Contacts of the helix formed by residues 670 - 680 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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653A PHE* 4.2 3.5 - - - -
660A ILE* 5.0 4.7 - - - +
668A PHE 4.2 0.2 - - - -
669A THR* 1.3 83.0 + - - +
671A VAL* 1.3 65.3 + - - +
672A GLU* 3.8 22.9 - - + +
673A GLU* 3.7 20.6 - - - +
674A SER* 3.0 28.4 + - - -
1003A SBJ 6.3 1.1 - - - +
465D PHE 3.3 17.9 - - - +
466D GLU* 3.8 22.8 + - + +
467D GLY* 4.4 2.4 + - - +
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Residues in contact with VAL 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649A MET* 4.3 22.2 - - + +
650A ILE* 6.5 0.9 - - + -
653A PHE* 4.0 20.2 - - + -
670A THR* 1.3 77.1 - - - +
672A GLU* 1.3 58.8 + - - +
674A SER* 3.5 5.6 + - - +
675A PHE* 2.9 27.1 + - + +
465D PHE* 3.3 49.9 + - + +
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Residues in contact with GLU 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670A THR* 3.8 18.7 - - + +
671A VAL* 1.3 76.6 - - - +
673A GLU* 1.3 73.3 + - + +
675A PHE* 3.3 11.4 + - + +
676A LYS* 2.9 51.6 + - - +
1003A SBJ 3.0 49.2 + - - +
702B ASN* 5.0 2.9 + - - +
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Residues in contact with GLU 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666A GLU* 3.0 38.9 - - + +
667A ALA* 4.3 1.4 - - - -
668A PHE 4.0 5.4 - - - +
669A THR* 4.4 1.3 - - - +
670A THR* 3.4 31.4 + - - +
671A VAL 3.3 0.6 - - - -
672A GLU* 1.3 89.1 - - + +
674A SER* 1.3 57.8 + - - +
676A LYS* 3.5 25.2 + - - +
677A THR* 2.4 39.5 + - - -
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Residues in contact with SER 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649A MET* 3.1 32.6 + - - +
652A MET* 5.0 0.2 - - - +
653A PHE* 4.1 13.9 - - - +
668A PHE* 3.8 32.9 - - - +
670A THR 3.0 17.0 + - - -
671A VAL 4.0 3.6 - - - -
673A GLU* 1.3 75.2 - - - +
675A PHE* 1.3 61.5 + - - +
678A LEU* 3.4 26.0 + - - +
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Residues in contact with PHE 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A PHE* 3.4 34.4 - + - -
649A MET* 3.7 18.8 - - - -
671A VAL* 2.9 20.0 + - + +
672A GLU* 3.5 12.1 - - + +
673A GLU 3.2 0.2 - - - -
674A SER* 1.3 78.2 - - - +
676A LYS* 1.3 61.1 + - + +
678A LEU 3.4 1.2 + - - -
679A PHE* 2.9 35.0 + + + +
1003A SBJ 3.6 58.6 - - + -
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Residues in contact with LYS 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672A GLU* 2.9 40.2 + - - +
673A GLU* 3.5 32.9 + - - +
675A PHE* 1.3 77.0 - - - +
677A THR* 1.3 65.1 + - - +
679A PHE* 4.2 6.5 - - - -
680A TRP* 2.9 47.3 + - + +
1003A SBJ 4.1 34.5 + - + -
701B GLU* 5.7 0.4 + - - -
702B ASN* 5.4 1.6 + - - -
705B TYR* 4.4 29.1 + - + +
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Residues in contact with THR 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667A ALA* 3.4 28.0 - - + +
668A PHE* 3.7 30.1 - - + -
673A GLU* 2.4 25.1 + - - -
675A PHE 3.4 0.2 - - - -
676A LYS* 1.3 78.9 - - - +
678A LEU* 1.3 60.6 + - - +
681A ALA* 3.4 12.6 + - - +
686A SER* 3.1 30.0 + - - +
690A SER* 3.9 15.3 - - - +
708A TYR* 4.1 3.1 + - - +
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Residues in contact with LEU 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A PHE* 3.3 18.4 - - + +
648A PHE* 3.7 17.9 - - + +
649A MET* 3.5 37.5 - - + +
652A MET* 3.8 15.0 - - + -
668A PHE* 3.6 25.6 - - + -
674A SER 3.4 14.7 + - - +
675A PHE 3.4 1.4 + - - -
676A LYS 3.3 0.2 - - - -
677A THR* 1.3 75.8 - - - +
679A PHE* 1.3 64.5 + - - +
681A ALA 3.8 2.2 + - - -
682A ILE* 3.7 4.3 - - - +
708A TYR* 4.1 6.3 - - + -
711A TYR* 2.5 51.9 + - + +
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Residues in contact with PHE 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A PHE* 3.4 14.3 - + + -
675A PHE* 2.9 30.0 + + + +
676A LYS* 3.3 7.2 + - - +
678A LEU* 1.3 78.1 - - - +
680A TRP* 1.3 75.3 + + - +
681A ALA 3.1 2.0 + - - -
682A ILE* 3.3 33.0 + - + +
683A PHE* 3.9 26.5 - + - -
1003A SBJ 3.8 53.4 - - + -
709B GLY* 3.9 15.3 - - - -
713B VAL* 4.1 19.1 - - + -
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Residues in contact with TRP 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676A LYS* 2.9 37.4 + - + +
679A PHE* 1.3 85.7 - + - +
681A ALA* 1.3 58.4 + - - +
682A ILE 3.3 0.9 - - - -
683A PHE* 3.7 18.2 + + - +
684A GLY 3.5 2.4 + - - -
685A LEU* 2.9 55.0 + - + +
686A SER* 3.7 13.0 - - - +
1003A SBJ 3.6 18.4 - - + +
688B VAL* 3.8 28.2 - - + +
705B TYR* 4.0 25.9 - + - -
708B TYR* 3.5 29.4 - + - -
709B GLY* 3.6 23.3 - - - -
712B ASN* 3.7 22.2 - - - -
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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