Contacts of the helix formed by residues 670 - 680 (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 THR 670 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465B PHE 3.3 18.4 - - - +
466B GLU* 3.8 22.2 + - + +
467B GLY* 4.4 3.0 + - - +
653C PHE* 4.2 3.3 - - - -
660C ILE* 5.0 4.5 - - - +
668C PHE 4.2 0.2 - - - -
669C THR* 1.3 83.6 + - - +
671C VAL* 1.3 64.5 + - - +
672C GLU* 3.3 23.3 - - + +
673C GLU* 3.4 19.8 + - - +
674C SER* 3.0 27.5 + - - -
1004C SBJ 6.3 1.1 - - - +
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Residues in contact with VAL 671 (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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465B PHE* 3.3 48.4 + - + +
649C MET* 4.3 22.4 - - + +
650C ILE* 6.5 0.7 - - + -
653C PHE* 4.0 20.0 - - + -
670C THR* 1.3 76.7 - - - +
672C GLU* 1.3 58.1 + - - +
674C SER* 3.5 5.9 + - - +
675C PHE* 2.9 28.0 + - + +
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Residues in contact with GLU 672 (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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670C THR* 3.8 17.9 - - + +
671C VAL* 1.3 77.3 - - - +
673C GLU* 1.3 73.6 + - + +
675C PHE* 3.3 10.7 + - + +
676C LYS* 2.9 51.7 + - - +
1004C SBJ 3.0 48.4 + - - +
702D ASN* 5.0 2.8 + - - +
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Residues in contact with GLU 673 (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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666C GLU* 3.0 39.6 - - + +
667C ALA* 4.3 1.1 - - - -
668C PHE 4.0 4.9 - - - +
669C THR* 4.4 1.1 - - - +
670C THR* 3.4 31.3 + - - +
671C VAL 3.3 0.6 - - - -
672C GLU* 1.3 89.8 - - + +
674C SER* 1.3 56.0 + - - +
676C LYS* 3.5 25.1 + - - +
677C THR* 2.4 40.0 + - - -
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Residues in contact with SER 674 (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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649C MET* 3.1 32.6 + - - +
652C MET* 5.0 0.2 - - - +
653C PHE* 4.1 13.2 - - - +
668C PHE* 3.8 33.8 - - - +
670C THR 3.0 16.8 + - - -
671C VAL 4.0 3.8 - - - -
673C GLU* 1.3 76.5 - - - +
675C PHE* 1.3 62.3 + - - +
677C THR 4.1 0.4 - - - -
678C LEU* 3.4 26.3 + - - +
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Residues in contact with PHE 675 (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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645C PHE* 3.4 33.6 - + - -
649C MET* 3.7 18.2 - - - -
671C VAL* 2.9 19.7 + - + +
672C GLU* 3.5 11.7 - - + +
673C GLU 3.2 0.2 - - - -
674C SER* 1.3 77.9 - - - +
676C LYS* 1.3 61.9 + - - +
678C LEU 3.4 1.4 + - - -
679C PHE* 2.9 34.8 + + + +
1004C SBJ 3.6 58.3 - - + -
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Residues in contact with LYS 676 (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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672C GLU* 2.9 41.3 + - - +
673C GLU* 3.5 32.7 + - - +
675C PHE* 1.3 77.4 - - + +
677C THR* 1.3 64.7 + - - +
679C PHE* 4.2 6.3 - - - -
680C TRP* 2.9 47.5 + - + +
1004C SBJ 4.1 33.6 + - + -
701D GLU* 5.7 0.4 + - - -
702D ASN* 5.4 1.8 + - - -
705D TYR* 4.4 29.5 + - + +
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Residues in contact with THR 677 (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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667C ALA* 3.4 28.2 - - + +
668C PHE* 3.7 31.2 - - + -
673C GLU* 2.4 25.6 + - - -
674C SER 4.4 0.2 - - - -
676C LYS* 1.3 79.1 - - - +
678C LEU* 1.3 60.2 + - - +
681C ALA* 3.4 12.8 + - - +
686C SER* 3.1 28.9 + - - +
690C SER* 3.9 15.0 - - - +
708C TYR* 4.1 2.8 + - - +
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Residues in contact with LEU 678 (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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645C PHE* 3.3 18.5 - - + +
648C PHE* 3.7 18.6 - - + +
649C MET* 3.5 36.8 - - + +
652C MET* 3.8 15.7 - - + -
668C PHE* 3.6 25.4 - - + -
674C SER 3.4 15.6 + - - +
675C PHE 3.4 1.4 + - - -
676C LYS 3.3 0.4 - - - -
677C THR* 1.3 75.2 - - - +
679C PHE* 1.3 63.8 + - - +
681C ALA 3.8 3.0 + - - -
682C ILE* 3.7 4.2 - - - +
708C TYR* 4.1 6.5 - - + -
711C TYR* 2.5 50.8 + - + +
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Residues in contact with PHE 679 (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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645C PHE* 3.6 14.6 - + + -
675C PHE* 2.9 29.8 + + + +
676C LYS* 3.3 6.5 + - - +
678C LEU* 1.3 78.3 - - - +
680C TRP* 1.3 77.7 + + - +
681C ALA 3.1 1.9 + - - -
682C ILE* 3.3 33.0 + - + +
683C PHE* 3.9 27.0 - + - -
1004C SBJ 3.8 54.1 - - + -
709D GLY* 3.9 14.6 - - - -
713D VAL* 4.1 19.1 - - + -
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Residues in contact with TRP 680 (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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676C LYS* 2.9 38.0 + - + +
679C PHE* 1.3 84.9 - + - +
681C ALA* 1.3 57.8 + - - +
682C ILE 3.3 0.4 - - - -
683C PHE* 3.7 17.3 + + - -
684C GLY 3.5 2.8 + - - -
685C LEU* 2.9 56.7 + - + +
686C SER* 3.7 12.6 - - - +
1004C SBJ 3.6 17.5 - - + +
688D VAL* 3.8 27.8 - - + +
705D TYR* 4.0 26.2 - + - -
708D TYR* 3.5 28.9 - + - -
709D GLY* 3.6 23.8 - - - -
712D ASN* 3.7 22.4 - - - -
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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