Contacts of the helix formed by residues 785 - 791 (chain A) in PDB entry 4NC6
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 785 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781A LYS* 3.0 41.9 + - + +
784A ARG* 1.3 88.5 - - + +
786A GLN* 1.3 78.8 + - + +
787A LEU 3.3 1.3 + - - -
788A PRO* 3.5 4.4 - - - +
789A LYS* 3.5 25.7 + - + +
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Residues in contact with GLN 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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778A GLY 5.4 0.8 + - - -
781A LYS* 3.2 29.4 - - - +
782A PHE* 3.2 47.5 + - + +
785A VAL* 1.3 88.2 - - + +
787A LEU* 1.3 65.1 + - - +
789A LYS* 3.2 10.0 + - + +
790A ARG* 3.1 23.0 + - - +
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Residues in contact with LEU 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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727A TRP* 4.0 13.2 - - + -
736A PHE* 3.9 24.0 - - + -
763A LEU* 4.3 15.9 - - + +
767A SER* 3.7 24.5 - - - +
782A PHE* 2.8 31.3 + - + +
783A PHE* 3.8 32.8 - - + +
786A GLN* 1.3 79.6 - - - +
788A PRO* 1.4 69.2 - - + +
790A ARG* 3.3 7.1 + - - +
791A TYR* 3.3 37.4 - - + -
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Residues in contact with PRO 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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735A LYS* 3.6 33.9 - - + +
736A PHE* 3.9 26.5 - - + -
737A PRO* 3.7 19.3 - - + +
783A PHE 3.5 13.9 - - - +
784A ARG 3.9 13.2 - - - +
785A VAL 3.5 11.7 - - - +
787A LEU* 1.4 93.9 - - + +
789A LYS* 1.3 61.0 + - - +
791A TYR* 3.1 11.8 + - - -
792A ARG* 3.7 0.8 + - - +
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Residues in contact with LYS 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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785A VAL* 3.5 19.1 + - + +
786A GLN* 3.2 15.0 + - + +
788A PRO* 1.3 77.9 - - - +
790A ARG* 1.3 65.2 + - - +
791A TYR 3.1 0.7 + - - -
792A ARG* 3.2 55.0 + - - +
793A SER 4.6 0.2 + - - -
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Residues in contact with ARG 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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766A THR* 3.6 23.5 - - - +
767A SER* 4.0 15.7 - - - -
782A PHE* 5.9 2.0 - - + -
786A GLN 3.1 11.1 + - - +
787A LEU* 3.5 12.6 - - - +
788A PRO 3.3 0.2 - - - -
789A LYS* 1.3 77.7 - - - +
791A TYR* 1.3 89.0 + - + +
792A ARG 3.4 3.1 + - - -
793A SER* 3.6 6.4 + - - -
796A ASN* 3.0 62.1 + - - +
799A LYS* 5.4 10.7 - - - +
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Residues in contact with TYR 791 (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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736A PHE* 4.3 4.9 - + - -
737A PRO* 3.6 22.5 - - + +
739A TYR* 5.6 2.8 - - - +
740A MET* 3.7 35.2 + - + +
763A LEU* 3.5 23.7 - - + +
766A THR* 3.5 18.0 - - - +
767A SER* 4.7 1.9 + - - -
787A LEU* 3.3 25.6 - - + -
788A PRO 3.1 9.1 + - - +
790A ARG* 1.3 107.1 + - + +
792A ARG* 1.3 64.4 + - - +
793A SER 3.1 10.1 + - - +
796A ASN* 3.5 30.5 - - + -
797A ALA* 4.2 6.4 - - - +
800A LEU* 3.7 25.2 - - + +
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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