Contacts of the strand formed by residues 472 - 481 (chain A) in PDB entry 6TAV
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 HIS 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469A PRO* 3.3 30.1 - - + +
470A CYS 3.2 2.0 - - - +
471A GLY* 1.3 82.3 + - - +
473A THR* 1.3 80.5 + - - +
474A GLN* 4.9 1.7 - - - +
530A VAL* 3.2 27.3 + - - +
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Residues in contact with THR 473 (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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472A HIS* 1.3 92.6 + - - +
474A GLN* 1.3 62.9 + - - +
475A THR* 5.5 4.0 - - - +
527A SER* 6.3 1.3 - - - -
528A ILE 3.7 6.7 - - - -
529A PRO* 3.7 30.3 - - + -
530A VAL 5.6 0.2 - - - +
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Residues in contact with GLN 474 (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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464A MET* 4.5 13.1 - - + +
466A HIS* 4.6 10.1 - - - -
468A LEU* 4.0 30.8 - - + +
469A PRO* 5.5 6.4 - - + +
472A HIS* 3.7 2.0 + - - -
473A THR* 1.3 75.7 + - - +
475A THR* 1.3 85.8 + - - +
476A VAL* 5.0 4.5 - - + -
527A SER* 4.5 0.2 - - - -
528A ILE* 2.8 47.7 + - + +
530A VAL* 3.9 18.6 - - + -
558A TYR* 6.3 1.6 - - + -
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Residues in contact with THR 475 (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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464A MET* 3.8 11.4 - - - +
473A THR* 5.5 4.5 - - - +
474A GLN* 1.3 97.9 + - - +
476A VAL* 1.3 62.1 + - - +
477A GLN* 5.3 2.0 - - - +
525A SER* 5.1 10.7 - - - -
526A ILE 3.5 9.4 - - - -
527A SER* 4.1 15.7 - - - -
528A ILE* 4.3 0.2 - - - -
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Residues in contact with VAL 476 (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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461A LEU* 4.1 11.0 - - + -
462A GLU 3.4 17.7 - - - +
464A MET* 3.8 12.6 - - - -
474A GLN* 5.0 4.5 - - + -
475A THR* 1.3 76.1 - - - +
477A GLN* 1.3 65.5 + - - +
478A ALA* 3.8 0.5 + - - +
525A SER* 3.2 4.1 - - - -
526A ILE* 2.8 41.4 + - + +
528A ILE* 3.7 23.1 - - + -
540A LEU* 4.3 16.2 - - + -
558A TYR* 3.1 33.0 - - + +
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Residues in contact with GLN 477 (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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461A LEU* 3.7 2.5 - - - -
462A GLU* 2.8 60.1 + - + +
464A MET* 3.9 12.1 - - + +
475A THR* 5.3 1.6 - - - +
476A VAL* 1.3 77.2 - - - +
478A ALA* 1.3 57.7 + - - +
479A HIS* 4.4 13.6 + - + +
523A HIS* 5.3 5.4 - - - +
524A PHE* 5.1 3.2 - - - +
525A SER* 3.6 28.0 + - - +
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Residues in contact with ALA 478 (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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459A VAL* 5.4 2.0 - - + -
460A HIS 3.1 12.3 - - - +
461A LEU* 4.5 5.2 - - + +
476A VAL 3.8 2.4 + - - +
477A GLN* 1.3 73.2 - - - +
479A HIS* 1.4 63.4 + - - +
480A TYR* 4.2 0.6 - - - -
523A HIS* 3.7 0.3 - - - -
524A PHE* 2.7 69.2 + - + +
525A SER* 5.2 0.2 - - - -
526A ILE* 5.6 4.0 - - + +
542A ILE* 4.3 17.7 - - + -
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Residues in contact with HIS 479 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A ILE* 4.4 24.0 - - + +
366A PHE* 4.7 9.3 - + - -
459A VAL* 3.5 3.2 - - - +
460A HIS* 2.7 62.5 + + + +
462A GLU* 3.6 31.0 + - + +
477A GLN* 4.4 20.3 - - + +
478A ALA* 1.4 75.6 - - - +
480A TYR* 1.3 59.8 + - - +
481A ILE* 5.8 0.2 - - - -
522A GLY 3.5 9.1 + - - +
523A HIS* 3.9 21.1 + - + +
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Residues in contact with TYR 480 (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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363A ILE* 6.0 0.2 - - - +
458A PHE 3.6 9.6 - - - +
459A VAL* 4.6 0.7 - - + -
478A ALA 4.2 0.9 - - - -
479A HIS* 1.3 77.9 - - - +
481A ILE* 1.4 66.5 + - - +
482A LEU* 3.4 22.9 - - + -
495A PHE* 4.3 19.5 - + + -
513A LEU* 3.4 41.3 - - + +
519A ASP* 4.1 10.3 + - - -
521A LYS* 3.1 33.7 + - - +
522A GLY* 3.2 41.5 + - - +
523A HIS 3.6 10.7 + - - -
524A PHE* 4.0 28.3 - + + +
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Residues in contact with ILE 481 (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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362A GLY* 3.1 30.5 - - - +
363A ILE* 4.1 19.3 - - + -
456A LYS 4.6 0.9 - - - +
457A SER* 3.3 6.2 - - - -
458A PHE* 2.9 59.5 + - + +
479A HIS 5.8 0.2 - - - -
480A TYR* 1.4 80.1 - - - +
482A LEU* 1.3 63.7 + - - +
483A ASN* 3.5 18.6 - - + +
520A MET* 3.1 22.7 - - + +
521A LYS* 4.1 13.0 - - + -
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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