Contacts of the helix formed by residues 491 - 498 (chain W) in PDB entry 5O9G
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 491 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-18I C 6.1 0.7 - - - -
432W VAL 3.7 5.8 - - - -
433W PRO* 4.2 4.0 - - + -
434W LEU* 3.5 49.1 - - + +
437W MET* 3.7 14.1 - - - +
457W MET* 5.5 0.3 - - - +
490W THR* 1.3 79.1 - - - +
492W TYR* 1.3 75.6 + - + +
493W GLU* 3.3 11.2 - - + +
494W TYR* 3.2 40.1 + - - -
495W ILE* 3.3 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 492 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431W VAL* 4.4 17.5 - - + -
433W PRO* 3.8 30.5 - - + +
490W THR 4.9 0.2 - - - -
491W THR* 1.3 81.9 - - + +
493W GLU* 1.3 62.4 + - - +
495W ILE* 3.3 23.0 + - + +
496W LEU* 3.4 21.0 - - + +
512W VAL* 3.6 20.4 - - + +
513W ASP 2.9 27.2 + - - -
514W GLU* 3.6 6.5 + - + -
515W ALA* 6.1 0.2 - - - -
517W ARG* 3.8 35.0 - - + -
525W LEU* 4.5 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 493 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-19I G 5.3 6.6 + - - +
-18I C 2.9 28.4 + - - +
-17I T 2.9 42.7 + - - +
434W LEU* 3.7 7.0 - - - +
491W THR* 4.3 10.5 - - + +
492W TYR* 1.3 76.7 - - - +
494W TYR* 1.3 81.9 + - + +
496W LEU* 3.4 7.1 + - - +
497W LYS* 2.9 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 494 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-17I T 4.4 10.8 + - - -
-16I T 4.8 11.8 + - - -
434W LEU* 6.0 2.2 - - + +
456W TYR* 3.3 47.9 - + + -
457W MET* 3.6 13.6 - - + +
458W GLY* 2.9 36.4 + - - -
459W ASN* 5.6 0.4 - - - -
490W THR* 3.7 8.5 - - + -
491W THR* 3.2 35.5 + - - +
493W GLU* 1.3 94.6 - - + +
495W ILE* 1.3 60.3 + - - +
497W LYS* 3.9 14.4 - - + -
498W ASP* 3.0 32.7 + - - +
502W LEU* 4.4 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 495 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429W ILE* 5.9 1.3 - - + -
431W VAL* 3.6 28.5 - - + -
490W THR* 3.8 12.1 - - + -
491W THR 3.3 14.8 - - - +
492W TYR* 3.5 13.0 - - + +
493W GLU 3.2 1.0 - - - -
494W TYR* 1.3 76.9 - - - +
496W LEU* 1.3 62.8 + - + +
498W ASP 3.1 19.9 - - - +
499W ARG* 3.2 14.4 - - - +
502W LEU* 4.4 6.5 - - + -
525W LEU* 4.0 21.5 - - + -
528W SER* 3.3 26.9 - - - +
529W LEU* 4.1 9.4 - - + -
532W PHE* 4.1 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 496 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J C 5.0 0.9 - - - +
20J G 3.2 45.3 - - - +
21J G 4.7 1.1 - - - +
492W TYR* 3.4 17.5 - - + +
493W GLU* 3.4 8.8 + - - +
495W ILE* 1.3 83.0 - - + +
497W LYS* 1.3 60.7 + - - +
499W ARG* 3.0 36.9 + - - +
524W SER* 3.7 22.4 - - - +
525W LEU* 4.2 31.0 - - + -
528W SER* 5.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 497 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-17I T 3.7 4.0 + - - -
-16I T 2.3 49.2 + - - +
459W ASN* 5.5 6.7 - - - +
463W ARG* 6.1 0.9 - - - +
493W GLU* 2.9 24.6 + - - +
494W TYR* 4.2 16.3 - - + +
496W LEU* 1.3 78.9 - - - +
498W ASP* 1.3 76.0 + - - +
499W ARG 4.0 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 498 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456W TYR* 2.4 35.3 + - + +
459W ASN 5.7 0.3 - - - +
463W ARG* 4.0 24.4 + - - -
494W TYR* 3.0 16.6 + - - +
495W ILE* 3.1 10.1 - - - +
497W LYS* 1.3 98.1 - - - +
499W ARG* 1.3 60.4 + - - +
500W ALA 3.6 0.9 - - - -
501W GLU* 3.4 27.1 - - + +
502W LEU* 3.8 21.5 - - + +
532W PHE* 5.5 0.2 - - - -
----------------------------------------------------------
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