Contacts of the strand formed by residues 692 - 697 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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668G HIS* 3.4 35.5 - - + +
669G LYS* 3.9 20.7 - - - +
686G THR 3.6 2.6 - - - +
687G GLY* 3.4 1.1 - - - -
688G ALA* 2.9 32.2 + - - +
690G ASP* 3.6 16.1 - - + +
691G GLY* 1.3 78.4 - - - +
693G VAL* 1.3 68.5 + - - +
694G LEU* 4.7 3.6 - - + +
706G GLU* 2.4 43.8 + - - +
707G LEU 3.1 14.6 + - - +
708G LYS* 4.3 23.0 - - + +
714G VAL* 3.9 0.8 - - - +
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Residues in contact with VAL 693 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685G ALA* 3.9 27.8 - - + -
686G THR 3.5 6.7 - - - +
687G GLY* 4.2 1.3 - - - -
692G ARG* 1.3 77.3 - - - +
694G LEU* 1.3 70.5 + - - +
695G LEU* 4.0 1.1 - - - +
705G GLY 3.4 0.3 - - - +
706G GLU* 3.4 7.1 - - - -
707G LEU* 2.8 63.0 + - + +
710G HIS* 4.7 11.4 - - + +
714G VAL* 4.6 13.0 - - + -
717G LEU* 4.5 20.6 - - + -
726G LEU* 4.8 2.9 - - + -
728G SER* 4.8 2.9 - - - +
738G TRP* 5.3 0.2 - - - +
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Residues in contact with LEU 694 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666G THR 5.0 0.7 - - - +
668G HIS* 3.5 49.4 - - + +
684G LEU 3.3 0.7 - - - +
685G ALA* 3.3 3.1 - - - -
686G THR* 2.9 37.9 + - - +
692G ARG* 4.7 3.6 - - - +
693G VAL* 1.3 83.3 - - - +
695G LEU* 1.3 63.8 + - - +
696G TRP* 3.4 44.1 - - + +
703G MET* 4.8 16.4 - - + -
705G GLY 3.2 9.2 - - - +
706G GLU* 4.5 10.5 - - + -
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Residues in contact with LEU 695 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683G PHE* 4.1 17.3 - - + -
684G LEU 3.0 19.5 - - - +
685G ALA* 4.7 1.3 - - - +
693G VAL* 4.0 3.3 - - + +
694G LEU* 1.3 71.2 - - - +
696G TRP* 1.3 60.9 + - - +
697G ASP* 4.7 2.7 - - - +
703G MET* 3.5 2.1 - - - -
704G VAL* 2.5 59.0 + - + -
705G GLY* 2.8 22.9 + - - +
707G LEU* 6.1 1.7 - - + +
719G PHE* 4.1 17.3 - - + -
724G GLU* 4.6 7.9 - - + +
742G LYS* 3.9 28.0 - - + +
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Residues in contact with TRP 696 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651G VAL* 5.3 2.3 - - + +
665G PHE* 3.6 49.9 - + + +
666G THR* 3.3 31.9 - - - -
668G HIS* 5.6 0.2 - - + -
683G PHE* 3.6 1.6 - - - +
684G LEU* 2.8 41.5 + - + +
686G THR* 2.7 43.9 + - + +
694G LEU* 3.4 41.1 - - + +
695G LEU* 1.3 73.5 - - - +
697G ASP* 1.3 72.0 + - - +
701G GLY 4.4 5.4 - - - -
702G LEU 3.2 11.9 - - - -
703G MET* 3.3 49.4 - - + -
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Residues in contact with ASP 697 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665G PHE* 3.2 19.4 - - - -
682G ARG 4.3 4.5 - - - +
683G PHE* 3.1 32.0 - - + -
684G LEU* 4.7 1.6 - - - -
695G LEU* 4.7 3.6 - - - +
696G TRP* 1.3 84.4 - - - +
698G ILE* 1.3 62.5 + - - +
700G HIS* 4.6 24.3 - - + -
701G GLY* 3.3 12.1 - - - -
702G LEU* 3.1 15.9 + - + +
704G VAL* 3.3 24.9 - - + +
744G PHE 5.2 5.2 - - - +
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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