Contacts of the helix formed by residues 477 - 494 (chain B) in PDB entry 4A9C
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 GLY 477 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B SER 3.7 2.8 + - - -
476B VAL* 1.3 76.9 - - - +
478B ASP* 1.3 57.2 + - - +
479B ARG 3.6 2.0 - - - -
480B GLU* 3.2 26.4 + - - -
481B TRP* 2.8 32.2 + - - +
509B LYS* 3.8 3.6 - - - -
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Residues in contact with ASP 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B GLY* 1.3 68.6 - - - +
479B ARG* 1.4 61.5 + - + +
481B TRP* 3.8 2.8 - - - +
482B LEU 3.1 21.1 + - - -
502B MET* 3.3 37.8 - - - +
504B SER* 3.0 28.9 + - - -
509B LYS* 2.8 35.9 + - - +
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Residues in contact with ARG 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B GLY 3.6 0.2 - - - -
478B ASP* 1.4 79.4 - - + +
480B GLU* 1.4 60.4 + - + +
482B LEU* 3.6 26.1 - - + +
483B ASP* 3.0 28.6 + - - +
486B ARG* 4.8 14.3 + - - +
502B MET* 5.8 1.6 - - - -
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Residues in contact with GLU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B VAL* 4.0 13.4 - - + +
477B GLY* 3.2 28.2 + - - +
479B ARG* 1.4 75.6 + - + +
481B TRP* 1.4 57.4 + - - +
483B ASP* 3.4 5.8 + - - +
484B LEU* 3.0 29.8 + - + +
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Residues in contact with TRP 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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433B MET* 4.8 7.9 - - + +
438B PRO* 5.5 2.9 - - + +
445B TRP* 5.6 2.4 - + - -
469B PHE* 3.3 29.4 - - + -
471B THR* 3.4 25.0 - - + +
474B ASN* 3.3 24.5 - - - +
476B VAL* 3.7 21.5 - - + +
477B GLY 2.8 20.9 + - - +
478B ASP 3.8 1.1 - - - +
480B GLU* 1.4 70.0 - - - +
482B LEU* 1.4 59.3 + - - +
484B LEU* 3.3 14.5 - - + +
485B LEU* 3.0 54.3 + - + +
502B MET* 3.6 20.2 - - + -
509B LYS* 3.5 35.0 - - + -
510B VAL 3.9 5.2 - - - -
511B ALA* 3.7 20.9 - - + -
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Residues in contact with LEU 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B ASP 3.1 10.5 + - - +
479B ARG* 3.6 28.7 - - + +
480B GLU 3.3 0.2 - - - -
481B TRP* 1.4 75.5 - - - +
483B ASP* 1.4 58.2 + - - +
485B LEU* 3.3 6.2 + - - +
486B ARG* 2.9 36.9 + - - +
499B PRO* 3.7 40.6 - - + -
501B ALA 5.2 1.8 - - - +
502B MET* 3.6 37.2 - - + +
511B ALA* 4.2 15.3 - - + -
513B LEU* 4.4 10.9 - - + +
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Residues in contact with ASP 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ARG 3.0 17.4 + - - +
480B GLU* 3.8 6.5 - - - +
482B LEU* 1.4 72.2 - - - +
484B LEU* 1.4 55.7 + - - +
486B ARG* 3.7 34.9 + - - +
487B GLY* 2.8 31.4 + - - -
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Residues in contact with LEU 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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438B PRO* 4.0 33.4 - - + -
439B PRO 5.5 3.4 - - - +
442B VAL* 5.2 12.3 - - + -
446B PHE* 5.4 1.9 - - + -
476B VAL* 4.6 15.5 - - + -
480B GLU 3.0 15.5 + - - +
481B TRP* 3.3 17.7 - - + +
482B LEU 3.3 0.2 - - - -
483B ASP* 1.4 76.8 - - - +
485B LEU* 1.4 60.5 + - + +
487B GLY* 4.0 1.0 - - - -
488B GLY* 3.0 24.3 + - - -
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Residues in contact with LEU 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B TRP* 4.9 6.1 - - + -
446B PHE* 4.4 12.1 - - + -
469B PHE* 3.6 46.2 - - + -
481B TRP* 3.0 57.8 + - + +
482B LEU* 3.3 7.4 + - - +
484B LEU* 1.4 77.1 - - + +
486B ARG* 1.4 57.5 + - - +
488B GLY* 3.3 2.5 + - - -
489B LEU* 3.0 37.2 + - - +
511B ALA* 3.9 17.3 - - + -
513B LEU* 4.2 12.8 - - + -
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Residues in contact with ARG 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ARG* 4.8 15.2 + - - +
482B LEU* 2.9 22.1 + - - +
483B ASP* 3.7 33.6 + - - +
485B LEU* 1.4 74.7 - - - +
487B GLY* 1.3 58.5 + - - +
489B LEU* 3.5 4.4 + - - +
490B LYS* 3.1 27.8 + - + +
495B LEU 5.2 0.7 - - - +
496B ASP* 3.9 22.5 + - - +
497B TYR* 3.4 26.6 + - - +
498B ARG* 5.5 0.2 - - - +
499B PRO* 4.1 21.5 - - - +
513B LEU* 4.1 14.1 - - + +
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Residues in contact with GLY 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B ASP* 2.8 23.0 + - - -
484B LEU* 4.1 1.1 - - - -
486B ARG* 1.3 70.6 - - - +
488B GLY* 1.3 63.4 + - - +
490B LYS* 3.3 7.6 + - - +
491B GLU* 3.2 23.0 + - - +
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Residues in contact with GLY 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B VAL* 6.2 0.2 - - - -
446B PHE* 4.0 24.1 - - - -
484B LEU 3.0 18.6 + - - -
485B LEU 3.3 2.2 + - - -
487B GLY* 1.3 77.5 - - - +
489B LEU* 1.3 58.9 + - - +
491B GLU* 3.7 5.9 + - - +
492B LEU* 3.4 20.8 + - - +
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Residues in contact with LEU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B PHE* 4.5 15.3 - - + -
467B TYR* 3.7 54.3 - - + -
469B PHE* 4.1 17.5 - - + -
485B LEU 3.0 20.5 + - - +
486B ARG 4.0 4.0 - - - +
488B GLY* 1.3 73.9 - - - +
490B LYS* 1.4 56.9 + - - +
491B GLU 3.4 0.2 - - - -
492B LEU* 4.5 6.5 - - + -
493B THR* 2.7 41.7 + - + +
495B LEU 4.3 1.1 - - - -
497B TYR* 3.8 37.2 - - + -
513B LEU* 4.2 11.0 - - + -
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Residues in contact with LYS 490 (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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486B ARG* 3.1 19.1 + - + +
487B GLY* 3.3 10.3 + - - +
489B LEU* 1.4 76.3 - - - +
491B GLU* 1.3 57.8 + - - +
494B ASP* 2.8 64.8 + - - +
495B LEU 3.6 20.2 + - - +
496B ASP* 4.2 26.1 + - - +
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Residues in contact with GLU 491 (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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487B GLY 3.2 15.4 + - - +
488B GLY* 4.0 5.6 - - - +
489B LEU 3.4 0.2 - - - -
490B LYS* 1.3 76.9 - - - +
492B LEU* 1.3 60.8 + - - +
494B ASP* 4.8 1.0 + - - +
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Residues in contact with LEU 492 (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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443B THR* 3.8 17.9 - - + -
446B PHE* 3.8 34.5 - - + +
447B THR* 3.6 27.8 - - + -
461B THR* 4.1 22.2 + - + +
467B TYR* 4.5 9.4 - - - +
488B GLY 3.4 14.4 + - - +
489B LEU* 3.9 7.6 - - + +
490B LYS 3.3 0.4 - - - -
491B GLU* 1.3 80.6 - - - +
493B THR* 1.3 70.8 + - + +
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Residues in contact with THR 493 (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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461B THR* 5.8 1.1 - - - +
463B PRO* 3.6 41.6 - - + +
467B TYR* 4.4 4.9 - - + +
489B LEU* 2.7 21.7 + - - +
492B LEU* 1.3 92.5 - - + +
494B ASP* 1.4 65.0 + - - +
495B LEU* 3.0 29.0 + - - +
497B TYR* 3.4 22.5 - - + +
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Residues in contact with ASP 494 (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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490B LYS* 2.8 53.7 + - - +
491B GLU 4.7 1.4 + - - +
492B LEU 3.8 0.6 - - - -
493B THR* 1.4 72.2 - - - +
495B LEU* 1.3 59.7 + - + +
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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