Contacts of the helix formed by residues 781 - 790 (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 VAL 781 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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727A ILE* 5.1 1.1 - - + -
757A VAL* 3.9 11.9 - - + -
759A VAL* 3.9 24.0 - - + -
777A ALA 2.9 10.5 + - - +
780A ILE* 1.3 90.0 - - + +
782A VAL* 1.3 68.9 + - + +
783A MET 3.5 1.1 + - - -
784A PRO* 3.5 1.3 - - - +
785A ILE* 3.2 47.0 + - + +
884A LEU* 3.7 27.1 - - + -
887A VAL* 4.1 16.6 - - + -
888A ILE* 4.7 8.1 - - + -
898A MET* 4.4 4.7 - - - -
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Residues in contact with VAL 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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704A VAL* 4.6 9.4 - - + -
727A ILE* 4.0 36.8 - - + +
729A LEU* 4.0 14.1 - - + -
759A VAL* 5.0 1.6 - - + -
777A ALA 3.0 16.1 + - - +
778A PHE* 3.8 47.8 - - + -
781A VAL* 1.3 75.8 - - + +
783A MET* 1.3 59.8 + - - +
786A ALA* 2.9 32.6 + - + +
827A LEU* 4.4 13.5 - - + -
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Residues in contact with MET 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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778A PHE* 3.1 25.1 + - + +
779A ARG* 5.0 1.6 - - - +
782A VAL* 1.3 77.7 - - - +
784A PRO* 1.3 70.0 - - + +
786A ALA* 3.6 1.7 - - - +
787A ARG* 2.8 69.0 + - - +
826A GLN* 3.2 57.0 - - + +
827A LEU* 4.1 18.6 - - - -
830A LEU* 4.1 19.7 - - + -
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Residues in contact with PRO 784 (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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778A PHE 3.6 2.5 - - - +
779A ARG 3.2 28.3 - - - +
780A ILE 3.5 13.5 - - - +
781A VAL 3.5 9.6 - - - +
783A MET* 1.3 92.1 - - + +
785A ILE* 1.3 57.0 + - - +
787A ARG* 3.4 8.1 + - + +
788A GLU* 3.0 28.2 + - - +
897A CYS* 3.7 27.0 - - + +
898A MET* 4.5 1.1 - - + -
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Residues in contact with ILE 785 (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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725A LEU* 3.8 15.3 - - + -
727A ILE* 4.4 7.6 - - + -
757A VAL* 4.0 20.9 - - + -
781A VAL* 3.2 36.4 + - + +
782A VAL 4.1 1.3 - - - +
784A PRO* 1.3 75.6 - - - +
786A ALA* 1.3 59.3 + - - +
788A GLU* 3.2 4.3 + - - +
789A PHE* 2.8 28.1 + - - +
887A VAL* 5.7 0.2 - - + -
891A HIS* 4.9 3.1 - - + -
895A TRP* 3.7 39.4 - - + +
897A CYS* 4.0 17.9 - - - -
898A MET* 4.1 18.8 - - + -
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Residues in contact with ALA 786 (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* 3.7 17.3 - - + -
725A LEU* 4.4 6.3 - - - +
727A ILE* 4.7 1.3 - - + +
782A VAL* 2.9 23.0 + - + +
783A MET* 3.6 5.4 - - - +
785A ILE* 1.3 75.1 - - - +
787A ARG* 1.3 53.1 + - - +
789A PHE* 3.3 6.0 + - - +
790A SER 2.7 30.7 + - - -
791A PRO* 3.3 9.8 - - - +
830A LEU* 3.6 29.6 - - + -
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Residues in contact with ARG 787 (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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783A MET* 2.8 59.8 + - - +
784A PRO* 3.7 6.7 - - + +
786A ALA* 1.3 70.4 - - - +
788A GLU* 1.3 65.9 + - - +
790A SER* 3.4 17.3 + - - +
829A ASN* 4.1 28.1 + - - +
830A LEU* 3.8 18.0 - - + +
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Residues in contact with GLU 788 (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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784A PRO 3.0 15.2 + - - +
785A ILE* 3.6 4.5 - - - +
787A ARG* 1.3 76.9 - - - +
789A PHE* 1.3 62.6 + - - +
790A SER* 4.4 2.6 - - - -
894A TYR 4.7 1.2 - - - +
895A TRP* 3.7 26.7 - - + -
896A GLY* 2.9 24.9 + - - -
897A CYS* 3.0 34.2 + - - +
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Residues in contact with PHE 789 (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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700A LYS* 2.8 67.2 + - + -
701A ILE 3.6 22.4 - - - -
702A LEU* 4.7 1.8 - - + -
722A PRO 3.5 19.7 - - - -
723A SER 3.8 16.6 - - - -
725A LEU* 3.4 43.3 - - + -
755A PHE* 3.9 25.1 - + - -
785A ILE 2.8 9.9 + - - +
786A ALA* 3.5 3.1 - - - +
788A GLU* 1.3 76.3 - - - +
790A SER* 1.3 54.5 + - - +
791A PRO* 3.9 17.3 - - + -
895A TRP* 4.0 7.1 - + + -
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Residues in contact with SER 790 (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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700A LYS* 3.1 21.0 + - - -
786A ALA 2.7 16.9 + - - -
787A ARG* 3.4 14.7 + - - +
788A GLU 4.4 2.2 - - - -
789A PHE* 1.3 78.9 - - - +
791A PRO* 1.3 68.0 + - - +
792A ASP* 4.9 2.3 - - - +
830A LEU* 6.0 0.4 - - - -
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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