Contacts of the helix formed by residues 471 - 489 (chain B) in PDB entry 4AY6
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 ASP 471 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469B TRP 3.3 1.8 + - - -
470B THR* 1.3 84.1 - - + +
472B TYR* 1.3 65.3 + - - +
473B ASP 3.2 2.2 - - - -
474B GLU* 3.1 26.2 + - + +
475B ARG* 2.9 21.3 + - + +
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Residues in contact with TYR 472 (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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464B GLN* 4.0 18.5 + - - -
469B TRP* 3.3 33.1 + + + +
470B THR 3.2 2.6 - - - -
471B ASP* 1.3 76.8 - - - +
473B ASP* 1.3 72.8 + - - +
475B ARG* 3.1 23.5 + - - +
476B MET* 2.9 68.1 + - + +
502B LEU 4.6 7.6 + - - -
844B ASP* 3.6 22.3 + - + +
845B PRO* 3.9 32.5 - - + -
916B LEU* 5.1 1.0 - - - +
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Residues in contact with ASP 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ASP 3.2 1.0 - - - -
472B TYR* 1.3 93.5 - - - +
474B GLU* 1.3 62.2 + - - +
476B MET* 3.4 5.9 + - - +
477B LYS* 3.1 34.3 + - + +
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Residues in contact with GLU 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B TYR* 4.8 6.9 + - - -
471B ASP* 3.1 28.1 + - + +
473B ASP* 1.3 79.2 - - - +
475B ARG* 1.3 57.7 + - - +
477B LYS* 3.8 7.8 - - + +
478B LYS* 2.8 41.3 + - + +
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Residues in contact with ARG 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B TYR* 3.4 30.1 + - + +
460B ALA* 3.8 36.3 + - + +
463B LEU* 3.8 22.1 - - + +
464B GLN* 4.2 12.9 + - - +
468B ASP* 2.5 37.4 + - - -
469B TRP* 3.5 6.1 - - - +
470B THR 3.5 21.1 + - - +
471B ASP* 2.9 12.9 + - + +
472B TYR* 3.1 27.2 + - - +
474B GLU* 1.3 79.2 + - - +
476B MET* 1.3 67.1 + - - +
478B LYS* 3.4 3.5 + - - +
479B LEU* 3.0 28.1 + - - +
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Residues in contact with MET 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B ALA* 5.6 0.4 - - + +
464B GLN* 4.6 1.1 - - - +
472B TYR* 2.9 61.3 + - + +
473B ASP* 3.8 6.7 - - - +
475B ARG* 1.3 96.9 - - - +
477B LYS* 1.3 67.6 + - + +
479B LEU* 3.0 20.1 + - + +
480B VAL* 3.1 18.7 + - - +
502B LEU 4.8 0.7 - - - +
503B TYR* 3.7 32.1 - - + -
504B PRO* 3.6 37.0 - - + +
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Residues in contact with LYS 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ASP* 3.1 21.3 + - - +
474B GLU* 3.8 7.6 - - + +
476B MET* 1.3 78.1 - - + +
478B LYS* 1.3 64.1 + - - +
480B VAL* 3.4 8.3 + - - +
481B SER* 3.0 24.4 + - - -
504B PRO* 5.5 0.2 - - - +
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Residues in contact with LYS 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B PRO 5.0 9.5 + - - -
456B TYR* 3.7 40.9 - - + +
474B GLU* 2.8 30.3 + - + +
475B ARG 3.5 5.8 - - - +
477B LYS* 1.3 75.8 - - - +
479B LEU* 1.3 62.2 + - - +
481B SER* 2.9 11.3 - - - +
482B ILE* 2.9 37.9 + - + +
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Residues in contact with LEU 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B TYR* 3.8 21.3 - - + -
457B CYS* 3.8 35.9 - - + -
460B ALA* 4.2 10.5 - - + -
475B ARG 3.0 15.3 + - - +
476B MET* 3.0 16.4 + - + +
478B LYS* 1.3 73.3 - - - +
480B VAL* 1.3 68.0 + - + +
482B ILE* 2.7 17.7 + - + +
483B VAL* 3.0 18.6 + - + +
495B VAL* 4.5 4.0 - - + -
503B TYR* 3.6 55.0 - - + -
505B LEU* 5.6 1.1 - - + -
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Residues in contact with VAL 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B MET 3.1 18.1 + - - +
477B LYS* 3.6 7.9 - - - +
479B LEU* 1.3 75.5 - - + +
481B SER* 1.3 54.3 + - - +
483B VAL* 3.2 2.4 + - - +
484B ALA* 2.8 37.1 + - + +
504B PRO* 3.5 34.3 - - + +
505B LEU* 4.0 24.9 - - + +
506B SER 5.7 0.7 - - - +
509B PHE* 4.3 11.3 - - + -
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Residues in contact with SER 481 (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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477B LYS 3.0 11.0 + - - -
478B LYS* 2.9 20.8 - - - +
480B VAL* 1.3 79.1 - - - +
482B ILE* 1.3 59.9 + - - +
484B ALA* 3.4 7.0 - - - +
485B ASP* 3.1 22.2 + - - +
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Residues in contact with ILE 482 (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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453B PRO* 3.9 27.4 - - + -
456B TYR* 3.7 38.6 - - + -
457B CYS* 4.4 9.6 - - - -
478B LYS* 2.9 33.5 + - + +
479B LEU* 2.7 17.3 + - + +
481B SER* 1.3 69.8 - - - +
483B VAL* 1.3 60.0 + - + +
485B ASP* 3.2 9.7 + - - +
486B GLN* 2.9 44.3 + - + +
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Residues in contact with VAL 483 (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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457B CYS* 5.4 0.4 - - - -
479B LEU 3.0 15.2 + - - +
480B VAL 3.5 5.2 - - - +
482B ILE* 1.3 74.3 - - + +
484B ALA* 1.3 58.9 + - - +
486B GLN* 2.9 13.3 + - - +
487B LEU* 2.8 54.5 + - + +
493B PRO* 4.4 6.3 - - + -
495B VAL* 3.8 31.4 - - + +
505B LEU* 4.2 13.5 - - + -
509B PHE* 4.2 8.5 - - + -
513B ILE* 4.0 22.4 - - + -
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Residues in contact with ALA 484 (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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480B VAL* 2.8 22.5 + - + +
481B SER* 3.4 9.6 - - - +
483B VAL* 1.3 73.3 - - - +
485B ASP* 1.3 62.6 + - - +
487B LEU* 3.5 2.5 + - - +
488B GLU* 3.2 23.4 + - - +
509B PHE* 3.5 29.3 - - + -
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Residues in contact with ASP 485 (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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481B SER 3.1 10.8 + - - +
482B ILE* 3.3 11.9 - - + +
484B ALA* 1.3 79.2 - - - +
486B GLN* 1.3 58.6 + - - +
488B GLU* 3.1 13.2 + - - +
489B LYS* 2.8 72.8 + - - +
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Residues in contact with GLN 486 (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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453B PRO* 3.8 14.8 - - + +
454B ASP* 5.2 0.8 + - - -
482B ILE* 2.9 37.3 + - + +
483B VAL* 2.9 9.6 + - - +
485B ASP* 1.3 81.0 - - - +
487B LEU* 1.3 65.7 + - - +
489B LYS* 3.5 3.8 + - - +
490B ASN 3.2 2.8 + - - -
491B ARG* 3.0 49.8 + - + +
492B LEU 3.6 16.6 + - - -
493B PRO* 3.6 7.8 - - + +
494B SER* 3.2 35.2 + - - -
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Residues in contact with LEU 487 (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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483B VAL* 2.8 28.4 + - + +
484B ALA 3.8 3.1 - - - +
486B GLN* 1.3 72.9 - - - +
488B GLU* 1.3 62.1 + - - +
490B ASN* 3.3 3.6 + - - +
493B PRO* 4.2 19.5 - - + +
509B PHE* 3.7 54.7 - - + +
512B ALA* 3.7 30.7 - - + -
513B ILE* 4.4 1.6 - - + +
516B ARG* 2.7 36.8 + - - +
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Residues in contact with GLU 488 (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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484B ALA 3.2 14.4 + - - +
485B ASP* 3.1 11.4 + - - +
487B LEU* 1.3 77.7 - - + +
489B LYS* 1.3 80.0 + - - +
490B ASN* 3.1 10.8 + - - +
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Residues in contact with LYS 489 (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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485B ASP* 2.8 50.8 + - - +
486B GLN* 4.3 3.6 - - - +
487B LEU 3.4 0.4 - - - -
488B GLU* 1.3 87.0 - - - +
490B ASN* 1.3 68.8 + - - +
491B ARG* 3.0 11.1 + - + +
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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