Contacts of the strand formed by residues 725 - 730 (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 ILE 725 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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719G PHE* 5.1 2.0 - - - +
720G SER* 2.7 44.5 + - - +
721G ARG 5.1 3.1 - - - +
723G GLY* 2.6 17.1 + - - +
724G GLU* 1.3 78.2 - - - +
726G LEU* 1.3 67.3 + - - +
737G LEU* 5.1 9.2 - - + -
738G TRP 3.5 3.8 - - - +
739G ASP* 3.6 24.7 - - - +
776G LYS* 4.1 22.9 - - - +
794G ALA* 5.3 11.4 - - + -
795G GLY* 6.5 0.9 - - - -
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Residues in contact with LEU 726 (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* 4.7 1.1 - - + -
693G VAL* 4.8 9.4 - - + -
707G LEU* 3.8 29.6 - - + -
717G LEU* 4.6 11.0 - - + -
718G ARG 3.3 17.5 - - - +
719G PHE* 3.5 34.5 - - + +
720G SER* 5.4 0.2 - - - -
724G GLU 3.9 1.0 - - - -
725G ILE* 1.3 76.3 - - - +
727G ALA* 1.3 75.5 + - - +
728G SER* 5.0 0.2 - - - -
737G LEU* 3.3 12.9 - - - +
738G TRP* 2.9 50.7 + - + +
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Residues in contact with ALA 727 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717G LEU* 3.7 0.2 - - - -
718G ARG* 2.9 42.6 + - + +
720G SER* 5.5 4.7 - - - -
725G ILE 3.7 1.2 + - - -
726G LEU* 1.3 78.6 - - - +
728G SER* 1.3 63.9 + - - +
735G VAL* 5.8 3.1 - - + -
736G ARG 3.9 3.1 - - - -
737G LEU* 4.1 11.9 - - + -
769G LEU* 4.0 18.6 - - + -
771G GLY* 5.9 2.0 - - - +
778G THR* 4.5 20.0 - - + +
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Residues in contact with SER 728 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693G VAL* 4.8 2.1 - - - +
710G HIS* 3.1 24.5 + - - -
714G VAL* 4.4 5.7 - - - +
716G SER* 3.2 8.1 - - - -
717G LEU* 3.8 20.4 - - - +
726G LEU* 5.0 1.3 - - - -
727G ALA* 1.3 77.9 - - - +
729G GLY* 1.3 60.9 + - - +
735G VAL* 3.2 10.1 - - - +
736G ARG 2.9 37.7 + - - +
738G TRP* 4.0 14.6 - - - -
769G LEU* 4.4 3.1 - - - +
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Residues in contact with GLY 729 (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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710G HIS* 4.5 3.8 - - - -
714G VAL* 4.0 2.9 - - - +
715G CYS* 3.1 8.3 + - - +
716G SER* 2.8 44.6 + - - +
728G SER* 1.3 79.6 + - - +
730G SER* 1.3 60.5 + - - -
734G THR 3.1 12.1 - - - -
766G GLN* 3.9 11.9 - - - -
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Residues in contact with SER 730 (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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710G HIS* 2.7 29.2 + - - +
713G THR 3.3 21.3 - - - -
714G VAL* 4.4 1.1 - - - -
715G CYS* 4.3 2.5 - - - +
729G GLY* 1.3 74.5 - - - -
731G MET* 1.3 54.5 + - - +
732G ASP* 2.4 26.6 + - - -
733G ASN* 2.9 15.6 + - - -
734G THR* 2.3 40.8 + - - +
766G GLN* 4.7 10.0 + - - +
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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