Contacts of the strand formed by residues 734 - 739 (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 734 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710G HIS* 3.8 12.8 + - - +
729G GLY* 3.1 4.7 - - - -
730G SER* 2.3 54.7 + - - +
732G ASP* 2.9 30.7 + - - +
733G ASN* 1.3 77.0 - - - +
735G VAL* 1.3 65.0 + - - +
736G ARG* 4.2 8.1 - - - +
758G HIS* 5.4 4.0 - - + -
760G ASN* 3.3 21.5 - - - +
766G GLN* 4.4 1.3 - - - +
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Residues in contact with VAL 735 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727G ALA* 5.8 2.7 - - + -
728G SER 3.2 15.5 - - - +
734G THR* 1.3 71.6 - - - +
736G ARG* 1.3 69.5 + - - +
737G LEU* 4.2 7.5 + - + +
758G HIS* 3.2 2.0 - - - +
759G ILE* 2.6 55.6 + - + +
761G LEU* 5.2 4.7 - - + -
766G GLN* 3.3 40.6 - - - +
769G LEU* 6.1 2.9 - - + -
778G THR* 6.2 1.3 - - + -
780G VAL* 5.1 7.4 - - + -
792G LEU* 5.1 22.2 - - + -
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Residues in contact with ARG 736 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708G LYS 2.8 30.1 + - - -
709G GLY* 2.8 33.7 + - - -
710G HIS* 3.4 30.3 + - + +
727G ALA* 3.8 0.5 - - - -
728G SER* 2.9 33.0 + - - -
734G THR* 5.5 6.0 - - - +
735G VAL* 1.3 77.3 - - - +
737G LEU* 1.3 71.2 + - - +
738G TRP* 3.6 22.0 - - + +
756G THR 5.5 3.4 - - - +
757G GLY* 4.9 1.8 - - - +
758G HIS* 3.6 32.2 + - + +
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Residues in contact with LEU 737 (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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459G PRO* 6.2 0.7 - - + -
725G ILE* 5.1 6.7 - - + -
726G LEU 3.3 14.8 - - - +
727G ALA* 4.1 16.2 - - + -
735G VAL* 4.1 8.2 + - + +
736G ARG* 1.3 81.8 - - - +
738G TRP* 1.3 75.5 + - - +
739G ASP* 5.1 5.8 - - - +
756G THR* 3.5 30.8 - - + -
757G GLY 4.0 8.4 + - - +
758G HIS 5.6 0.2 - - - -
759G ILE* 5.3 12.7 - - + +
778G THR* 5.4 6.1 - - + +
792G LEU* 5.5 8.3 - - + -
793G ALA 4.2 9.2 - - - +
794G ALA* 3.9 29.4 - - + -
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Residues in contact with TRP 738 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693G VAL* 5.3 0.2 - - - +
707G LEU* 3.7 53.2 - - + +
708G LYS 4.2 7.4 - - - -
710G HIS* 3.5 21.7 + + - -
724G GLU 3.8 0.5 - - - +
725G ILE* 3.5 5.8 - - - -
726G LEU* 2.9 57.8 + - + +
728G SER* 4.0 7.1 - - - -
736G ARG* 3.6 44.3 - - + +
737G LEU* 1.3 86.5 - - - +
739G ASP* 1.3 62.6 + - - +
740G ALA* 3.4 11.3 + - + +
753G THR* 6.0 2.7 - - - -
754G THR 5.4 3.1 - - - -
755G ALA* 3.6 31.6 - - + -
756G THR* 3.3 17.0 - - - -
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Residues in contact with ASP 739 (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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724G GLU 4.4 3.1 - - - -
725G ILE* 3.6 29.7 - - - +
737G LEU* 5.2 4.2 - - - +
738G TRP* 1.3 68.6 + - - +
740G ALA* 1.3 58.9 + - - +
741G ILE* 4.2 1.3 - - - -
755G ALA* 3.4 21.9 - - - +
756G THR* 2.4 35.0 + - - +
796G ALA* 3.4 34.0 + - - +
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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