Contacts of the strand formed by residues 778 - 782 (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 THR 778 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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720G SER* 5.6 4.2 - - - -
727G ALA* 4.5 16.8 - - + +
735G VAL* 6.2 1.8 - - + -
737G LEU* 5.4 6.0 - - + +
769G LEU* 3.9 24.9 - - + -
770G LEU 3.8 5.4 - - - +
771G GLY* 4.8 4.0 - - - -
777G SER* 1.3 85.2 + - - +
779G PRO* 1.3 64.6 - - - +
780G VAL* 4.5 2.5 - - + -
791G VAL* 3.5 0.8 - - - +
792G LEU* 2.8 65.4 + - + +
793G ALA* 5.3 2.8 - - - -
794G ALA* 5.6 4.3 - - - +
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Residues in contact with PRO 779 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464G TYR* 5.9 0.2 - - - +
477G ASP* 5.1 10.3 - - - +
480G ASP* 6.1 0.2 - - - +
769G LEU* 3.3 4.9 - - - +
770G LEU* 3.2 43.5 + - + +
772G THR* 3.2 20.4 - - + +
777G SER* 4.9 0.7 - - - -
778G THR* 1.3 87.6 - - - +
780G VAL* 1.3 60.7 + - - +
781G VAL* 5.8 0.2 - - - -
789G ASN* 3.5 20.4 - - - +
790G LEU 3.6 5.2 - - - +
791G VAL* 4.1 19.7 - - + -
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Residues in contact with VAL 780 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735G VAL* 5.1 4.7 - - + -
766G GLN* 3.3 38.8 - - + +
768G LEU 3.2 21.8 - - - +
769G LEU* 3.7 22.7 - - + -
778G THR* 4.5 4.7 - - + +
779G PRO* 1.3 77.5 - - + +
781G VAL* 1.3 65.3 + - - +
782G HIS* 3.3 14.6 - - - +
789G ASN* 2.8 18.3 - - - +
790G LEU 2.9 24.8 + - - +
792G LEU* 4.2 19.1 - - + -
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Residues in contact with VAL 781 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475G ALA* 3.6 40.8 - - + +
476G VAL* 5.9 0.7 - - - -
477G ASP* 5.8 6.7 - - - +
483G SER* 5.7 8.5 - - - -
485G ILE* 5.2 7.9 - - + -
766G GLN* 3.4 26.2 - - - +
767G GLU* 3.5 11.9 + - + +
768G LEU 3.3 18.5 + - - +
769G LEU 4.9 0.9 - - - +
779G PRO 5.8 0.2 - - - -
780G VAL* 1.3 80.1 - - - +
782G HIS* 1.3 66.5 + - - +
783G LEU* 4.2 10.5 - - + -
787G ARG 5.8 3.1 - - - +
788G ARG 5.7 0.2 - - - -
789G ASN* 4.6 14.6 - - + +
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Residues in contact with HIS 782 (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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761G LEU* 3.3 26.5 - - + +
764G ASN* 3.4 21.9 + - + +
765G SER 3.7 4.5 - - - -
766G GLN* 3.3 25.4 + - - -
780G VAL* 3.1 40.4 + - + +
781G VAL* 1.3 76.6 - - - +
783G LEU* 1.3 64.6 + - - +
786G THR 2.8 22.6 - - - +
788G ARG* 3.1 28.2 + - + +
790G LEU* 3.2 38.0 + - + +
792G LEU* 5.6 2.9 - - + -
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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