Contacts of the helix formed by residues 499 - 510 (chain A) in PDB entry 4P0S
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 THR 499 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ARG* 5.7 1.1 + - - +
475A PHE* 3.9 8.9 - - - -
497A TYR 3.1 1.6 + - - -
498A SER* 1.3 80.9 - - - +
500A PRO* 1.3 81.7 - - - +
501A ALA 3.8 2.2 + - - +
502A SER* 2.8 39.9 + - - +
503A LEU 3.2 5.0 + - - -
556B GLN 4.3 0.2 + - - -
559B THR* 2.1 40.3 + - - +
560B LEU* 3.2 27.8 - - + +
561B GLN 5.3 1.8 - - - -
562B PRO* 5.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ARG* 5.9 1.3 - - - +
475A PHE* 3.7 41.0 - - + -
478A GLN* 4.1 0.4 - - - +
499A THR* 1.3 92.7 - - - +
501A ALA* 1.3 61.3 + - - +
502A SER 3.3 0.2 + - - -
503A LEU* 3.4 4.2 + - + +
504A LEU* 3.2 25.3 + - - +
544A TYR* 5.8 3.9 - - + -
556B GLN* 3.0 28.5 - - - +
557B MET* 3.5 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A THR* 3.1 2.9 + - + +
500A PRO* 1.3 80.1 - - - +
502A SER* 1.3 57.7 + - - +
504A LEU* 3.3 10.8 + - + +
505A ALA* 3.0 28.6 + - - +
557B MET 3.3 5.4 + - - +
558B THR* 2.8 41.1 - - + +
559B THR 4.3 2.9 - - - +
560B LEU* 4.3 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ARG 4.8 1.0 + - - -
497A TYR* 3.7 25.8 - - - -
498A SER* 4.0 7.9 + - - -
499A THR* 2.8 34.4 + - - +
501A ALA* 1.3 76.7 - - - +
503A LEU* 1.3 63.2 + - - -
505A ALA* 3.3 13.4 + - - +
506A ALA* 3.4 9.4 + - - +
560B LEU* 3.5 16.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A PHE* 4.4 13.7 - - + -
479A LEU* 5.5 1.8 - - + -
497A TYR* 3.7 32.3 - - + +
499A THR 3.2 5.9 + - - +
500A PRO* 3.8 7.2 - - + +
502A SER* 1.3 78.6 - - - +
504A LEU* 1.3 58.8 + - + +
506A ALA* 3.4 1.7 + - - +
507A TYR* 3.0 59.8 + - + +
519A LEU* 5.3 1.3 - - + -
520A LEU* 3.7 27.4 - - + -
540A LEU* 5.6 2.0 - - + -
544A TYR* 3.6 35.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A PRO* 3.2 16.7 + - + +
501A ALA* 3.5 15.7 - - + +
502A SER 3.2 0.2 - - - -
503A LEU* 1.3 79.0 - - + +
505A ALA* 1.3 59.7 + - - +
507A TYR* 4.1 5.5 - - + +
508A ASP* 2.9 34.5 + - + +
544A TYR* 4.0 39.0 - - + +
507B PRO* 5.6 3.8 - - + +
508B GLN* 4.2 9.9 - - - +
511B VAL* 3.5 41.3 - - + -
557B MET* 4.4 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A ALA 3.0 16.7 + - - +
502A SER* 3.8 7.4 - - - +
503A LEU 3.3 0.2 - - - -
504A LEU* 1.3 76.1 - - - +
506A ALA* 1.3 60.0 + - - +
508A ASP* 3.7 4.3 - - - +
509A ALA* 2.8 32.2 + - - +
560B LEU* 5.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A TYR* 3.6 32.1 - - + +
502A SER 3.4 5.4 + - - +
503A LEU 3.9 4.7 - - - +
504A LEU 3.3 0.2 - - - -
505A ALA* 1.3 77.4 - - - +
507A TYR* 1.3 64.4 + - - +
509A ALA* 3.2 13.3 + - - +
510A CYS* 3.1 20.6 + - - -
519A LEU* 3.7 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A LEU* 3.0 46.3 + - + +
504A LEU* 4.1 6.1 - - + +
506A ALA* 1.3 75.9 - - - +
508A ASP* 1.3 57.9 + - - +
510A CYS* 3.5 8.4 - - - +
516A GLN* 2.8 73.5 + - + +
519A LEU* 4.0 17.0 - - + -
520A LEU* 3.2 26.9 - - + +
537A SER 3.7 4.2 + - - -
540A LEU* 3.7 14.5 - - - +
541A SER* 3.5 25.1 + - - -
544A TYR* 4.2 9.2 - - + -
545A CYS* 3.8 20.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A LEU* 2.9 20.8 + - + +
505A ALA* 4.0 4.3 - - - +
507A TYR* 1.3 73.9 - - - +
509A ALA* 1.3 59.2 + - - +
510A CYS 3.1 13.3 + - - +
516A GLN* 4.7 2.5 - - - +
547A TYR* 4.9 8.2 + - - -
508B GLN* 6.1 3.6 - - - +
515B GLN* 5.2 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ALA 2.8 21.3 + - - +
506A ALA* 3.2 9.1 + - - +
508A ASP* 1.3 71.4 - - - +
510A CYS* 1.3 68.0 + - - +
511A ALA* 5.2 0.3 - - - +
515A GLU* 4.6 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A ALA 3.1 24.0 + - - -
507A TYR* 3.5 16.2 - - - +
508A ASP 3.1 10.4 - - - +
509A ALA* 1.3 85.6 - - - +
511A ALA* 1.3 62.5 + - - +
512A THR 4.2 1.1 - - - +
515A GLU* 3.0 50.0 - - + +
516A GLN* 4.0 12.5 + - + +
519A LEU* 4.1 16.6 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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