Contacts of the strand formed by residues 683 - 688 (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 PHE 683 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677G PHE* 3.3 25.1 - - - +
678G SER* 3.0 9.7 + - - -
680G ASN* 5.0 10.5 - - - -
682G ARG* 1.3 130.4 - - + +
684G LEU* 1.3 69.0 + - - +
695G LEU* 4.1 9.2 - - + -
696G TRP 3.6 4.0 - - - +
697G ASP* 3.1 32.5 - - + -
719G PHE* 3.8 17.3 - + + -
724G GLU* 3.2 34.3 - - + -
742G LYS 4.4 7.4 - - - -
743G ALA* 5.4 9.0 - - + -
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Residues in contact with LEU 684 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643G ALA* 5.4 0.9 - - + -
651G VAL* 5.2 2.0 - - + -
653G LEU* 5.6 3.1 - - + -
665G PHE* 3.7 36.8 - - + -
675G LEU* 4.3 9.6 - - + -
676G THR 3.4 3.8 - - - +
677G PHE* 3.5 34.1 - - + -
682G ARG 4.8 1.8 - - - +
683G PHE* 1.3 81.4 - - - +
685G ALA* 1.3 58.5 + - - +
686G THR* 4.0 16.4 - - + -
695G LEU* 3.0 12.3 - - - +
696G TRP* 2.8 49.0 + - + +
697G ASP 4.7 6.1 - - - -
698G ILE* 4.7 8.7 - - + +
719G PHE* 3.5 6.7 - - - -
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Residues in contact with ALA 685 (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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675G LEU* 3.3 3.1 - - - -
676G THR* 2.8 45.3 + - - +
684G LEU* 1.3 73.7 - - - +
686G THR* 1.3 63.1 + - - +
693G VAL* 3.9 18.6 - - + -
694G LEU 3.3 4.7 - - - -
695G LEU* 5.4 0.4 - - - -
717G LEU* 4.0 14.8 - - + -
719G PHE* 3.4 21.8 - - + -
726G LEU* 4.7 3.1 - - + -
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Residues in contact with THR 686 (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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651G VAL* 4.5 12.8 - - + -
668G HIS* 5.6 1.0 - - - +
672G ILE* 5.4 5.6 - - - -
674G SER 3.6 7.9 - - - -
675G LEU* 3.8 24.2 - - + -
684G LEU* 4.0 9.6 - - + -
685G ALA* 1.3 78.7 - - - +
687G GLY* 1.3 62.2 + - - +
688G ALA* 5.1 1.7 - - - +
692G ARG 3.6 1.9 - - - +
693G VAL* 3.5 1.9 - - - -
694G LEU* 2.9 35.9 + - - +
696G TRP* 2.7 39.7 + - + +
717G LEU* 4.1 0.7 - - - -
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Residues in contact with GLY 687 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672G ILE* 4.0 3.3 - - - +
673G HIS 3.6 5.4 + - - -
674G SER* 3.2 29.2 + - - +
686G THR* 1.3 74.4 - - - +
688G ALA* 1.3 59.2 + - - +
692G ARG 3.4 6.5 - - - -
693G VAL* 4.2 4.9 - - - -
714G VAL* 3.7 29.3 - - - +
717G LEU* 3.4 9.4 - - - +
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Residues in contact with ALA 688 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668G HIS* 3.5 44.9 - - + +
670G GLY 4.4 6.3 - - - +
671G PRO 4.3 5.8 - - - +
672G ILE* 4.7 7.6 - - + +
673G HIS* 4.8 1.8 - - - +
686G THR 5.1 1.1 - - - +
687G GLY* 1.3 75.8 - - - +
689G THR* 1.3 53.3 + - - +
690G ASP 3.0 3.1 - - - +
691G GLY* 2.9 26.9 + - - -
692G ARG 2.9 13.4 + - - +
714G VAL* 3.7 10.6 + - - +
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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
------------------------------------------------------------
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