Contacts of the helix formed by residues 499 - 507 (chain B) in PDB entry 1JQI
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 TYR 499 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B VAL 3.0 10.3 + - - +
495B ASN* 3.6 18.2 - - - +
498B LEU* 1.3 78.0 - - - +
500B LEU* 1.3 81.6 + - + +
501B GLY 3.4 0.2 - - - -
502B PRO* 3.2 14.3 - - - +
503B ILE* 3.3 32.8 - - + +
515B TRP* 2.9 42.3 + - - +
519B PHE* 3.6 19.2 - + - -
526B GLY* 3.8 25.8 - - - -
527B CYS 4.1 8.7 - - - +
570B ALA* 3.4 36.0 - - + +
571B THR 4.4 1.6 - - - -
572B VAL* 3.9 17.9 - - + +
590B LEU* 4.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B LEU 3.5 24.9 - - - +
457B ALA* 3.5 23.3 - - + -
460B VAL* 3.9 17.9 - - + -
495B ASN* 3.1 21.4 + - - +
496B ASN* 3.7 5.8 - - - +
499B TYR* 1.3 104.5 - - + +
501B GLY* 1.3 65.9 + - - +
503B ILE* 3.3 5.2 + - - +
504B LEU* 2.9 27.9 + - - +
516B ILE* 4.0 34.1 - - + +
519B PHE* 4.1 7.6 - - + +
520B THR* 4.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B TYR* 5.6 0.7 - - - -
496B ASN 3.1 14.6 + - - -
497B SER* 3.5 9.4 + - - -
500B LEU* 1.3 76.4 - - - +
502B PRO* 1.3 68.4 - - - +
504B LEU* 3.3 7.7 + - - +
505B LYS* 3.1 23.9 + - - +
646B MET* 3.8 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B SER 3.3 14.8 - - - +
498B LEU 3.1 22.9 - - - +
499B TYR* 3.2 13.0 - - - +
501B GLY* 1.3 88.3 - - - +
503B ILE* 1.3 56.3 + - - +
505B LYS* 4.7 0.7 - - + -
506B PHE* 2.9 41.7 + - + +
507B GLY 3.9 0.2 + - - -
528B PHE* 5.2 1.3 - - + -
572B VAL* 4.5 13.5 - - + -
630B LEU* 4.2 16.5 - - + +
639B ILE* 4.3 7.6 - - + -
643B THR* 3.5 26.9 - - + +
646B MET* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B TYR* 3.3 59.9 - - + +
500B LEU* 3.3 7.0 + - - +
502B PRO* 1.3 76.0 - - - +
504B LEU* 1.3 58.3 + - - +
507B GLY* 2.8 32.8 + - - +
511B GLN* 4.1 22.0 - - + +
512B LYS* 3.6 7.8 - - + +
515B TRP* 3.9 10.3 - - + +
516B ILE* 3.5 22.9 - - + -
572B VAL* 4.6 2.7 - - + -
590B LEU* 3.9 26.0 - - + -
630B LEU* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B ASP* 3.9 32.3 - - + +
460B VAL* 4.5 11.4 - - + -
461B PRO* 3.9 24.0 - - + -
464B LEU* 4.1 10.5 - - + -
500B LEU 2.9 18.0 + - - +
501B GLY* 3.7 7.0 - - - +
503B ILE* 1.3 78.5 - - - +
505B LYS* 1.3 61.7 + - - +
507B GLY 4.7 0.3 + - - +
512B LYS* 4.2 20.7 + - - +
516B ILE* 3.8 19.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B GLY 3.1 16.5 + - - +
504B LEU* 1.3 81.0 - - + +
506B PHE* 1.3 94.5 + - + +
507B GLY 3.7 0.8 - - - +
642B GLN* 3.5 29.7 + - + +
646B MET* 4.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B PRO* 2.9 24.4 + - + +
505B LYS* 1.3 107.8 - - + +
507B GLY* 1.3 66.3 + - - +
508B SER 3.9 0.7 + - - -
511B GLN* 4.5 0.5 - - - +
630B LEU* 4.0 12.8 - - + -
631B GLY* 4.1 15.1 + - - -
635B MET* 3.4 33.0 - - + -
638B LYS* 4.9 5.8 - - - -
639B ILE* 3.8 37.9 - - + -
642B GLN* 3.3 35.2 - - + -
643B THR* 4.8 2.0 - - - -
646B MET* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B ILE* 2.8 22.7 + - - -
504B LEU 5.0 0.7 - - - +
505B LYS 3.7 1.1 - - - +
506B PHE* 1.3 80.6 - - - +
508B SER* 1.3 66.5 + - - -
511B GLN* 3.5 15.5 - - - -
512B LYS* 3.4 15.5 + - - +
630B LEU* 3.8 9.3 - - - +
----------------------------------------------------------
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