Contacts of the strand formed by residues 688 - 691 (chain M) in PDB entry 1ZYR
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 ILE 688 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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682M TYR 4.4 2.0 - - - -
683M ASN* 4.0 3.6 - - - -
686M ASP 3.7 8.5 - - - +
687M ALA* 1.3 81.3 - - - +
689M VAL* 1.3 63.4 + - - +
690M ILE* 4.9 2.7 - - + -
839M LEU* 3.4 39.3 - - + +
845M ASN* 5.2 7.4 - - - +
846M LYS* 6.0 0.2 - - - -
847M GLY* 4.5 10.8 - - - +
848M VAL 3.1 9.8 + - - +
849M VAL* 3.3 11.1 - - - +
850M ALA 3.1 20.6 + - - -
851M LYS 4.0 0.2 + - - -
869M VAL* 3.0 35.0 - - + -
870M ILE 4.7 1.3 - - - +
871M LEU* 3.4 29.2 - - + -
994M ILE* 5.2 2.2 - - + -
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Residues in contact with VAL 689 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679M PHE* 4.1 7.9 - - + -
682M TYR* 4.3 16.8 - - + -
683M ASN* 3.7 19.5 - - + +
688M ILE* 1.3 76.1 - - - +
690M ILE* 1.3 53.9 + - - +
851M LYS 3.5 14.8 - - - +
853M LEU* 3.5 33.9 - - + -
858M MET* 5.4 0.7 - - + -
869M VAL* 2.9 31.2 - - - +
870M ILE* 3.2 49.4 + - + +
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Residues in contact with ILE 690 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688M ILE* 4.9 0.4 - - + -
689M VAL* 1.3 80.4 - - - +
691M SER* 1.3 67.7 + - - +
692M GLU* 4.9 0.2 - - - -
694M LEU* 3.3 26.5 - - + -
695M LEU* 5.2 5.4 - - + -
700M TYR* 5.4 2.5 - - + -
833M LEU* 4.0 21.8 - - + -
839M LEU* 4.2 8.3 - - + -
849M VAL* 3.6 28.3 - - + -
851M LYS 2.8 13.1 + - - +
852M ILE* 2.9 30.3 - - + -
853M LEU* 2.5 33.1 + - - -
858M MET* 4.5 2.9 - - - -
868M ASP 3.7 1.3 - - - -
869M VAL* 4.1 12.1 - - + -
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Residues in contact with SER 691 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690M ILE* 1.3 73.4 - - - +
692M GLU* 1.3 67.7 + - - +
693M GLU* 2.9 25.1 + - - +
694M LEU* 2.9 16.8 + - - +
853M LEU 3.3 8.2 + - - -
855M VAL* 4.7 6.5 - - - +
858M MET* 2.7 33.3 - - - -
866M PRO* 6.0 0.7 - - - +
867M VAL 3.8 7.0 + - - -
868M ASP* 2.9 19.4 + - - -
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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