Contacts of the strand formed by residues 692 - 697 (chain F) in PDB entry 6MZL
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 ARG 692 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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668F HIS* 3.4 38.1 + - + +
669F LYS* 3.1 26.6 - - - +
686F THR 3.5 4.0 - - - +
688F ALA* 3.3 23.6 + - - +
690F ASP* 3.3 16.3 - - + +
691F GLY* 1.3 78.3 - - - +
693F VAL* 1.3 67.5 + - - +
694F LEU* 4.2 5.9 - - - +
706F GLU* 2.4 42.2 + - - +
707F LEU 3.3 16.8 - - - +
708F LYS* 4.4 16.1 - - + +
714F VAL* 4.0 0.6 - - - +
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Residues in contact with VAL 693 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685F ALA* 3.9 17.0 - - + -
686F THR 3.3 20.4 - - - +
687F GLY* 4.0 9.4 - - - -
692F ARG* 1.3 76.4 - - - +
694F LEU* 1.3 66.4 + - - +
695F LEU* 4.1 1.2 + - - +
705F GLY 3.6 4.3 - - - +
706F GLU* 3.7 1.7 - - - -
707F LEU* 3.0 42.0 + - + +
710F HIS* 4.3 15.0 - - + +
714F VAL* 4.2 11.7 - - + -
717F LEU* 3.8 26.0 - - + -
726F LEU* 5.0 11.0 - - + -
728F SER* 4.8 0.2 - - - +
738F TRP* 5.8 0.9 - - - +
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Residues in contact with LEU 694 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666F THR 5.2 0.2 - - - +
668F HIS* 3.4 54.3 - - + +
684F LEU 3.6 2.1 - - - +
685F ALA* 3.7 0.3 - - - -
686F THR* 3.0 38.8 + - - +
692F ARG* 4.2 13.9 - - - +
693F VAL* 1.3 78.1 - - - +
695F LEU* 1.3 60.9 + - - +
696F TRP* 3.3 40.8 + - + +
703F MET* 4.8 19.5 - - + -
705F GLY 3.4 10.1 - - - +
706F GLU* 4.7 4.9 - - + -
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Residues in contact with LEU 695 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683F PHE* 4.6 12.3 - - + -
684F LEU 3.3 16.8 - - - +
685F ALA* 5.1 1.1 - - + +
693F VAL* 4.1 1.6 + - - +
694F LEU* 1.3 70.5 - - - +
696F TRP* 1.3 62.8 + - - +
697F ASP* 5.1 1.8 - - - +
702F LEU 3.6 0.3 - - - +
703F MET* 3.6 2.1 - - - -
704F VAL* 2.7 52.1 + - + +
705F GLY* 2.8 26.3 + - - +
719F PHE* 3.9 20.4 - - + -
724F GLU* 5.3 6.3 - - - +
726F LEU* 6.3 1.8 - - + -
740F ALA 6.1 0.2 - - - +
742F LYS* 4.0 32.5 - - + +
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Residues in contact with TRP 696 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651F VAL* 5.5 2.5 - - + +
665F PHE* 3.7 49.1 - + + -
666F THR* 3.5 34.1 - - - -
683F PHE* 3.8 3.8 - - - +
684F LEU* 3.2 40.5 + - + +
686F THR* 3.0 42.3 + - + +
694F LEU* 3.3 43.4 + - + +
695F LEU* 1.3 74.6 - - - +
697F ASP* 1.3 69.8 + - - +
701F GLY 4.4 6.5 - - - -
702F LEU 3.4 22.0 - - - -
703F MET* 3.6 37.0 - - + -
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Residues in contact with ASP 697 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665F PHE* 3.2 20.3 - - - -
682F ARG* 4.3 4.5 - - + +
683F PHE* 3.2 26.7 - - + -
684F LEU* 4.4 2.0 - - - -
695F LEU* 5.1 2.6 - - - +
696F TRP* 1.3 83.2 - - - +
698F ILE* 1.3 60.0 + - - +
699F GLY 4.7 0.7 - - - +
700F HIS* 4.5 20.5 - - + +
701F GLY* 3.3 21.5 + - - +
702F LEU* 3.4 15.4 + - - +
704F VAL* 3.3 24.5 - - - +
744F PHE 5.0 7.4 - - - +
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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