Contacts of the helix formed by residues 673 - 683 (chain B) in PDB entry 3T6A
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 TYR 673 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621B GLU* 4.9 2.1 + - - +
624B ALA* 3.9 8.1 - - + -
625B ALA* 3.3 41.9 - - - +
628B SER* 3.3 28.5 - - - +
669B LEU* 2.7 40.2 + - + +
672B GLN* 1.3 101.3 - - + +
674B THR* 1.3 52.8 + - - +
675B GLN* 3.4 3.4 - - - -
676B THR* 3.1 9.8 + - - +
677B ALA 2.8 30.5 + - - -
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Residues in contact with THR 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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670B ARG* 2.6 36.3 + - - +
671B HIS 3.6 10.7 + - - -
672B GLN 3.6 1.7 + - - -
673B TYR* 1.3 72.8 - - - +
675B GLN* 1.3 68.6 + - - +
677B ALA* 3.3 2.8 + - - +
678B ILE* 3.0 43.2 + - + +
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Residues in contact with GLN 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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673B TYR 3.4 0.6 - - - -
674B THR* 1.3 78.7 - - - +
676B THR* 1.3 57.7 + - - +
678B ILE* 3.9 6.4 - - - +
679B LEU* 3.0 30.7 + - - +
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Residues in contact with THR 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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628B SER* 4.1 21.3 + - - +
631B ILE* 3.4 37.2 - - + +
632B GLN* 4.3 17.9 + - + +
669B LEU* 4.9 1.3 - - + -
673B TYR* 3.1 15.8 + - - +
675B GLN* 1.3 77.5 - - - +
677B ALA* 1.3 65.4 + - - +
679B LEU* 3.5 12.1 + - + +
680B TYR* 3.0 22.2 + - - +
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Residues in contact with ALA 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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666B TRP* 5.5 0.6 - - + +
669B LEU* 3.5 33.8 - - + +
670B ARG* 3.9 28.9 - - + +
673B TYR 2.8 19.5 + - - +
674B THR 3.3 4.0 + - - +
676B THR* 1.3 73.5 - - - +
678B ILE* 1.3 60.9 + - - +
680B TYR* 3.4 6.5 + - - +
681B GLU* 3.1 24.6 + - - +
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Residues in contact with ILE 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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670B ARG* 2.9 35.7 - - - +
674B THR* 3.0 40.3 + - + +
675B GLN* 3.9 6.5 - - - +
677B ALA* 1.3 73.5 - - - +
679B LEU* 1.3 57.0 + - - +
681B GLU* 3.1 4.8 + - - -
682B LYS* 2.7 52.6 + - + +
683B GLN* 5.9 0.9 - - - +
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Residues in contact with LEU 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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631B ILE* 5.1 2.5 - - + -
635B VAL* 3.6 35.7 - - + -
639B ASP* 6.0 1.8 - - - +
675B GLN 3.0 19.1 + - - +
676B THR* 3.7 14.4 - - + +
678B ILE* 1.3 77.4 - - - +
680B TYR* 1.3 58.5 + - - +
683B GLN* 3.0 60.7 + - + +
684B LEU* 3.2 14.9 + - + +
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Residues in contact with TYR 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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631B ILE* 3.8 21.1 - - + -
651B MET* 3.7 21.7 - - + +
654B LEU* 3.7 47.2 + - + +
655B GLU* 4.1 9.9 - - - +
666B TRP* 3.5 32.9 - + - -
676B THR 3.0 18.5 + - - +
677B ALA* 3.5 5.6 - - - +
678B ILE 3.1 0.2 - - - -
679B LEU* 1.3 79.4 - - - +
681B GLU* 1.3 69.7 + - + +
684B LEU* 3.4 20.5 - - + +
685B LYS* 3.0 59.0 + - + +
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Residues in contact with GLU 681 (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 TRP* 6.2 0.9 - - + -
670B ARG* 6.0 2.2 - - - +
677B ALA 3.1 15.2 + - - +
678B ILE* 3.1 6.5 + - - +
680B TYR* 1.3 86.1 - - + +
682B LYS* 1.3 75.3 + - + +
683B GLN 3.6 0.2 - - - -
685B LYS* 2.6 42.4 + - - +
686B PRO* 3.5 15.6 - - - +
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Residues in contact with LYS 682 (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 ARG* 6.0 4.3 - - - +
678B ILE* 2.7 38.2 + - + +
681B GLU* 1.3 86.5 + - + +
683B GLN* 1.3 72.8 + - - +
686B PRO* 3.3 15.6 - - - +
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Residues in contact with GLN 683 (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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638B LYS* 5.4 4.0 - - - +
678B ILE* 5.9 0.9 - - - +
679B LEU* 3.0 42.8 + - + +
682B LYS* 1.3 88.9 + - + +
684B LEU* 1.3 66.7 + - + +
686B PRO* 3.3 5.0 - - - +
687B PHE* 3.1 30.7 + - - +
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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