Contacts of the strand formed by residues 477 - 486 (chain A) in PDB entry 1QF6
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 ALA 477 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469A THR* 3.9 11.4 - - - +
470A LEU 3.7 4.3 - - - -
471A TYR* 3.5 23.4 - - + +
475A ASP 4.1 0.2 + - - -
476A ARG* 1.3 74.9 - - - +
478A TRP* 1.3 73.3 + - - +
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Residues in contact with TRP 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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369A SER 5.8 0.2 - - - -
371A HIS* 4.1 31.9 - + + -
374A MET* 3.7 39.9 - - + +
375A ARG* 4.3 12.8 - - + -
469A THR* 4.1 2.7 + - - -
470A LEU 3.0 32.5 + - - +
472A ASP* 3.4 33.0 + - + +
476A ARG* 3.5 25.7 + - + +
477A ALA* 1.3 80.5 - - - +
479A GLN* 1.3 65.7 + - - +
480A CYS* 3.4 4.0 + - - -
520A ARG* 4.0 35.2 - - - -
524A ILE* 4.1 18.4 - - + -
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Residues in contact with GLN 479 (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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465A LYS* 4.8 7.9 + - - +
467A GLU* 2.9 35.2 - - + +
468A PHE 3.9 6.7 - - - +
469A THR* 4.2 7.4 - - - -
478A TRP* 1.3 72.8 - - - +
480A CYS* 1.3 60.9 + - - +
482A THR* 3.2 24.7 - - + +
520A ARG* 2.8 36.8 + - - +
1002A AMP 2.9 41.5 + - - +
76B A 5.0 7.9 + - - -
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Residues in contact with CYS 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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408A TYR* 3.5 11.0 - - - +
468A PHE 2.8 13.0 + - - +
470A LEU* 4.0 28.3 - - + -
478A TRP 3.4 10.0 + - - -
479A GLN* 1.3 79.6 - - - +
481A GLY* 1.3 68.0 + - - +
482A THR* 3.6 0.9 + - - +
513A ALA* 4.9 0.5 - - - +
515A LEU 3.4 16.6 - - - +
516A GLY* 3.4 14.3 - - - -
520A ARG* 4.3 16.6 - - - -
521A PHE* 4.6 6.3 - - + -
524A ILE* 4.8 5.8 - - - -
1002A AMP 2.9 24.2 + - - +
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Residues in contact with GLY 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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404A VAL* 5.0 1.8 - - - -
408A TYR* 2.9 11.5 + - - -
468A PHE* 2.8 34.6 + - - +
480A CYS* 1.3 81.2 - - - +
482A THR* 1.3 67.2 + - - +
513A ALA 2.9 15.7 - - - -
514A ILE* 3.1 14.1 + - - -
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Residues in contact with THR 482 (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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404A VAL* 5.6 0.4 - - - +
465A LYS* 5.3 6.5 - - - -
466A ILE 3.1 13.5 - - - +
467A GLU* 4.2 6.3 - - + -
468A PHE* 4.5 1.1 - - - -
479A GLN* 3.2 41.1 - - + +
480A CYS 3.6 5.1 + - - +
481A GLY* 1.3 85.4 - - - +
483A VAL* 1.3 69.2 + - - +
484A GLN* 4.6 9.1 + - - +
511A HIS 4.6 0.2 - - - -
512A ARG* 3.2 6.3 - - - +
513A ALA* 2.9 34.5 + - - +
1002A AMP 3.6 16.6 + - - +
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Residues in contact with VAL 483 (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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397A VAL* 4.7 11.0 - - + -
400A CYS* 4.2 25.4 - - + -
401A ILE* 5.0 3.8 - - + +
404A VAL* 5.5 3.6 - - + -
441A LEU* 4.5 15.8 - - + +
464A PRO 3.9 0.3 - - - +
465A LYS* 3.3 4.1 - - - -
466A ILE* 2.9 44.7 + - + +
468A PHE* 4.4 18.6 - - + -
482A THR* 1.3 82.2 - - - +
484A GLN* 1.3 63.1 + - - +
485A LEU 4.3 0.2 + - - -
510A ILE* 3.9 23.3 - - + -
511A HIS 3.5 3.1 - - - +
512A ARG* 4.5 5.8 - - + -
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Residues in contact with GLN 484 (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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460A ALA* 4.1 2.3 - - - +
462A TYR* 2.6 39.3 + - + -
463A GLY 5.1 2.2 - - - +
464A PRO 3.4 10.3 - - - +
465A LYS* 3.1 38.7 - - + +
482A THR* 4.6 8.3 + - - +
483A VAL* 1.3 78.3 - - - +
485A LEU* 1.3 61.0 + - - +
486A ASP 3.9 0.4 + - - -
510A ILE* 3.4 10.1 - - - +
511A HIS* 2.8 58.0 + - + +
1002A AMP 4.0 5.7 + - - -
76B A 3.1 23.5 + - - -
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Residues in contact with LEU 485 (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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393A ILE* 3.9 24.0 - - + -
397A VAL* 4.0 7.2 - - + -
437A ALA* 4.3 16.6 - - + +
440A ASP* 4.3 10.1 - - + -
441A LEU* 3.5 30.2 - - + +
462A TYR 3.9 0.5 - - - +
463A GLY* 3.6 21.4 - - - -
464A PRO* 3.4 15.9 + - + +
483A VAL 4.3 0.4 + - - -
484A GLN* 1.3 71.1 - - - +
486A ASP* 1.3 64.5 + - - +
487A PHE* 4.0 23.6 + - + -
508A VAL* 3.9 26.0 - - + -
510A ILE* 4.1 11.9 - - + -
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Residues in contact with ASP 486 (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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462A TYR* 3.5 24.5 - - + +
484A GLN 3.9 0.4 + - - -
485A LEU* 1.3 75.5 - - - +
487A PHE* 1.3 62.6 + - - +
488A SER* 3.0 15.9 + - - -
489A LEU* 2.9 34.8 + - - +
490A PRO* 3.3 8.8 - - - +
508A VAL* 4.2 1.2 - - - -
509A MET* 2.9 38.4 + - - +
511A HIS* 3.0 34.9 + - + +
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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