Contacts of the helix formed by residues 466 - 478 (chain A) in PDB entry 1Q6X
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 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A CYS* 6.3 0.4 - - - +
44A HIS* 3.7 5.6 + - - -
442A LEU* 4.3 0.3 - - - +
463A ARG 3.3 19.7 - - - +
464A SER* 2.8 15.6 + - - +
465A ALA* 1.3 76.3 - - - +
467A PRO* 1.3 74.8 - - + +
468A GLU* 3.4 13.1 + - - +
469A ALA* 3.0 24.2 + - - +
470A LEU* 3.0 18.7 + - - +
495A ALA 5.2 1.6 + - - -
498A ALA* 4.3 16.1 - - + +
499A GLN* 4.5 7.4 - - - +
502A TYR* 4.9 11.2 - - + -
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Residues in contact with PRO 467 (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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40A GLN* 3.9 33.4 - - + +
41A CYS* 5.4 3.1 - - - -
44A HIS* 3.8 26.2 - - + +
466A THR* 1.3 84.8 - - - +
468A GLU* 1.3 77.0 + - - +
470A LEU* 3.2 9.9 + - + +
471A ALA* 3.1 21.8 + - - +
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Residues in contact with GLU 468 (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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40A GLN* 5.7 3.8 + - - -
466A THR* 3.4 9.8 - - - +
467A PRO* 1.3 93.9 - - + +
469A ALA* 1.3 63.8 + - - +
471A ALA* 3.3 8.8 + - - +
472A PHE* 3.1 20.4 + - - +
491A LEU* 4.6 2.1 - - - +
494A THR* 4.0 16.8 + - - +
495A ALA* 3.9 24.0 - - - +
498A ALA* 3.7 20.2 - - + +
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Residues in contact with ALA 469 (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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429A VAL* 5.5 9.0 - - + -
432A GLN* 4.4 17.5 - - + -
442A LEU* 4.4 4.3 - - + -
464A SER 3.8 16.2 - - - +
466A THR* 3.0 22.6 + - - +
468A GLU* 1.3 73.3 - - - +
470A LEU* 1.3 66.4 + - - +
472A PHE* 3.2 4.6 + - - +
473A VAL* 3.0 28.6 + - + +
495A ALA* 4.3 12.8 - - + +
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Residues in contact with LEU 470 (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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44A HIS* 3.6 35.7 - - + +
436A TYR* 4.2 12.6 - - + -
441A ARG* 5.7 0.9 - - - -
442A LEU* 3.9 20.1 - - + +
466A THR 3.0 13.3 + - - +
467A PRO* 3.2 11.9 + - + +
469A ALA* 1.3 77.1 - - - +
471A ALA* 1.3 62.2 + - - +
473A VAL* 3.1 18.9 - - + +
474A GLN* 3.0 54.2 - - + +
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Residues in contact with ALA 471 (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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467A PRO 3.1 10.8 + - - +
468A GLU* 3.5 12.6 - - - +
469A ALA 3.2 0.2 - - - -
470A LEU* 1.3 78.0 - - - +
472A PHE* 1.3 61.5 + - - +
474A GLN* 3.5 12.4 + - - +
475A ALA* 3.3 23.6 + - - +
491A LEU* 3.9 23.5 - - + +
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Residues in contact with PHE 472 (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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429A VAL* 3.7 30.5 - - + -
433A LEU* 4.6 9.4 - - + -
468A GLU 3.1 13.2 + - - +
469A ALA 3.2 6.5 + - - +
471A ALA* 1.3 77.2 - - - +
473A VAL* 1.3 70.3 + - + +
475A ALA* 3.3 3.7 + - + +
476A MET* 3.1 65.3 + - + +
488A LYS* 3.9 9.2 - - - -
491A LEU* 4.1 18.3 - - + +
492A LEU* 3.5 49.4 - - + -
495A ALA* 4.3 5.2 - - + -
610A MET* 4.3 15.7 - - + -
613A LEU* 3.9 3.1 - - + -
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Residues in contact with VAL 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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429A VAL* 4.9 1.1 - - + +
432A GLN* 3.8 12.3 - - + +
433A LEU* 3.6 44.2 - - + +
436A TYR* 3.6 36.1 - - + -
442A LEU* 4.4 3.4 - - + -
469A ALA* 3.0 19.9 + - - +
470A LEU* 3.1 24.7 - - + +
472A PHE* 1.3 82.5 - - + +
474A GLN* 1.3 61.3 + - - +
476A MET* 3.3 2.0 + - - +
477A THR* 3.1 29.1 + - - +
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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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436A TYR* 3.7 21.5 + - + +
470A LEU* 3.0 53.8 + - + +
471A ALA* 3.8 9.6 - - - +
473A VAL* 1.3 76.7 - - - +
475A ALA* 1.3 58.5 + - - +
478A ASP* 2.7 49.3 + - + +
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Residues in contact with ALA 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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471A ALA 3.3 5.5 + - - +
472A PHE 3.3 4.0 + - - +
474A GLN* 1.3 78.7 - - - +
476A MET* 1.3 62.7 + - + +
479A HIS* 3.4 25.7 + - - +
483A MET* 3.6 25.7 - - + +
488A LYS* 3.6 13.5 - - + -
491A LEU* 3.5 31.9 - - + -
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Residues in contact with MET 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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433A LEU* 4.0 19.5 - - + -
472A PHE* 3.1 59.8 + - + +
473A VAL 3.8 4.7 - - - +
474A GLN 3.2 0.4 - - - -
475A ALA* 1.3 78.6 - - + +
477A THR* 1.3 63.2 + - + +
479A HIS* 4.0 13.6 + - - -
488A LYS* 3.9 26.2 - - + -
609A ASP* 4.2 35.2 - - + +
610A MET* 4.8 1.3 - - - +
613A LEU* 4.0 16.4 - - + -
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Residues in contact with THR 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A LEU* 3.8 24.5 - - + -
436A TYR* 3.4 20.6 - - - -
437A ARG* 4.0 30.6 - - + +
473A VAL 3.1 12.7 + - - -
476A MET* 1.3 83.1 - - + +
478A ASP* 1.3 65.6 + - - +
479A HIS* 3.4 7.7 + - - -
480A LYS* 4.5 14.0 - - - +
609A ASP* 5.8 1.3 - - - +
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Residues in contact with ASP 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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436A TYR* 2.7 42.1 + - - -
440A GLN* 5.6 4.9 - - - +
474A GLN* 2.7 26.7 + - + +
477A THR* 1.3 79.6 + - - +
479A HIS* 1.3 60.2 + - - +
480A LYS* 3.8 2.7 - - - -
482A ALA* 5.1 0.3 - - - +
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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