Residues in contact with SER 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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669A HIS* 4.0 4.3 - - - +
685A VAL* 3.4 19.1 - - - +
703A ILE* 5.0 3.2 - - - +
704A VAL 2.8 7.5 + - - -
705A ASP* 3.4 34.8 + - - +
706A TRP* 3.3 22.2 + - - -
707A ASP* 3.7 0.5 + - - +
714A THR* 4.8 2.4 + - - -
726A TYR* 5.8 0.2 - - - -
795A LEU 4.2 0.6 - - - -
796A VAL* 1.3 68.0 - - - +
798A ALA* 1.3 58.8 + - - +
799A GLY 3.3 6.9 + - - -
838A ALA 3.8 1.3 - - - -
840A GLU* 2.7 33.3 + - - -
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Residues in contact with ALA 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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661A PHE* 5.2 1.3 - - + -
706A TRP* 3.3 30.5 - - + +
796A VAL* 3.1 8.1 + - + -
797A SER* 1.3 68.7 - - - +
799A GLY* 1.3 62.6 + - - +
800A PHE* 3.6 22.1 - - + -
837A LEU* 4.0 17.9 - - + -
838A ALA 2.9 15.7 + - - +
839A LEU* 3.5 7.0 - - - +
840A GLU 3.4 14.6 + - - -
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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