Contacts of the helix formed by residues 498 - 512 (chain B) in PDB entry 4OL0
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 PHE 498 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B VAL* 3.8 33.2 - - + -
463B LEU* 4.0 28.0 - - + -
464B GLU* 3.8 31.4 - - + -
467B VAL* 6.0 1.6 - - + -
492B VAL* 4.3 6.3 - - + -
495B ASN* 3.0 30.8 + - + +
496B PRO 2.9 1.0 + - - -
497B GLN* 1.3 103.7 - - + +
499B LEU* 1.3 58.2 + - - +
500B ASP 3.4 0.4 - - - -
501B PRO* 3.4 11.0 - - + +
502B VAL* 2.9 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B VAL* 3.8 19.6 - - + +
496B PRO* 2.8 18.4 + - + +
498B PHE* 1.3 78.8 - - - +
500B ASP* 1.3 57.9 + - - +
502B VAL* 3.8 0.6 - - + +
503B LEU* 3.0 36.4 + - + +
526B ILE* 4.0 20.2 - - + -
530B CYS* 4.6 5.2 - - + -
533B HIS* 3.4 46.4 - - + +
534B MET* 3.8 22.0 - - + -
537B HIS* 3.8 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B PRO 4.5 0.8 + - - -
497B GLN 4.4 1.5 + - - +
499B LEU* 1.3 78.7 - - - +
501B PRO* 1.3 70.8 - - + +
503B LEU* 3.6 3.3 + - - +
504B GLY* 3.2 18.9 + - - -
537B HIS* 4.0 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B VAL* 4.0 17.0 - - + +
497B GLN 3.3 23.6 - - - +
498B PHE* 3.4 13.7 - - + +
500B ASP* 1.3 95.9 - - + +
502B VAL* 1.3 61.1 + - + +
504B GLY* 3.5 2.1 + - - -
505B TYR* 3.2 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B LEU* 4.2 11.4 - - + -
467B VAL* 3.9 22.2 - - + -
485B VAL* 3.7 18.4 - - + -
492B VAL* 4.0 21.1 - - + -
498B PHE* 2.9 29.7 + - + +
499B LEU* 3.8 4.9 - - + +
500B ASP 3.3 0.2 - - - -
501B PRO* 1.3 74.2 - - + +
503B LEU* 1.3 59.9 + - - +
505B TYR* 2.7 29.4 + - - +
506B LEU* 2.9 12.2 + - + +
526B ILE* 3.5 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B LEU* 3.0 26.4 + - + +
500B ASP* 4.0 4.3 - - - +
502B VAL* 1.3 75.2 - - + +
504B GLY* 1.3 54.7 + - - +
506B LEU* 2.7 13.0 + - + +
507B MET* 2.7 58.3 + - + +
523B ILE* 4.8 20.6 - - + -
526B ILE* 4.7 11.7 - - + -
534B MET* 3.8 33.0 - - + -
537B HIS* 3.4 40.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B ASP* 3.2 12.4 + - - -
501B PRO* 3.8 4.9 - - - -
502B VAL 3.3 0.2 - - - -
503B LEU* 1.3 78.9 - - - +
505B TYR* 1.3 58.3 + - - +
507B MET* 4.5 7.8 - - - +
508B LYS* 3.4 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B VAL 3.4 15.0 - - - -
467B VAL* 3.1 36.6 - - + +
469B LEU* 3.4 23.7 - - + +
478B ARG* 3.6 21.1 + - + +
481B SER* 2.7 24.4 + - - -
482B ILE* 3.9 22.5 - - + +
485B VAL* 4.1 17.3 - - + -
501B PRO 3.2 11.5 + - - +
502B VAL 2.7 15.0 + - - +
504B GLY* 1.3 73.6 - - - +
506B LEU* 1.3 74.1 + - + +
508B LYS* 4.0 8.4 - - + +
509B GLY* 3.5 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ILE* 4.0 18.6 - - + -
485B VAL* 4.0 15.7 - - + -
502B VAL* 2.9 17.1 + - + +
503B LEU* 2.7 11.8 + - + +
505B TYR* 1.3 86.4 - - + +
507B MET* 1.3 59.8 + - - +
509B GLY* 3.2 2.3 + - - -
510B LEU* 2.9 22.9 + - - +
519B ALA* 3.3 13.6 - - + +
522B ALA* 3.6 31.0 - - + -
523B ILE* 3.7 27.4 - - + +
526B ILE* 3.4 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B LEU* 2.7 53.7 + - + +
504B GLY* 4.5 5.6 - - - +
506B LEU* 1.3 69.3 - - - +
508B LYS* 1.3 65.8 + - - +
510B LEU* 2.8 26.2 + - + +
511B CYS* 3.3 12.5 + - - -
523B ILE* 4.5 6.1 - - + -
537B HIS* 5.3 4.9 - - + +
540B GLY* 4.7 18.2 - - - +
541B LEU* 4.9 6.1 - - + -
544B ILE* 3.9 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B GLU* 4.4 23.1 + - - +
478B ARG* 6.0 3.1 - - - +
504B GLY 3.4 19.9 + - - +
505B TYR* 4.0 10.1 - - + +
507B MET* 1.3 77.6 - - - +
509B GLY* 1.3 58.0 + - - +
511B CYS* 2.8 31.0 + - - +
512B GLU* 3.6 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B ARG* 5.9 1.3 - - - -
482B ILE* 4.5 9.0 - - - -
505B TYR 3.5 9.7 + - - -
506B LEU 3.2 9.2 + - - -
508B LYS* 1.3 78.2 - - - +
510B LEU* 1.3 58.2 + - - +
511B CYS 3.2 0.2 - - - -
512B GLU* 3.3 20.6 + - - +
515B LEU* 3.5 30.3 - - - +
516B ALA 3.7 3.1 + - - -
519B ALA* 4.0 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B LEU 2.9 11.4 + - - +
507B MET* 2.8 16.2 + - + +
509B GLY* 1.3 78.4 - - - +
511B CYS* 1.3 60.3 + - - +
512B GLU 3.4 0.4 - - - -
516B ALA* 3.7 33.2 - - - +
519B ALA* 3.9 9.4 - - + -
520B ALA* 4.3 3.4 - - - +
523B ILE* 4.4 8.1 - - + -
544B ILE* 4.0 27.8 - - + -
551B PHE* 3.4 59.6 - - + +
553B LEU* 4.4 2.7 - - + -
561B LEU* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B MET 3.7 13.7 - - - -
508B LYS* 2.8 11.3 + - - +
510B LEU* 1.3 78.3 - - - +
512B GLU* 1.3 63.1 + - + +
513B LYS* 3.6 5.0 + - - +
551B PHE* 4.1 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B GLU* 3.7 18.5 - - - +
475B THR* 5.8 1.0 - - - +
478B ARG* 2.8 39.5 + - - -
508B LYS* 3.6 12.7 + - - +
509B GLY* 3.3 11.1 + - - +
510B LEU 3.4 0.9 - - - -
511B CYS* 1.3 79.5 - - + +
513B LYS* 1.3 69.6 + - - +
514B PRO* 4.4 6.6 - - + +
515B LEU* 3.2 20.4 + - + +
516B ALA* 3.1 18.5 + - - +
----------------------------------------------------------
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