Contacts of the strand formed by residues 413 - 417 (chain A) in PDB entry 1JQP
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 413 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ARG* 3.5 48.7 - - - +
221A VAL* 3.3 27.4 - - - +
222A SER 4.3 3.1 + - - -
224A VAL* 3.7 17.1 - - + +
358A TYR* 3.8 0.5 - - - -
385A VAL* 4.1 11.4 - - + -
399A ILE* 4.3 9.2 - - + -
400A VAL 3.1 24.5 - - - +
401A LYS* 3.4 27.7 - - + +
408A TRP* 3.9 1.7 - - - -
409A GLY* 3.7 2.4 - - - -
410A GLU* 2.7 46.1 + - + +
411A SER* 3.6 12.1 - - - -
412A GLY* 1.3 82.4 - - - +
414A PHE* 1.3 63.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A PHE* 4.0 17.7 - + - -
355A PHE* 3.7 37.2 - + + -
358A TYR* 3.2 27.8 - - + -
363A TYR* 5.0 0.9 - - + -
382A VAL* 4.5 7.0 - - + -
398A TRP 3.8 0.7 - - - +
399A ILE* 3.9 1.9 - - - -
400A VAL* 3.0 66.0 + - + -
402A ASN* 4.3 11.0 - - + -
408A TRP* 3.7 16.6 - + + -
410A GLU* 4.6 3.1 - - - -
413A TYR* 1.3 77.3 - - - +
415A ARG* 1.3 70.7 + - - +
416A ILE* 3.6 29.2 - - + -
425A ILE* 4.5 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ARG* 6.2 0.9 - - - +
358A TYR* 3.1 7.0 + - - -
361A GLY* 3.3 30.9 - - - +
362A ILE* 3.9 18.5 - - + +
363A TYR* 2.8 27.1 + - - +
390A ASP* 5.1 5.5 + - - -
397A TYR* 3.1 56.7 + - + -
398A TRP 3.3 4.5 - - - +
399A ILE* 4.7 10.1 - - + +
410A GLU* 2.9 35.2 + - - -
414A PHE* 1.3 74.5 - - - +
416A ILE* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A PHE* 4.7 9.2 - - + -
362A ILE* 3.6 4.7 - - - -
363A TYR* 3.7 26.7 - - + +
397A TYR* 3.0 2.6 - - - -
398A TRP* 2.7 59.7 + - + +
400A VAL* 4.2 1.6 - - + -
414A PHE* 3.6 18.6 - - + -
415A ARG* 1.3 76.4 - - - +
417A ARG* 1.3 66.8 + - - +
422A GLU* 3.6 34.3 - - + +
423A CYS* 4.9 0.2 - - + -
425A ILE* 3.9 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ILE* 3.4 9.1 + - + +
363A TYR 3.1 14.5 + - - +
364A HIS* 3.6 42.0 + - - +
395A LEU* 3.6 39.4 - - + +
396A ASP 3.6 9.6 - - - +
398A TRP* 3.8 7.8 - - - -
416A ILE* 1.3 79.6 - - - +
418A ARG* 1.3 66.9 + - - +
420A THR* 3.7 26.7 - - + +
422A GLU* 3.5 33.5 + - + +
425A ILE* 4.6 0.9 - - - +
426A GLU* 4.3 1.9 - - - +
----------------------------------------------------------
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