Contacts of the helix formed by residues 503 - 516 (chain B) in PDB entry 3R9A
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 GLU 503 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468B PHE* 4.8 0.7 - - - -
472B LYS* 3.9 15.7 + - - +
498B PHE* 2.7 35.8 + - + +
501B SER* 2.7 33.7 + - - +
502B GLY* 1.3 76.8 - - - +
504B TYR* 1.3 63.6 + - - +
505B ASP* 3.3 3.4 - - - -
506B LYS* 2.7 41.0 + - + -
507B ALA 3.1 15.8 + - - -
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Residues in contact with TYR 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B ASN* 3.5 48.7 + - - -
502B GLY* 3.2 26.1 + - - -
503B GLU* 1.3 69.1 - - - +
505B ASP* 1.3 56.7 + - - +
507B ALA* 3.0 7.0 + - - +
508B VAL* 2.8 39.1 + - + +
531B THR* 3.5 15.4 - - + +
534B ASN* 3.5 47.5 + - + +
535B GLY* 3.9 9.9 - - - +
537B GLN* 5.8 0.9 - - - +
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Residues in contact with ASP 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B GLU 3.3 1.3 - - - -
504B TYR* 1.3 80.4 - - - +
506B LYS* 1.3 64.5 + - + +
508B VAL* 3.4 7.6 + - - +
509B ASP* 3.3 24.8 + - - +
535B GLY* 6.1 0.5 - - - -
537B GLN* 3.8 18.4 - - - +
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Residues in contact with LYS 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B LYS* 4.8 6.8 - - - +
498B PHE* 3.7 34.3 - - + -
503B GLU* 2.7 41.4 + - + +
505B ASP* 1.3 78.3 - - + +
507B ALA* 1.3 63.7 + - - +
509B ASP* 3.5 14.5 + - + +
510B CYS* 3.2 26.2 + - - -
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Residues in contact with ALA 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B GLY* 3.4 31.0 - - - +
498B PHE* 3.7 14.7 - - + +
499B ASN* 3.6 5.8 - - - +
503B GLU 3.1 7.0 + - - +
504B TYR* 3.0 5.5 + - - +
506B LYS* 1.3 74.9 - - - +
508B VAL* 1.3 64.4 + - - +
510B CYS* 3.0 12.5 + - - +
511B PHE* 3.0 18.8 + - + -
531B THR* 3.4 24.7 - - + -
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Residues in contact with VAL 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B TYR 2.8 22.7 + - - +
505B ASP* 3.5 10.5 - - - +
507B ALA* 1.3 72.4 - - - +
509B ASP* 1.3 63.8 + - - +
512B THR* 2.7 38.0 + - - +
528B LEU* 3.7 19.6 - - + +
531B THR* 3.6 15.9 - - + +
532B LEU* 3.8 34.3 - - + +
537B GLN* 4.2 12.3 - - - +
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Residues in contact with ASP 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B GLN* 4.9 0.2 - - - -
505B ASP 3.3 14.3 + - - +
506B LYS* 3.5 17.5 - - - +
507B ALA 3.2 0.4 - - - -
508B VAL* 1.3 81.0 - - - +
510B CYS* 1.3 57.7 - - - +
512B THR* 3.4 6.0 + - - -
513B ALA* 2.9 31.1 + - - +
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Residues in contact with CYS 510 (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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491B GLN* 3.2 46.7 - - - +
494B LEU* 3.6 38.8 - - - -
495B GLY* 3.7 10.8 - - - -
498B PHE* 4.0 7.0 - - - -
506B LYS 3.2 14.3 + - - -
507B ALA 3.0 9.5 + - - +
509B ASP* 1.3 79.5 - - - +
511B PHE* 1.3 57.4 + - - +
513B ALA* 3.4 1.2 + - - +
514B ALA* 3.1 21.8 + - - +
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Residues in contact with PHE 511 (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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392A LEU* 4.3 2.5 - - + -
492B CYS* 3.6 28.3 - - - -
495B GLY* 3.6 25.1 - - - -
496B VAL* 3.8 6.5 - - + -
499B ASN* 3.7 12.1 - - - -
507B ALA 3.0 18.8 + - - +
510B CYS* 1.3 73.3 - - - +
512B THR* 1.3 60.7 + - - +
514B ALA* 3.3 3.9 + - - +
515B LEU* 2.9 35.2 + - - +
524B LEU* 4.2 17.3 - - + +
527B LYS* 3.7 43.7 - - + -
528B LEU* 4.0 22.4 - - + +
531B THR* 3.2 28.3 - - - -
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Residues in contact with THR 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B VAL* 2.7 28.5 + - - +
509B ASP* 3.6 6.5 - - - -
511B PHE* 1.3 78.1 - - - +
513B ALA* 1.3 61.6 + - - +
515B LEU* 3.3 10.9 + - + +
516B SER* 3.1 21.9 + - - -
528B LEU* 3.5 18.5 - - + +
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Residues in contact with ALA 513 (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 ILE* 3.7 24.1 - - + +
491B GLN* 3.7 21.3 - - + +
509B ASP 2.9 18.8 + - - +
510B CYS 3.6 5.2 - - - +
512B THR* 1.3 76.6 - - - +
514B ALA* 1.3 60.7 + - - +
516B SER* 2.7 25.8 + - - -
517B VAL* 3.8 1.6 - - - +
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Residues in contact with ALA 514 (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 ILE* 4.7 0.4 - - - -
488B PRO* 3.5 39.6 - - + +
491B GLN* 4.1 2.9 - - + +
492B CYS 4.7 1.6 - - - +
510B CYS 3.1 17.4 + - - +
511B PHE* 3.7 5.2 - - - +
513B ALA* 1.3 75.8 - - - +
515B LEU* 1.3 57.9 + - - +
517B VAL* 3.2 7.1 + - - +
518B ARG 3.0 21.7 + - - -
524B LEU* 3.6 28.5 - - + +
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Residues in contact with LEU 515 (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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511B PHE 2.9 19.7 + - - +
512B THR* 3.6 7.0 - - + +
513B ALA 3.3 0.2 - - - -
514B ALA* 1.3 73.5 - - - +
516B SER* 1.3 55.5 + - - +
517B VAL 3.1 5.4 - - - -
518B ARG 3.6 15.7 - - - +
519B PRO* 3.0 35.6 - - + +
521B ASP 3.9 0.4 - - - +
524B LEU* 3.5 25.8 - - + +
525B TRP* 3.4 59.0 - - + +
528B LEU* 3.8 31.0 - - + -
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Residues in contact with SER 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B ILE* 3.7 17.7 - - - +
512B THR 3.1 11.5 + - - -
513B ALA* 2.7 21.2 + - - -
515B LEU* 1.3 74.6 - - - +
517B VAL* 1.3 59.7 + - - +
519B PRO* 4.8 4.0 - - - +
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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