Contacts of the helix formed by residues 466 - 485 (chain A) in PDB entry 3W6R
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 PRO 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A GLU* 5.5 1.8 - - - +
435A THR* 4.0 20.4 - - + -
437A ARG* 5.1 4.5 - - - +
464A GLU 4.1 4.3 - - - +
465A LEU* 1.3 88.2 - - + +
467A GLN* 1.3 67.4 + - - +
468A ALA* 3.3 2.7 - - + +
469A ASN* 3.2 25.7 + - - +
470A ARG* 3.1 16.7 + - - +
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Residues in contact with GLN 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A SER* 2.8 30.7 + - - -
361A MET* 3.6 24.8 - - - +
465A LEU 3.7 1.0 + - - -
466A PRO* 1.3 71.5 - - - +
468A ALA* 1.3 58.7 + - - +
470A ARG* 3.2 21.1 + - - +
471A ASP* 2.8 56.0 + - - +
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Residues in contact with ALA 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 3.6 15.9 - - + -
352A ALA* 4.7 10.1 - - + +
355A VAL* 3.9 27.6 - - + -
361A MET* 3.3 20.2 - - + +
466A PRO* 3.3 2.1 - - + +
467A GLN* 1.3 77.5 - - - +
469A ASN* 1.3 60.1 + - - +
472A THR* 2.8 37.2 + - - -
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Residues in contact with ASN 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 3.5 24.6 - - - +
431A GLU* 4.5 5.9 + - - +
432A PRO 4.1 2.4 + - - -
433A LEU* 2.8 37.8 + - - +
435A THR* 3.7 13.1 - - - +
465A LEU* 4.0 13.7 - - + -
466A PRO* 3.2 33.7 + - + +
468A ALA* 1.3 79.5 - - - +
470A ARG* 1.3 56.4 + - - +
473A LEU* 2.9 32.4 + - - +
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Residues in contact with ARG 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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462A VAL* 3.0 40.1 + - + -
463A GLY* 3.4 17.7 + - - -
465A LEU* 2.8 39.5 + - + +
466A PRO 3.1 7.6 + - - +
467A GLN* 3.8 26.8 - - - +
469A ASN* 1.3 76.0 - - - +
471A ASP* 1.3 58.4 + - - +
473A LEU* 3.3 3.5 + - - +
474A ALA* 2.8 36.4 + - - +
539A TRP* 4.9 1.0 - - + -
542A PHE* 3.6 42.4 - - + -
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Residues in contact with ASP 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A SER* 4.5 0.2 - - - -
360A PRO* 3.4 9.0 - - + +
361A MET* 2.8 38.6 + - - +
362A ILE* 3.8 3.2 - - - +
467A GLN* 2.8 50.4 + - - +
470A ARG* 1.3 78.1 + - - +
472A THR* 1.3 57.6 + - - +
474A ALA* 3.5 4.0 + - - -
475A PHE* 3.1 27.9 + - - +
542A PHE* 3.7 25.2 - - - +
543A MET* 3.6 9.5 - - - +
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Residues in contact with THR 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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351A LEU* 3.9 10.2 - - + +
361A MET 3.0 12.1 + - - -
362A ILE* 3.7 12.1 - - + -
363A PRO* 3.4 27.0 - - + +
366A VAL* 4.4 15.4 - - + +
426A LEU* 4.4 8.5 - - + -
433A LEU* 3.9 20.4 - - + -
468A ALA 2.8 22.5 + - - -
471A ASP* 1.3 73.4 - - - +
473A LEU* 1.3 61.3 + - - +
475A PHE* 3.4 2.9 + - - +
476A LEU* 2.9 28.7 + - + +
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Residues in contact with LEU 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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433A LEU* 3.9 25.5 - - + +
434A LEU* 3.8 22.2 - - + -
462A VAL* 4.5 3.4 - - + -
465A LEU* 3.8 16.6 - - + -
469A ASN 2.9 20.1 + - - +
470A ARG 3.6 3.6 - - - +
472A THR* 1.3 76.5 - - - +
474A ALA* 1.3 56.2 - - - +
476A LEU* 3.2 2.8 + - - +
477A MET* 2.8 48.8 + - + +
504A ILE* 4.0 21.3 - - + -
531A LEU* 4.0 12.1 - - + -
539A TRP* 3.7 28.5 - - + -
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Residues in contact with ALA 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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470A ARG 2.8 21.5 + - - +
471A ASP 3.7 4.9 - - - +
473A LEU* 1.3 72.5 - - - +
475A PHE* 1.3 62.5 + - - +
477A MET* 3.3 1.9 + - - +
478A ILE* 3.1 31.7 + - - +
539A TRP* 3.5 45.0 - - + +
542A PHE* 4.1 9.0 - - + -
543A MET* 3.8 9.4 - - + -
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Residues in contact with PHE 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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362A ILE* 3.6 28.5 - - + -
366A VAL* 3.9 18.2 - - + -
367A VAL* 3.8 34.5 - - + -
370A VAL* 3.6 40.4 - - + -
371A ASN* 4.7 4.3 - - - -
471A ASP 3.1 17.9 + - - +
472A THR 3.6 4.5 - - - +
474A ALA* 1.3 77.2 - - - +
476A LEU* 1.3 61.9 + - - +
478A ILE* 3.5 9.1 + - + +
479A HIS* 3.2 21.5 + - - +
543A MET* 4.0 16.3 - - + +
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Residues in contact with LEU 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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366A VAL* 5.5 5.4 - - + -
370A VAL* 5.1 3.1 - - + -
422A LEU* 4.2 25.6 - - + -
426A LEU* 3.8 17.0 - - + -
433A LEU* 4.4 6.3 - - + -
472A THR* 2.9 18.5 + - + +
473A LEU* 3.6 4.7 - - - +
475A PHE* 1.3 78.9 - - - +
477A MET* 1.3 66.9 + - + +
479A HIS* 3.2 12.1 + - + +
480A LEU* 2.8 49.3 + - + +
500A PHE* 4.1 15.5 - - + -
504A ILE* 3.8 29.2 - - + -
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Residues in contact with MET 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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473A LEU* 2.8 39.4 + - + +
474A ALA 3.7 2.2 - - - +
476A LEU* 1.3 79.7 - - + +
478A ILE* 1.3 60.3 + - - +
480A LEU* 3.4 24.4 + - + -
481A GLN* 3.0 38.0 + - - +
504A ILE* 4.4 10.5 - - + -
528A VAL* 4.9 3.6 - - + -
531A LEU* 3.7 25.6 - - - -
532A LEU* 3.7 25.7 - - + +
539A TRP* 3.5 40.4 - - + +
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Residues in contact with ILE 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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474A ALA 3.1 20.4 + - - +
475A PHE* 3.8 7.9 - - + +
477A MET* 1.3 76.1 - - - +
479A HIS* 1.3 62.3 + - - +
481A GLN* 3.6 10.5 + - - +
482A ARG* 3.4 34.9 + - + +
536A LEU* 3.9 25.8 - - + -
539A TRP* 3.7 16.8 - - + +
540A SER* 4.0 26.9 - - - +
543A MET* 4.2 17.3 - - + -
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Residues in contact with HIS 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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370A VAL* 3.5 47.9 + - + +
373A ILE* 3.6 28.9 - - + +
374A GLU* 4.4 12.2 + - - -
378A LEU* 5.2 2.2 - - + +
384A TYR* 2.8 34.3 + - - -
475A PHE 3.2 11.3 + - - +
476A LEU* 3.5 11.7 - - + +
478A ILE* 1.3 79.7 - - - +
480A LEU* 1.3 72.2 + - + +
482A ARG* 3.1 13.7 + - - +
483A VAL* 3.1 34.0 + - + +
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Residues in contact with LEU 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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384A TYR* 3.7 24.2 - - + -
476A LEU* 2.8 41.0 + - + +
477A MET* 3.9 14.8 - - + -
479A HIS* 1.3 77.8 - - + +
481A GLN* 1.3 60.4 + - - +
483A VAL* 3.2 6.9 + - + +
484A ALA* 2.9 24.8 + - - +
496A LEU* 3.5 19.2 - - + +
500A PHE* 3.6 47.8 - - + -
528A VAL* 5.6 0.2 - - + -
532A LEU* 3.6 22.2 - - + -
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Residues in contact with GLN 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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477A MET 3.0 22.0 + - - +
478A ILE* 3.7 11.3 - - - +
479A HIS 3.3 0.2 - - - -
480A LEU* 1.3 76.8 - - - +
482A ARG* 1.3 56.9 + - + +
484A ALA* 3.3 8.5 + - - +
485A GLN* 3.0 48.9 + - - +
493A VAL* 6.0 2.2 - - + -
532A LEU* 2.9 28.8 + - + +
534A LEU 2.8 29.7 + - - -
535A PRO* 4.0 1.2 - - - +
536A LEU* 3.7 30.9 + - - +
539A TRP* 3.9 9.4 - - - +
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Residues in contact with ARG 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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374A GLU* 2.9 44.3 + - - +
378A LEU* 4.2 13.0 - - + +
478A ILE* 3.4 28.4 + - + +
479A HIS* 3.1 12.4 + - - +
481A GLN* 1.3 73.4 - - + +
483A VAL* 1.3 65.0 + - - +
485A GLN* 3.2 13.8 + - - +
486A SER* 3.2 22.0 + - - -
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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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378A LEU* 3.9 17.3 - - + -
383A LEU* 4.1 23.6 - - + -
384A TYR* 4.2 6.7 - - + -
479A HIS* 3.1 41.9 + - + +
480A LEU* 3.4 11.4 - - - +
482A ARG* 1.3 76.8 - - - +
484A ALA* 1.3 59.1 + - - +
485A GLN 3.3 0.9 + - - -
486A SER 3.4 5.5 + - - -
489A THR* 2.8 37.7 + - + +
491A MET* 4.5 4.7 - - + -
496A LEU* 4.0 23.8 - - + -
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Residues in contact with ALA 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU 2.9 16.1 + - - +
481A GLN* 3.3 8.0 + - - +
483A VAL* 1.3 75.6 - - - +
485A GLN* 1.3 61.5 + - + +
486A SER 3.5 4.1 + - - +
489A THR* 5.1 0.2 + - - -
491A MET 3.3 21.2 - - - +
492A ASP* 4.4 5.4 - - - +
493A VAL* 4.1 28.7 - - + +
496A LEU* 4.0 7.4 - - + -
532A LEU* 6.3 0.2 - - + -
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Residues in contact with GLN 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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481A GLN* 3.0 36.7 + - - +
482A ARG* 3.2 13.7 + - - +
483A VAL 3.2 0.4 - - - -
484A ALA* 1.3 79.1 - - + +
486A SER* 1.3 61.9 + - - +
487A PRO* 3.8 6.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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