Contacts of the strand formed by residues 380 - 389 (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 HIS 380 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLN* 3.6 4.7 + - - -
233A CYS* 3.4 36.1 - - + +
348A ALA* 3.0 26.9 - - - +
349A PHE* 3.1 25.1 + + + +
351A VAL* 3.5 27.4 - - + -
378A THR* 3.9 1.0 - - - -
379A ASN* 1.3 83.0 + - - +
381A ALA* 1.3 62.3 + - - +
382A VAL* 3.4 22.2 - - + +
402A ASN* 2.9 24.7 + - - -
403A SER* 4.1 0.9 - - - -
404A TRP* 3.5 31.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A CYS* 3.6 23.8 - - - +
234A TYR* 3.5 35.7 - - + +
237A ALA* 3.7 9.2 + - + +
276A GLY 5.5 0.7 - - - +
278A PRO* 4.3 12.8 - - + -
347A VAL 3.5 7.4 - - - +
348A ALA* 4.3 4.7 - - + +
380A HIS* 1.3 78.3 + - - +
382A VAL* 1.3 68.5 + - - +
403A SER* 4.7 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ALA* 3.7 10.5 - - - +
346A ALA* 3.5 4.7 - - - -
347A VAL* 2.9 45.2 + - + +
349A PHE* 4.0 20.9 - - + -
380A HIS* 3.4 28.7 - - + +
381A ALA* 1.3 80.0 - - - +
383A LEU* 1.3 59.9 + - - +
400A VAL* 3.2 23.8 - - + -
401A LYS 3.5 13.0 - - - +
402A ASN* 3.8 15.0 - - - +
403A SER* 5.1 0.7 - - - +
414A PHE* 4.5 2.5 - - + -
425A ILE* 4.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A VAL* 4.7 5.8 - - + -
236A PHE 5.7 0.2 - - - +
237A ALA* 3.8 12.5 - - - +
240A GLY* 3.5 25.4 - - - +
241A MET* 3.6 28.3 - - + +
244A ALA* 5.0 0.2 - - + -
344A PRO* 3.9 12.3 - - + -
345A MET 3.4 27.8 - - - +
346A ALA 4.2 0.2 - - - +
382A VAL* 1.3 74.9 - - - +
384A LEU* 1.3 69.7 + - - +
385A VAL* 3.4 8.1 + - + -
400A VAL* 3.3 3.8 - - - +
401A LYS* 2.8 64.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A MET* 3.6 31.4 - - + -
339A LEU* 3.9 10.7 - - + +
344A PRO* 3.2 29.3 - - - +
345A MET* 2.7 41.7 + - + +
347A VAL* 4.0 14.4 - - + +
382A VAL 3.9 2.0 + - - -
383A LEU* 1.3 70.4 - - - +
385A VAL* 1.3 62.0 + - - +
386A GLY 3.8 6.1 - - - +
398A TRP* 3.4 50.9 - - + -
399A ILE 3.9 4.7 - - - +
400A VAL* 4.4 8.3 - - + -
425A ILE* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ASP* 4.0 18.4 - - - +
212A TRP* 3.2 33.4 + - + +
213A ARG* 4.1 20.0 - - + +
221A VAL* 4.1 15.5 - - + -
339A LEU* 4.0 7.2 - - - -
344A PRO* 4.4 5.4 - - + -
383A LEU* 3.4 28.5 + - + +
384A LEU* 1.3 77.8 - - - +
386A GLY* 1.3 56.8 + - - +
399A ILE* 2.8 19.7 + - + +
401A LYS* 4.1 1.8 - - + -
413A TYR* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A TRP 3.2 13.9 - - - -
211A ASP* 4.2 0.7 - - - -
339A LEU* 3.5 15.2 - - - +
384A LEU* 3.8 1.1 - - - +
385A VAL* 1.3 78.8 - - - +
387A TYR* 1.3 61.5 + - - +
398A TRP* 3.5 9.2 - - - -
399A ILE* 2.7 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A LEU* 4.1 3.1 - - - +
207A PRO* 2.8 35.4 + - - +
208A GLU 3.4 18.6 - - - -
209A SER* 3.5 6.1 - - - -
210A TRP* 2.8 49.2 + - + +
336A LYS* 3.9 38.1 - - + +
339A LEU* 3.7 18.8 - - + -
340A VAL* 3.6 24.7 - - + +
386A GLY* 1.3 74.7 - - - +
388A GLY* 1.3 60.7 + - - +
397A TYR* 3.4 19.3 - - - +
398A TRP* 3.7 9.0 - + + -
399A ILE* 3.8 7.0 - - - +
418A ARG* 3.7 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLU 4.3 3.4 - - - -
209A SER* 3.7 14.6 - - - -
387A TYR* 1.3 77.8 - - - +
389A LYS* 1.3 60.5 + - - -
396A ASP* 3.5 0.2 - - - -
397A TYR* 3.1 37.8 + - - -
418A ARG* 2.6 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLU* 4.1 31.4 + - + +
209A SER* 4.6 3.4 + - - -
388A GLY* 1.3 76.1 - - - +
390A ASP* 1.3 70.4 + - - +
391A PRO* 3.1 9.3 - - + +
394A GLY* 3.5 34.5 + - - +
395A LEU 3.6 5.2 - - - -
396A ASP* 2.8 26.5 + - - +
397A TYR* 3.3 8.3 + - - -
418A ARG* 4.8 1.8 - - - +
----------------------------------------------------------
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