Contacts of the helix formed by residues 478 - 491 (chain B) in PDB entry 2I91
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 HIS 478 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B MET* 3.7 15.6 + - + +
6B ASP 3.0 15.9 + - - -
7B GLN* 3.6 16.1 - - - +
9B GLN 2.6 29.4 + - - -
11B LEU* 3.5 29.0 - - + +
15B GLN* 3.6 18.0 + - - -
23B TYR* 3.6 25.3 + - + -
25B TRP* 6.1 1.2 - - + -
448B ALA* 4.2 0.2 - - - -
476B ASP 3.6 0.2 + - - -
477B VAL* 1.3 74.0 - - - +
479B PRO* 1.3 70.8 - - + +
480B ALA* 4.3 1.6 - - + +
481B THR* 2.8 34.3 + - - +
482B ALA* 2.8 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLN* 4.6 10.8 - - + +
23B TYR 6.0 0.4 - - - +
25B TRP* 6.2 0.4 - - + -
447B CYS* 3.4 25.6 - - + +
448B ALA* 3.7 15.3 - - + +
451B MET* 3.6 15.6 - - + +
472B THR* 5.1 5.2 - - + +
477B VAL 3.6 3.3 - - - +
478B HIS* 1.3 89.1 - - + +
480B ALA* 1.3 62.7 + - + +
482B ALA* 3.0 3.6 + - + +
483B LEU* 2.9 20.8 + - - +
496B LEU* 5.5 1.8 - - + -
508B ILE* 3.5 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 480 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 4.4 8.1 - - + -
25B TRP* 3.9 34.8 - - + -
478B HIS* 3.2 0.8 - - + -
479B PRO* 1.3 81.7 - - - +
481B THR* 1.3 61.5 + - - +
483B LEU* 3.4 4.9 + - - +
484B LYS* 3.2 31.4 + - - +
496B LEU* 5.6 0.7 - - - -
508B ILE 4.4 3.7 + - - +
510B ASP* 4.4 2.5 - - + +
516B MET* 4.2 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 481 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B MET* 5.7 2.5 - - + +
11B LEU* 3.8 19.1 - - - +
477B VAL* 4.3 11.7 - - + -
478B HIS* 2.8 31.4 + - - +
480B ALA* 1.3 76.8 - - - +
482B ALA* 1.3 57.4 + - - +
484B LYS* 3.3 11.3 + - + +
485B GLN* 3.0 49.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 482 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B ALA* 3.8 24.7 - - + +
451B MET* 3.7 21.4 - - + +
452B LEU* 4.1 12.6 - - + +
455B GLN* 5.4 0.3 - - - +
477B VAL* 4.1 7.4 - - + +
478B HIS 2.8 11.4 + - - +
479B PRO* 3.2 9.2 - - + +
481B THR* 1.3 77.8 - - - +
483B LEU* 1.3 60.0 + - - +
485B GLN* 3.6 10.0 + - - +
486B TYR* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 483 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B MET* 3.7 22.4 - - + +
464B PHE* 4.1 15.7 - - + -
479B PRO 2.9 11.9 + - - +
480B ALA* 3.7 8.3 - - - +
481B THR 3.2 0.2 - - - -
482B ALA* 1.3 74.5 - - - +
484B LYS* 1.3 60.5 + - - +
486B TYR* 2.9 6.6 + - + +
487B ARG* 2.8 59.8 + - - +
494B ALA* 3.9 26.2 - - + +
495B LYS 4.4 3.6 - - - +
496B LEU* 3.4 30.1 - - + +
516B MET* 3.8 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B ALA* 3.2 16.2 + - - +
481B THR* 3.6 11.4 - - + +
483B LEU* 1.3 77.3 - - - +
485B GLN* 1.3 64.4 + - + +
487B ARG* 3.0 17.1 + - - +
488B GLU* 3.0 35.8 + - - +
510B ASP* 5.3 8.1 - - - -
513B ASP* 3.9 23.6 + - - +
516B MET* 5.2 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LEU* 4.2 21.8 - - + +
455B GLN* 3.7 12.9 + - - +
477B VAL* 4.7 13.0 - - - +
481B THR* 3.0 37.5 + - + +
482B ALA* 3.8 6.0 - - - +
484B LYS* 1.3 75.8 - - + +
486B TYR* 1.3 56.0 + - - +
488B GLU* 4.0 12.6 - - - +
489B LYS* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B MET* 3.8 10.8 - - + +
454B ALA* 3.6 21.1 - - + -
455B GLN* 3.7 26.7 + - + -
459B THR 2.7 21.9 + - - -
460B ALA* 3.4 3.5 - - - -
461B ALA* 3.2 21.6 + - - +
464B PHE* 3.8 15.0 - + - -
482B ALA 3.1 14.7 + - - +
483B LEU* 2.9 14.0 + - + +
485B GLN* 1.3 74.4 - - - +
487B ARG* 1.3 70.3 + - - +
489B LYS* 3.1 2.0 + - - -
490B MET* 2.8 54.7 + - + +
492B ILE* 4.2 6.0 - - + +
494B ALA* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B LEU* 2.8 50.6 + - - +
484B LYS* 3.0 15.0 + - - +
486B TYR* 1.3 73.9 - - - +
488B GLU* 1.3 56.9 + - + +
491B GLY* 2.6 38.3 + - - -
492B ILE 3.3 24.2 + - - +
493B PRO* 4.2 12.7 + - + +
494B ALA* 3.5 28.8 + - + +
513B ASP* 2.8 42.7 + - - -
515B GLY* 4.1 9.9 - - - +
516B MET* 3.5 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B LYS* 3.0 25.8 + - + +
485B GLN* 4.0 13.9 + - - +
487B ARG* 1.3 78.4 - - + +
489B LYS* 1.3 65.4 + - - +
491B GLY* 3.6 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B GLN* 3.4 42.4 - - + +
485B GLN 3.0 20.7 + - - +
486B TYR 3.7 2.2 - - - +
488B GLU* 1.3 80.2 - - - +
490B MET* 1.3 63.2 - - - +
491B GLY 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 490 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B GLN* 4.2 13.9 - - - +
458B ASN* 3.4 54.5 - - - +
459B THR 3.7 13.0 - - - +
460B ALA* 4.1 9.6 - - + +
486B TYR* 2.8 57.9 + - + +
489B LYS* 1.3 77.2 - - + +
491B GLY* 1.3 61.1 + - - +
492B ILE* 3.4 16.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 491 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B ARG 2.6 19.2 + - - -
488B GLU* 3.6 5.7 + - - -
489B LYS 3.4 2.6 + - - -
490B MET* 1.3 75.5 - - - +
492B ILE* 1.3 58.6 + - - +
493B PRO* 4.4 3.2 - - - +
----------------------------------------------------------
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