Contacts of the helix formed by residues 490 - 497 (chain A) in PDB entry 1JPW
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 GLY 490 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A VAL* 3.7 19.7 - - - -
485A VAL* 2.6 29.9 + - - -
486A ARG 4.1 0.2 + - - -
488A HIS 3.5 0.8 - - - -
489A TYR* 1.3 73.8 - - - +
491A LEU* 1.3 64.4 + - - +
492A PRO 3.3 1.1 - - - -
493A VAL* 3.1 24.4 - - - +
494A VAL* 3.1 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A VAL* 3.9 2.4 + - + -
486A ARG* 3.6 34.3 - - + -
489A TYR* 6.1 0.2 - - - -
490A GLY* 1.3 75.0 - - - +
492A PRO* 1.3 73.3 - - + +
494A VAL* 3.1 4.7 + - + -
495A VAL* 3.0 27.5 + - - +
517A LEU* 4.1 24.7 - - + -
523A ASN* 4.3 12.6 - - - +
526A PRO* 3.4 35.7 - - + +
527A LEU* 3.8 25.8 - - + +
530A GLN* 4.5 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LEU* 6.3 1.1 - - + -
489A TYR* 3.9 18.8 - - + +
490A GLY 3.5 3.4 - - - -
491A LEU* 1.3 93.7 - - + +
493A VAL* 1.3 57.8 + - + +
495A VAL* 4.2 2.1 - - - +
496A LYS* 3.2 27.1 + - - +
530A GLN* 3.9 34.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A VAL* 4.8 4.3 - - + +
451A VAL* 3.3 34.8 - - + -
452A LEU* 3.6 39.0 - - + +
489A TYR 4.9 1.1 - - - +
490A GLY* 3.1 21.5 + - - +
492A PRO* 1.3 77.6 - - - +
494A VAL* 1.3 68.3 + - + +
496A LYS* 3.8 14.3 - - + +
497A LEU* 3.0 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A VAL* 6.1 0.4 - - + -
451A VAL* 6.2 0.7 - - + -
465A ILE* 4.6 7.0 - - + -
468A LEU* 5.2 3.1 - - + -
485A VAL* 4.8 4.3 - - + -
490A GLY* 3.1 21.7 + - - +
491A LEU* 3.1 11.2 + - + +
493A VAL* 1.3 78.6 - - + +
495A VAL* 1.3 63.5 + - + +
497A LEU* 2.9 33.4 + - - +
510A THR* 3.4 17.7 - - + +
513A LEU* 4.1 31.6 - - + -
514A ILE* 4.0 24.9 - - + -
517A LEU* 4.5 10.5 - - + -
527A LEU* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A LEU 3.0 14.8 + - - +
492A PRO 4.2 2.2 - - - +
494A VAL* 1.3 81.9 - - + +
496A LYS* 1.3 62.0 + - - +
498A LEU* 3.3 28.0 + - + +
499A HIS* 4.3 11.8 + - + +
514A ILE* 4.8 7.2 - - + -
527A LEU* 3.9 27.8 - - + -
530A GLN* 3.6 38.1 - - + +
531A GLY 4.1 13.9 - - - +
532A ALA* 4.1 15.5 - - + -
535A ARG* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A PRO 3.2 20.5 + - - +
493A VAL* 3.8 14.4 - - + +
494A VAL 3.1 1.0 - - - -
495A VAL* 1.3 76.8 - - - +
497A LEU* 1.3 59.4 + - + +
498A LEU 3.1 0.4 - - - -
499A HIS* 3.0 42.6 + - + +
500A PRO 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A VAL* 3.7 17.7 - - + -
455A GLY 4.7 8.1 - - - +
461A THR* 4.4 15.7 - - + -
465A ILE* 3.6 35.7 - - + -
493A VAL* 3.0 24.5 - - + +
494A VAL* 2.9 12.5 + - - +
496A LYS* 1.3 77.0 - - + +
498A LEU* 1.3 59.3 + - - +
499A HIS 3.2 0.4 - - - -
502A SER* 2.7 31.7 + - - +
506A LEU* 3.7 25.9 - - + +
507A ILE* 4.0 4.3 - - - +
510A THR* 3.8 14.6 - - - +
----------------------------------------------------------
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