Contacts of the helix formed by residues 494 - 503 (chain B) in PDB entry 4OSI
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 494 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B CYS* 3.2 4.8 - - - -
493B LEU* 1.3 74.3 - - - +
495B PRO* 1.3 65.1 - - - +
496B GLN* 3.1 19.7 + - - +
497B GLN* 2.8 36.1 + - + +
498B VAL* 2.7 33.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B HIS 5.2 7.6 - - - +
458B GLY 5.4 6.5 - - - +
459B LEU* 5.1 9.6 - - + -
463B GLN* 6.1 1.1 - - - +
484B LEU* 4.1 26.1 - - + +
488B CYS* 4.6 4.0 - - - -
494B THR* 1.3 89.2 - - - +
496B GLN* 1.3 69.5 + - - +
498B VAL* 3.0 6.6 + - - +
499B VAL* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B GLN* 4.4 20.7 - - - +
494B THR* 3.1 12.2 + - - +
495B PRO* 1.3 90.2 - - + +
497B GLN* 1.3 57.7 + - - +
499B VAL* 3.0 11.3 + - - +
500B ALA* 2.9 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 497 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B LEU* 2.3 48.8 - - + +
494B THR* 2.8 33.8 + - - +
496B GLN* 1.3 75.5 - - - +
498B VAL* 1.3 63.5 + - - +
500B ALA* 3.5 6.4 + - - +
501B ILE* 3.1 31.9 + - - +
529B PRO* 5.2 6.1 + - - +
530B GLN* 6.0 1.2 - - - +
533B VAL* 3.7 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B VAL* 4.9 8.6 - - + +
483B LEU 5.5 0.4 - - - -
484B LEU* 4.0 24.0 - - + +
487B LEU* 3.8 37.2 - - + -
488B CYS* 4.3 3.6 - - - -
493B LEU* 4.1 7.4 - - + -
494B THR 2.7 26.2 - - - +
495B PRO* 3.0 11.2 + - + +
497B GLN* 1.3 77.6 - - - +
499B VAL* 1.3 61.9 + - + +
501B ILE* 3.9 8.0 - - - +
502B ALA* 3.4 18.5 + - - +
511B LEU* 3.8 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B LEU* 3.8 27.4 - - + -
463B GLN* 4.4 26.5 - - + +
466B ALA* 6.0 1.3 - - + -
467B ILE* 4.1 18.4 - - + -
480B VAL* 5.6 3.1 - - + -
484B LEU* 6.0 0.9 - - + -
495B PRO 2.9 14.2 + - - +
496B GLN* 3.0 12.5 + - - +
498B VAL* 1.3 75.0 - - + +
500B ALA* 1.3 63.2 + - + +
501B ILE 3.0 1.3 - - - -
502B ALA* 2.6 30.1 + - - +
503B SER* 3.0 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B GLN 2.9 13.7 + - - +
497B GLN* 4.0 7.2 - - - +
499B VAL* 1.3 81.3 - - + +
501B ILE* 1.3 60.2 + - - +
503B SER* 3.4 12.5 + - - -
504B ASN* 3.3 17.8 + - - +
533B VAL* 6.0 2.7 - - + -
537B SER* 3.6 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B LEU* 5.3 1.6 - - + -
493B LEU* 4.6 7.6 - - + -
497B GLN 3.1 25.8 + - - +
498B VAL* 3.9 10.1 - - - +
499B VAL 3.0 0.6 - - - -
500B ALA* 1.3 75.4 - - - +
502B ALA* 1.3 59.5 + - - +
503B SER 3.2 0.2 - - - -
504B ASN* 2.6 20.6 - - - +
507B GLY* 3.9 7.8 - - - -
510B ALA* 3.6 28.5 - - + +
511B LEU* 3.7 23.1 - - + +
514B VAL* 4.9 12.3 - - + -
533B VAL* 4.3 19.7 - - + +
536B ALA* 3.8 21.5 - - + +
537B SER* 3.3 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ILE* 3.9 12.4 - - + +
470B ASN* 4.1 2.8 + - - -
476B ALA* 3.8 21.3 - - + +
480B VAL* 3.4 33.2 - - + -
498B VAL 3.4 7.8 + - - +
499B VAL* 2.6 16.2 + - - +
501B ILE* 1.3 75.4 - - - +
503B SER* 1.3 54.8 + - - -
504B ASN 3.3 9.4 + - - +
507B GLY* 4.0 11.7 - - - -
511B LEU* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B ALA* 4.1 17.4 - - - +
467B ILE* 3.8 21.0 + - - +
470B ASN* 3.3 22.6 - - - +
499B VAL* 3.0 20.8 + - - +
500B ALA* 3.4 10.3 + - - -
501B ILE 3.2 2.8 - - - -
502B ALA* 1.3 75.4 - - - +
504B ASN* 1.3 66.8 + - - +
----------------------------------------------------------
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