Contacts of the strand formed by residues 672 - 677 (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 672 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631G ASN* 2.5 33.1 + - - +
632G CYS* 4.4 13.7 - - - -
645G GLY* 3.8 3.8 - - - -
646G SER 3.3 22.2 + - - +
649G ARG 3.6 26.0 - - - +
650G THR 3.6 18.8 - - - +
651G VAL* 3.7 21.3 - - + -
668G HIS* 5.7 2.2 - - + +
670G GLY 4.5 3.1 - - - +
671G PRO* 1.3 72.8 - - - +
673G HIS* 1.3 65.1 + - - +
674G SER 3.4 26.5 - - - +
675G LEU* 5.2 2.5 - - + -
686G THR* 5.4 6.5 - - - -
687G GLY 4.0 7.6 - - - +
688G ALA* 4.7 6.7 - - + +
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Residues in contact with HIS 673 (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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631G ASN* 4.8 1.6 - - - -
632G CYS* 4.8 10.3 - - - +
671G PRO* 3.3 22.0 + - + +
672G ILE* 1.3 76.3 - - - +
674G SER* 1.3 66.3 + - - +
687G GLY 3.6 5.6 + - - +
688G ALA 5.3 0.4 - - - -
689G THR* 3.3 34.8 + - - +
713G THR* 4.3 23.7 - - + +
714G VAL 3.6 17.9 - - - +
715G CYS* 4.5 7.3 - - - +
59I HIS* 3.1 38.1 + - + +
60I MET* 3.3 32.0 - - + +
62I LYS* 5.8 7.0 + - - +
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Residues in contact with SER 674 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632G CYS* 4.3 4.9 - - - -
672G ILE* 3.4 12.1 - - - +
673G HIS* 1.3 82.9 + - - +
675G LEU* 1.3 63.3 + - - +
686G THR* 3.6 1.7 - - - -
687G GLY 3.2 26.2 + - - +
714G VAL* 2.6 26.2 + - - -
715G CYS 2.8 24.1 + - - -
717G LEU* 3.7 23.6 - - - -
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Residues in contact with LEU 675 (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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632G CYS* 3.6 25.4 - - - +
634G ARG* 3.6 29.7 + - + +
643G ALA* 3.7 16.8 - - + -
645G GLY* 4.7 4.7 - - - +
651G VAL* 3.7 32.5 - - + -
672G ILE* 5.5 1.3 - - + -
674G SER* 1.3 78.0 - - - +
676G THR* 1.3 86.8 + - - +
677G PHE* 3.7 30.5 - - + -
684G LEU* 4.3 2.5 - - + -
685G ALA 3.3 7.9 - - - -
686G THR* 3.8 20.0 - - + -
717G LEU* 4.1 2.2 - - - +
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Residues in contact with THR 676 (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* 3.4 13.5 - - - +
675G LEU* 1.3 81.6 - - - +
677G PHE* 1.3 84.5 + - - +
684G LEU* 3.4 5.0 - - - +
685G ALA* 2.8 45.8 + - - +
717G LEU* 3.3 37.9 - - + +
718G ARG* 4.0 14.8 - - - +
719G PHE* 4.3 9.3 - - - -
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Residues in contact with PHE 677 (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* 3.7 11.5 - - + +
635G PHE 3.2 28.5 - - - +
636G HIS* 3.3 42.0 - + + +
637G PRO* 4.0 11.9 - - + -
641G TYR* 4.7 2.0 - - + -
642G VAL 4.9 0.4 - - - -
643G ALA* 3.6 22.9 - - + -
653G LEU* 4.1 13.5 - - + -
675G LEU* 3.7 14.4 - - + -
676G THR* 1.3 89.0 - - - +
678G SER* 1.3 63.6 + - - +
679G PRO* 4.5 0.3 - - - +
683G PHE 3.3 8.1 - - - +
684G LEU* 3.5 32.5 - - + -
698G ILE* 6.6 0.2 - - + -
718G ARG* 5.4 3.5 + - - -
719G PHE* 3.2 20.4 + - - +
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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