Contacts of the strand formed by residues 714 - 719 (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 VAL 714 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673G HIS* 3.6 13.3 - - - +
674G SER* 2.6 24.3 + - - -
687G GLY* 3.7 27.6 - - - +
688G ALA 3.7 21.8 + - - +
691G GLY* 3.8 22.4 - - - +
692G ARG 3.9 2.5 - - - +
693G VAL* 4.6 7.2 - - + -
710G HIS* 4.5 12.1 - - + -
712G ASP 4.1 0.4 - - - -
713G THR* 1.3 69.5 - - - +
715G CYS* 1.3 51.9 + - - +
716G SER 4.6 0.4 - - - +
717G LEU* 3.8 29.6 - - + -
728G SER* 4.4 8.5 - - - +
729G GLY 4.1 6.3 - - - +
730G SER* 4.4 1.6 - - - -
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Residues in contact with CYS 715 (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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673G HIS* 4.5 6.5 - - - +
674G SER* 2.8 19.6 + - - -
713G THR* 3.0 35.3 + - - +
714G VAL* 1.3 71.8 - - - +
716G SER* 1.3 59.9 + - - +
717G LEU 4.1 0.2 + - - -
729G GLY 3.1 6.7 + - - +
730G SER* 5.0 1.8 - - - -
731G MET* 4.7 12.8 - - - -
765G SER* 6.4 0.4 - - - -
766G GLN 3.4 22.0 - - - +
767G GLU 4.0 9.8 - - - +
768G LEU* 5.6 1.9 - - - +
62I LYS* 4.3 33.4 + - - +
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Residues in contact with SER 716 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714G VAL* 3.7 1.2 - - - -
715G CYS* 1.3 79.1 - - - +
717G LEU* 1.3 62.8 + - - +
728G SER* 3.2 6.8 + - - -
729G GLY* 2.8 42.6 + - - +
766G GLN* 3.8 14.0 + - - -
767G GLU 4.4 11.2 - - - -
768G LEU* 4.4 5.6 - - - +
769G LEU* 3.4 31.2 - - - +
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Residues in contact with LEU 717 (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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674G SER* 3.7 19.8 - - - -
675G LEU 4.1 0.7 - - - +
676G THR* 3.3 26.4 - - + +
685G ALA* 3.9 24.7 - - + +
687G GLY* 3.4 30.7 - - - +
693G VAL* 4.5 15.5 - - + -
714G VAL* 3.8 15.0 - - + -
715G CYS 4.1 1.6 + - - -
716G SER* 1.3 76.3 - - - +
718G ARG* 1.3 73.5 + - - +
726G LEU* 4.6 4.0 - - + -
727G ALA 3.7 2.7 - - - +
728G SER* 3.8 26.2 - - - +
769G LEU* 4.6 3.6 - - - +
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Residues in contact with ARG 718 (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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634G ARG* 3.2 35.6 - - - +
676G THR* 4.1 11.3 - - - +
677G PHE 5.4 2.6 + - - -
717G LEU* 1.3 83.4 + - - +
719G PHE* 1.3 83.1 + - - +
720G SER* 3.2 1.7 + - - +
726G LEU* 3.3 5.5 - - - +
727G ALA* 2.9 44.7 + - + +
768G LEU* 4.8 10.9 - - - +
769G LEU* 4.0 33.5 + - + -
770G LEU* 4.6 9.1 - - - +
771G GLY* 3.4 32.5 - - - +
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Residues in contact with PHE 719 (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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676G THR* 4.3 6.8 + - - +
677G PHE 3.2 24.5 + - - +
678G SER* 3.5 13.0 - - - -
679G PRO* 4.0 16.2 - - + +
683G PHE* 3.8 31.9 - - + -
684G LEU* 3.5 8.3 - - - -
685G ALA* 3.4 37.5 - - + -
695G LEU* 4.1 13.5 - - + -
718G ARG* 1.3 87.0 - - - +
720G SER* 1.3 66.9 + - - +
723G GLY 5.6 3.4 - - - +
724G GLU* 6.1 9.6 - - + -
725G ILE 4.4 3.8 - - - -
726G LEU* 3.5 28.7 - - + -
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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