Contacts of the strand formed by residues 756 - 761 (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 ASN 756 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715A GLN* 2.9 45.4 + - - +
718A PHE 5.6 2.2 + - - +
719A TYR* 4.1 8.4 - - + +
726A TYR* 3.3 34.5 - - - +
746A GLU 3.1 16.6 - - - +
747A VAL* 3.2 28.3 + - - -
748A GLY* 3.7 6.3 - - - +
754A GLY 3.3 0.2 - - - -
755A PHE* 1.3 79.1 + - - +
757A VAL* 1.3 61.7 + - - +
758A ASN* 3.6 5.7 + - - +
891A HIS* 3.1 18.2 + - - -
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Residues in contact with VAL 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A LEU* 4.1 16.8 - - + -
726A TYR* 2.8 12.8 + - - +
727A ILE* 3.2 15.8 - - + +
728A SER 2.9 26.5 + - - +
754A GLY 4.1 7.2 - - - +
756A ASN* 1.3 75.3 - - - +
758A ASN* 1.3 64.3 + - - +
759A VAL* 4.6 2.5 - - + -
781A VAL* 3.9 26.9 - - + -
785A ILE* 4.0 18.2 - - + -
887A VAL* 4.0 12.3 - - + -
891A HIS* 3.5 28.9 - - + +
895A TRP* 4.5 0.2 - - - +
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Residues in contact with ASN 758 (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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710A HIS* 3.1 22.3 + - - -
715A GLN* 3.0 22.1 + - - +
726A TYR* 4.3 1.9 - - - -
728A SER* 3.7 11.5 - - - -
730A HIS* 3.8 2.9 - - - +
742A GLY* 3.2 31.2 - - - +
743A ALA 3.1 23.7 + - - +
744A VAL* 3.8 13.3 + - - +
746A GLU* 3.5 14.7 + - - +
756A ASN* 3.9 4.6 + - - +
757A VAL* 1.3 73.8 - - - +
759A VAL* 1.3 61.2 + - - +
760A ALA 3.0 6.1 + - - -
887A VAL* 3.6 14.5 - - - +
891A HIS* 4.7 2.7 + - - -
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Residues in contact with VAL 759 (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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727A ILE* 4.6 9.4 - - + -
728A SER 2.7 17.8 + - - +
729A LEU* 3.5 15.6 - - + -
730A HIS* 3.1 24.6 + - - -
757A VAL* 4.6 1.6 - - + -
758A ASN* 1.3 68.7 - - - +
760A ALA* 1.3 58.4 + - - +
761A TRP* 3.4 30.7 + - + -
777A ALA* 4.4 4.0 - - + -
781A VAL* 3.9 31.2 - - + -
782A VAL* 5.0 2.0 - - + -
883A SER* 5.8 0.9 - - - -
884A LEU* 3.6 26.2 - - + +
887A VAL* 3.9 12.1 - - + -
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Residues in contact with ALA 760 (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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730A HIS* 3.7 9.0 - - + -
732A HIS* 3.7 21.1 - - + +
742A GLY 3.4 25.4 - - - +
744A VAL* 3.9 26.7 - - + +
758A ASN 3.0 5.0 + - - +
759A VAL* 1.3 69.3 - - - +
761A TRP* 1.3 65.6 + - - +
762A ALA* 3.4 5.2 + - - +
883A SER* 3.8 13.0 + - - +
887A VAL* 4.5 1.6 - - - +
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Residues in contact with TRP 761 (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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729A LEU* 4.2 9.8 - - + +
730A HIS 2.8 35.0 + - - +
732A HIS* 2.8 28.5 + - - +
733A ASP* 3.1 9.3 + - - +
759A VAL* 3.4 15.0 + - + -
760A ALA* 1.3 70.2 - - - +
762A ALA* 1.3 57.7 + - - +
769A MET* 4.1 13.2 - - + -
773A GLU* 3.4 30.5 - - + -
774A TYR* 3.4 33.7 + + - -
777A ALA* 3.9 19.7 - - + -
813A TYR* 3.3 33.4 - + - +
880A ALA* 3.4 39.0 - - + -
883A SER* 3.7 13.7 - - - -
884A LEU* 4.1 10.1 - - + -
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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