Contacts of the helix formed by residues 770 - 781 (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 GLY 770 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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768A PRO 4.0 0.8 + - - -
769A MET* 1.3 75.6 - - - +
771A ASP* 1.3 66.2 + - - -
772A PRO* 4.3 1.6 - - - -
773A GLU* 2.8 17.1 + - - +
774A TYR* 3.1 28.1 + - - -
814A HIS* 3.7 20.2 - - - -
815A VAL* 4.1 7.0 - - - -
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Residues in contact with ASP 771 (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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770A GLY* 1.3 70.5 - - - -
772A PRO* 1.3 73.5 - - + +
774A TYR 3.2 0.2 + - - -
775A LEU* 2.8 31.3 + - + +
814A HIS 3.8 3.0 + - - +
815A VAL* 3.4 4.3 - - - -
816A SER* 2.6 47.9 + - - -
819A CYS* 3.3 23.3 - - - +
872A TRP* 2.8 32.8 + - + +
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Residues in contact with PRO 772 (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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770A GLY* 3.5 1.6 - - - -
771A ASP* 1.3 93.4 - - + +
773A GLU* 1.3 77.0 + - - +
775A LEU* 4.0 7.3 - - + +
776A ALA* 3.0 28.8 + - - +
779A ARG* 5.0 1.4 + - - -
871A GLY 3.6 24.0 - - - +
872A TRP* 5.5 2.9 - - - +
874A GLN* 3.5 26.5 - - + +
875A LYS 4.2 1.6 - - - +
876A PRO* 3.8 12.8 - - + +
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Residues in contact with GLU 773 (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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761A TRP* 3.4 19.8 - - + -
768A PRO 3.9 3.8 - - - +
769A MET* 3.9 9.6 - - - -
770A GLY 2.8 34.1 + - - +
772A PRO* 1.3 87.9 - - - +
774A TYR* 1.3 63.7 + - + +
776A ALA* 3.4 3.4 + - - +
777A ALA 2.9 22.2 + - - -
875A LYS 4.4 0.7 - - - +
876A PRO* 3.3 11.2 - - + +
877A ASN* 2.9 41.4 + - - +
880A ALA* 3.2 32.3 - - + -
884A LEU* 4.7 0.2 - - - +
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Residues in contact with TYR 774 (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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706A TRP* 4.5 16.1 + - + -
708A VAL* 4.6 4.2 - - - +
729A LEU* 3.8 38.1 + - + -
761A TRP* 3.4 32.4 + + - -
769A MET* 5.3 1.1 - - + -
770A GLY* 3.1 22.9 + - - +
771A ASP 4.1 2.0 - - - +
773A GLU* 1.3 77.2 - - + +
775A LEU* 1.3 64.5 + - - +
777A ALA* 3.3 7.5 + - - +
778A PHE* 3.0 27.5 + - - -
802A ALA* 4.0 9.1 - - + +
813A TYR* 3.6 31.7 - + - -
815A VAL* 3.9 19.3 - - + -
819A CYS* 4.4 14.8 - - - -
820A PHE* 6.1 1.8 - + - -
823A MET* 4.3 20.6 - - + -
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Residues in contact with LEU 775 (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 ASP* 2.8 25.1 + - + +
772A PRO* 4.0 4.9 - - + +
774A TYR* 1.3 77.2 - - - +
776A ALA* 1.3 58.1 + - - +
778A PHE* 3.1 6.2 + - - +
779A ARG* 2.9 45.0 + - - +
819A CYS* 4.1 17.3 - - - +
822A TYR* 3.6 35.0 - - + -
823A MET* 5.4 3.8 - - + -
826A GLN* 4.3 7.0 + - - +
872A TRP* 3.6 48.7 - - + +
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Residues in contact with ALA 776 (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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772A PRO 3.0 21.2 + - - +
773A GLU 3.4 6.5 - - - +
774A TYR 3.3 0.2 - - - -
775A LEU* 1.3 77.2 - - - +
777A ALA* 1.3 62.3 + - - +
779A ARG* 3.4 22.9 + - - +
780A ILE* 3.0 35.9 + - + +
876A PRO* 3.9 19.3 - - + -
884A LEU* 4.1 13.2 - - + -
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Residues in contact with ALA 777 (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* 3.6 26.9 - - + -
759A VAL* 4.4 3.1 - - + -
761A TRP* 3.9 13.5 - - + -
773A GLU 2.9 14.5 + - - +
774A TYR 3.4 9.2 - - - +
776A ALA* 1.3 75.3 - - - +
778A PHE* 1.3 58.9 + - - +
781A VAL* 2.9 26.2 + - - +
782A VAL* 3.0 11.5 + - + +
884A LEU* 4.0 18.3 - - + +
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Residues in contact with PHE 778 (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* 4.5 3.4 - - + -
706A TRP* 4.2 12.6 - + - -
729A LEU* 4.3 17.5 - - + -
774A TYR 3.0 18.1 + - - +
775A LEU* 3.6 8.7 - - - +
777A ALA* 1.3 75.5 - - - +
779A ARG* 1.3 65.7 + - - +
780A ILE 3.4 0.3 + - - -
782A VAL* 3.8 29.6 - - + -
783A MET* 3.1 43.5 + - + +
823A MET* 3.7 56.3 - - + -
826A GLN* 3.9 28.0 - - - +
827A LEU* 4.0 21.8 - - + -
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Residues in contact with ARG 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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772A PRO 5.0 1.4 + - - -
775A LEU* 2.9 35.4 + - - +
776A ALA* 3.6 25.2 - - - +
778A PHE* 1.3 74.8 - - - +
780A ILE* 1.3 70.0 + - + +
783A MET* 5.0 1.7 - - - +
784A PRO* 3.2 21.7 - - - +
826A GLN* 4.9 6.2 + - - +
876A PRO* 5.1 9.1 - - - +
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Residues in contact with ILE 780 (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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776A ALA* 3.0 25.8 + - + +
779A ARG* 1.3 91.6 - - + +
781A VAL* 1.3 66.9 + - + +
784A PRO* 3.5 7.7 - - - +
884A LEU* 4.3 17.7 - - + -
888A ILE* 3.7 30.7 - - + -
898A MET* 3.2 20.7 - - + +
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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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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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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