Contacts of the helix formed by residues 670 - 680 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A ARG 5.1 0.2 - - - -
465A PHE 3.3 17.7 - - - +
466A GLU* 3.8 22.0 + - + -
467A GLY* 4.4 2.3 + - - +
653B PHE* 4.2 3.5 - - - -
660B ILE* 5.0 4.3 - - - +
668B PHE 4.2 0.2 - - - -
669B THR* 1.3 84.2 + - - +
671B VAL* 1.3 64.5 + - - +
672B GLU* 3.3 22.0 - - + +
673B GLU* 3.7 19.4 - - - +
674B SER* 3.0 28.1 + - - -
1004B SBJ 6.3 0.9 - - - +
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Residues in contact with VAL 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A PHE* 3.3 49.5 + - + +
649B MET* 4.3 22.4 - - + +
650B ILE* 6.5 0.7 - - + -
653B PHE* 4.0 20.0 - - + -
670B THR* 1.3 77.9 - - - +
672B GLU* 1.3 57.8 + - - +
674B SER* 3.5 5.8 + - - -
675B PHE* 2.9 27.6 + - + +
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Residues in contact with GLU 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670B THR* 3.8 18.6 - - + +
671B VAL* 1.3 77.9 - - - +
673B GLU* 1.3 74.0 + - + +
675B PHE* 3.3 11.5 + - + +
676B LYS* 2.9 52.4 + - - +
1004B SBJ 3.0 47.9 + - - +
702C ASN* 5.0 2.9 + - - +
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Residues in contact with GLU 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666B GLU* 3.0 38.1 - - + +
667B ALA* 4.3 1.4 - - - -
668B PHE 4.0 5.4 - - - +
669B THR* 4.4 1.8 - - - +
670B THR* 3.4 31.5 + - - +
671B VAL 3.3 0.4 - - - -
672B GLU* 1.3 89.6 - - + +
674B SER* 1.3 56.2 + - - +
676B LYS* 3.4 25.1 + - - +
677B THR* 2.4 40.3 + - - -
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Residues in contact with SER 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649B MET* 3.1 32.2 + - - +
653B PHE* 4.2 12.8 - - - -
668B PHE* 3.8 34.1 - - - +
670B THR 3.0 17.4 + - - -
671B VAL* 4.0 3.8 - - - -
673B GLU* 1.3 75.4 - - - +
675B PHE* 1.3 61.2 + - - +
677B THR* 4.1 0.7 - - - -
678B LEU* 3.4 26.7 + - - +
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Residues in contact with PHE 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645B PHE* 3.4 34.4 - + - -
649B MET* 3.7 18.8 - - + -
671B VAL* 2.9 18.9 + - + +
672B GLU* 3.5 11.2 - - + +
673B GLU 3.2 0.2 - - - -
674B SER* 1.3 77.0 - - - +
676B LYS* 1.3 62.8 + - + +
678B LEU 3.4 1.4 + - - -
679B PHE* 2.9 33.7 + + + +
1004B SBJ 3.6 59.9 - - + -
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Residues in contact with LYS 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672B GLU* 2.9 41.8 + - - +
673B GLU* 3.5 32.4 + - - +
675B PHE* 1.3 76.3 - - - +
677B THR* 1.3 64.5 + - - +
679B PHE* 4.2 6.5 - - - -
680B TRP* 2.9 48.5 + - + +
1004B SBJ 4.1 33.3 + - + -
701C GLU* 5.7 0.6 + - - -
702C ASN* 5.4 1.8 + - - -
705C TYR* 4.4 29.7 + - + +
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Residues in contact with THR 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667B ALA* 3.4 28.3 - - + +
668B PHE* 3.7 30.5 + - + -
673B GLU* 2.4 25.1 + - - +
674B SER 4.4 0.2 - - - -
676B LYS* 1.3 79.4 - - - +
678B LEU* 1.3 60.5 + - - +
681B ALA* 3.4 12.0 + - - +
686B SER* 3.1 30.2 + - - +
690B SER* 3.9 14.6 - - - +
708B TYR* 4.1 3.2 + - - +
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Residues in contact with LEU 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645B PHE* 3.3 18.7 - - + +
648B PHE* 3.7 19.1 - - + +
649B MET* 3.5 37.0 - - + +
652B MET* 3.8 15.9 - - + -
668B PHE* 3.6 24.5 - - + -
674B SER 3.4 14.7 + - - +
675B PHE 3.4 1.6 + - - -
676B LYS 3.3 0.4 - - - -
677B THR* 1.3 74.8 - - - +
679B PHE* 1.3 63.8 + - - +
681B ALA* 3.8 2.9 + - - -
682B ILE* 3.7 4.3 - - - +
708B TYR* 4.1 6.5 - - + -
711B TYR* 2.5 50.6 + - + +
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Residues in contact with PHE 679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645B PHE* 3.4 13.7 - + + -
675B PHE* 2.9 30.9 + + + +
676B LYS* 3.3 6.7 + - - +
678B LEU* 1.3 78.4 - - - +
680B TRP* 1.3 76.5 + + - +
681B ALA 3.1 2.4 + - - -
682B ILE* 3.3 32.9 + - + +
683B PHE* 3.9 27.4 - + - -
1004B SBJ 3.8 52.7 - - + -
709C GLY* 3.9 14.4 - - - -
713C VAL* 4.1 19.3 - - + -
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Residues in contact with TRP 680 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676B LYS* 2.9 38.2 + - + +
679B PHE* 1.3 83.3 - + - +
681B ALA* 1.3 58.5 + - - +
682B ILE 3.3 0.7 - - - -
683B PHE* 3.7 17.5 + + - +
684B GLY 3.5 2.3 + - - -
685B LEU* 2.9 55.8 + - + +
686B SER* 3.7 13.0 - - - +
1004B SBJ 3.6 18.8 - - + +
688C VAL* 3.8 28.3 - - + +
705C TYR* 4.0 27.2 - + - -
708C TYR* 3.5 29.8 - + + -
709C GLY* 3.6 23.6 - - - -
712C ASN* 3.7 21.5 - - - -
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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