Contacts of the helix formed by residues 691 - 695 (chain A) in PDB entry 3HZJ
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 GLU 691 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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671A GLU* 3.4 10.3 - - - +
689A ASN* 3.5 14.2 + - - +
690A LEU* 1.3 76.9 - - - +
692A ALA* 1.3 66.3 + - - +
693A HIS* 3.0 32.0 + - + +
694A MSE 3.1 25.1 + - + +
695A TYR* 3.2 14.3 - - - -
671B GLU* 2.8 37.9 - - - +
691B GLU* 3.1 33.6 - - + +
693B HIS* 4.6 3.5 - - - -
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Residues in contact with ALA 692 (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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667A PHE* 3.9 26.9 - - + +
670A LEU* 4.5 12.8 - - + -
671A GLU* 2.8 30.8 + - + +
691A GLU* 1.3 72.7 - - - +
693A HIS* 1.3 56.5 - - - +
694A MSE 3.0 0.6 + - - -
695A TYR* 3.2 20.9 + - + +
696A ALA* 2.9 34.6 + - - +
902A UNX 3.8 1.6 - - - -
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Residues in contact with HIS 693 (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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664A HIS* 5.7 1.6 - - + -
667A PHE* 3.4 38.4 - - + +
691A GLU* 3.0 40.7 + - + +
692A ALA* 1.3 77.4 - - - +
694A MSE 1.3 80.5 + - + +
696A ALA 4.6 1.1 - - - -
697A SER* 4.3 13.2 - - - -
664B HIS* 5.5 6.1 - + + -
691B GLU* 4.5 5.4 - - - -
693B HIS* 5.6 5.8 - + - -
793B TYR* 4.1 19.7 - + - -
796B MSE 5.3 1.8 - - + +
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Residues in contact with MSE 694 (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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689A ASN 3.8 11.7 - - - +
690A LEU* 4.1 2.7 - - + -
691A GLU* 3.4 31.6 - - + +
692A ALA 3.0 0.8 - - - -
693A HIS* 1.3 102.5 - - + +
695A TYR* 1.3 58.6 + - + +
748A PHE* 3.6 28.9 - - + -
752A LEU* 3.9 15.9 - - + +
910A UNX 3.8 9.0 - - - -
668B TYR* 4.0 16.6 - - + -
793B TYR* 3.7 28.0 - - + -
796B MSE 3.7 33.5 - - + +
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Residues in contact with TYR 695 (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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670A LEU* 4.6 4.2 - - + +
674A MSE 3.3 19.6 - - - +
685A PHE* 3.7 16.3 - + - -
690A LEU* 4.2 14.8 - - + -
691A GLU 3.2 23.8 - - - -
692A ALA* 3.2 12.3 + - - +
694A MSE 1.3 79.1 - - + +
696A ALA* 1.3 68.1 + - + +
697A SER 3.7 1.8 - - - -
698A GLN 5.3 0.2 + - - -
699A TRP* 3.7 42.9 + + - -
707A LYS* 4.7 0.2 + - - -
736A LEU* 4.5 4.0 - - + -
752A LEU* 4.4 5.6 - - + -
755A PHE* 3.5 42.0 - + + -
902A UNX 2.9 21.6 - - - -
909A UNX 2.7 26.8 - - - -
910A UNX 3.9 3.3 - - - -
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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