Contacts of the helix formed by residues 687 - 692 (chain C) in PDB entry 6UZA
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 GLU 687 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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685B LEU* 4.9 5.2 - - + -
687B GLU* 5.3 8.7 - - - +
665C ASN* 5.6 3.3 + - - +
685C LEU 4.4 9.0 - - - +
686C SER* 1.3 80.6 - - - +
688C VAL* 1.3 60.9 + - - +
689C LYS* 3.2 30.4 - - + +
690C SER* 2.9 25.2 + - - -
708C TYR* 4.0 5.6 - - - -
687D GLU* 5.3 8.3 - - - +
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Residues in contact with VAL 688 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680B TRP* 3.8 35.0 - - + +
685B LEU* 3.7 45.8 - - + +
687C GLU* 1.3 72.3 - - - +
689C LYS* 1.3 59.5 + - - +
690C SER 3.1 6.0 + - - -
691C VAL* 3.3 19.7 - - + +
692C VAL* 4.0 5.2 - - - +
705C TYR* 3.6 28.6 + - + +
708C TYR* 4.7 6.7 - - + -
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Residues in contact with LYS 689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664C GLN* 3.6 50.4 + - + +
665C ASN* 3.5 22.6 - - - +
687C GLU* 3.8 25.5 - - + +
688C VAL* 1.3 77.7 - - - +
690C SER* 1.3 57.1 + - - +
691C VAL 3.3 3.2 + - - -
692C VAL* 3.7 14.3 + - + +
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Residues in contact with SER 690 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663C LYS* 2.7 27.7 + - - -
665C ASN* 3.4 24.9 - - - +
667C ALA* 3.8 15.5 - - - -
668C PHE* 3.4 17.3 - - - -
677C THR* 3.9 16.1 - - - +
686C SER* 5.2 0.6 - - - -
687C GLU 2.9 23.9 + - - -
688C VAL 3.1 0.2 - - - -
689C LYS* 1.3 77.5 - - - +
691C VAL* 1.3 56.5 + - - +
708C TYR* 4.5 3.8 - - - -
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Residues in contact with VAL 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652C MET* 5.3 0.4 - - - -
656C TYR* 2.5 35.1 + - + +
663C LYS* 3.5 5.8 - - - +
668C PHE* 4.0 17.0 - - + -
688C VAL* 3.3 19.7 - - + +
689C LYS 3.3 0.2 - - - -
690C SER* 1.3 83.6 - - - +
692C VAL* 1.3 59.9 + - - +
701C GLU* 3.6 11.6 - - - +
704C GLY 4.0 18.8 - - - +
705C TYR* 3.8 36.1 - - + -
708C TYR* 4.1 21.1 - - + -
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Residues in contact with VAL 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663C LYS* 3.5 7.2 - - - +
664C GLN* 3.2 42.9 + - + +
688C VAL 4.0 11.2 - - - +
689C LYS* 3.7 14.5 + - + +
690C SER 3.6 0.4 - - - -
691C VAL* 1.3 81.2 - - - +
693C ILE* 1.3 74.4 + - - +
694C ASN* 5.4 0.2 - - - +
698C LYS* 5.3 1.3 - - - +
701C GLU* 4.2 17.7 - - - +
705C TYR* 3.6 24.2 - - + +
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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