Contacts of the strand formed by residues 702 - 705 (chain A) in PDB entry 4ZGA
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 MET 702 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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628A MET* 4.3 2.1 - - - +
629A PRO* 4.9 0.7 - - - +
653A VAL* 4.7 15.0 - - + -
665A GLN* 2.8 46.2 + - + +
666A ASN 5.1 3.8 - - - +
667A CYS* 5.3 5.2 - - - -
670A TYR* 3.9 20.9 - - + -
678A TYR* 3.7 39.3 - - + -
679A GLY 3.3 4.3 - - - -
680A PHE* 4.1 7.6 - - + -
698A LEU 4.1 7.2 - - - +
699A VAL* 3.2 44.3 + - + +
700A THR 3.5 0.8 - - - -
701A ASN* 1.3 78.0 - - - +
703A VAL* 1.3 66.9 + - - +
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Residues in contact with VAL 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A MET* 3.9 26.9 - - + -
629A PRO* 4.3 4.3 - - + +
670A TYR* 3.5 5.2 - - - -
678A TYR* 3.1 4.9 - - - +
679A GLY 2.7 44.0 + - - +
680A PHE 4.7 0.2 - - - -
681A LEU* 3.9 29.8 - - + -
702A MET* 1.3 80.6 - - - +
704A PRO* 1.3 63.9 - - + +
705A MET* 3.4 28.0 - - + -
737A PRO* 5.4 0.9 - - + -
768A TYR* 3.2 20.2 - - + +
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Residues in contact with PRO 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A MET* 3.8 16.2 - - + -
665A GLN* 4.4 2.9 - - - +
670A TYR* 3.3 20.6 - - + +
676A MET* 3.7 24.2 - - + -
677A SER 3.5 4.7 - - - +
703A VAL* 1.3 86.9 - - + +
705A MET* 1.3 57.9 + - - +
757A VAL* 4.3 8.1 - - + -
762A ILE* 4.7 0.4 - - + -
763A PRO 3.7 11.7 - - - +
764A VAL* 4.1 4.9 - - + -
765A PRO* 3.6 21.5 - - + -
768A TYR* 2.4 24.0 + - - +
798A HIS* 3.3 11.1 - - - -
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Residues in contact with MET 705 (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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676A MET* 3.6 5.1 - - - -
677A SER* 3.0 33.9 + - - -
679A GLY* 3.7 24.0 - - - +
703A VAL* 3.4 26.8 + - + +
704A PRO* 1.3 78.4 - - - +
706A TYR* 1.3 65.1 + - - +
709A PHE* 3.7 25.8 - - + -
710A LYS* 3.6 21.4 - - + +
713A TRP* 3.4 50.7 - - + +
768A TYR* 4.2 10.8 - - + +
798A HIS* 3.5 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