Contacts of the strand formed by residues 418 - 429 (chain A) in PDB entry 2Y1X
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 GLN 418 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A VAL* 3.4 6.9 - - - +
342A ASP 3.0 32.1 + - - +
343A THR* 2.6 36.3 + - - -
344A PHE* 3.8 19.0 + - + -
390A PHE 3.5 14.1 - - - +
391A TRP* 4.0 8.1 - - + +
407A THR 3.0 25.2 + - - +
408A ALA 3.7 3.0 + - - -
409A PRO* 3.6 31.0 - - + +
411A GLU 5.4 1.4 + - - -
413A LEU* 4.7 8.7 - - - +
414A THR 5.8 1.0 - - - +
416A TRP 4.0 0.9 - - - -
417A TYR* 1.3 85.5 + - - +
419A VAL* 1.3 69.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A TYR* 4.1 14.8 - - + -
263A MET* 3.7 50.3 - - + +
339A PRO* 3.7 28.7 - - + -
340A VAL 3.3 6.1 - - - +
341A VAL* 4.3 10.8 - - + -
389A ALA* 3.4 3.5 - - - +
390A PHE* 2.7 39.6 + - + +
416A TRP 5.0 3.6 - - - +
418A GLN* 1.3 83.1 - - - +
420A ARG* 1.3 68.6 + - - +
421A CYS* 4.8 2.0 - - - -
470A LEU* 5.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A PHE* 3.8 27.6 - - + -
300A ASP* 2.8 29.1 + - - +
303A LEU* 3.5 17.7 - - + +
339A PRO* 3.5 2.4 - - - +
340A VAL* 2.7 53.3 + - + +
342A ASP* 2.9 36.2 + - - -
343A THR 4.1 4.0 + - - -
344A PHE* 3.3 32.3 - - + +
348A ILE* 3.6 16.0 - - - +
388A LEU 3.5 2.7 - - - -
389A ALA* 3.8 17.0 - - + -
419A VAL* 1.3 80.5 - - - +
421A CYS* 1.3 61.8 + - - +
422A LEU* 4.2 0.9 - - + -
476A ARG* 3.5 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A PHE* 4.7 1.1 - - - -
338A GLN 5.3 0.2 - - - -
339A PRO* 4.1 13.7 - - - -
387A GLY* 3.4 1.1 - - - -
388A LEU* 2.9 32.1 + - - +
390A PHE* 3.8 18.8 - - - -
419A VAL* 4.8 2.5 - - - -
420A ARG* 1.3 77.4 - - - +
422A LEU* 1.3 63.7 + - - +
423A PHE* 5.3 0.7 - - - -
451A ILE* 4.1 16.2 - - - -
453A ILE* 3.8 16.0 - - + +
468A LEU* 3.7 39.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A PHE* 3.7 25.6 - - + -
303A LEU* 4.0 18.8 - - + -
304A TYR* 4.4 11.0 - - + +
307A GLN* 3.7 40.2 - - + +
336A PHE* 4.0 19.1 - - + +
338A GLN 5.7 0.4 + - - -
340A VAL* 5.3 9.0 - - + -
386A HIS* 3.3 21.3 - - + +
420A ARG 4.3 0.9 + - - +
421A CYS* 1.3 75.6 - - - +
423A PHE* 1.3 71.6 + - - +
453A ILE* 6.0 0.4 - - - +
466A ASN* 3.0 29.2 - - - +
468A LEU* 4.5 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A TYR* 3.7 6.6 - - - -
336A PHE* 3.5 13.4 - - - -
385A VAL* 3.6 39.0 - - + -
386A HIS 2.7 9.9 + - - +
387A GLY* 3.6 18.1 - - - -
388A LEU* 3.8 26.2 - - + -
421A CYS 5.3 0.7 - - - -
422A LEU* 1.3 79.1 - - - +
424A GLN* 1.3 65.1 + - - +
425A SER 3.4 19.4 + - - +
427A LEU* 4.6 11.4 - - + -
435A LEU* 4.7 2.7 - - + -
453A ILE* 3.7 31.0 - - + -
455A ALA* 3.7 27.8 - - + -
464A SER* 3.7 13.2 - - - +
465A SER 4.0 11.0 - - - +
466A ASN* 4.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A TYR* 2.5 25.6 + - - -
308A PHE* 4.9 2.1 - - - -
336A PHE* 4.1 18.8 - - + -
422A LEU 3.9 0.6 + - - -
423A PHE* 1.3 72.4 - - - +
425A SER* 1.3 58.5 + - - +
464A SER* 3.7 3.8 + - - +
465A SER* 3.0 31.9 + - - +
466A ASN* 3.6 30.4 - - - +
467A LEU* 4.6 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A TYR* 3.5 4.0 - - - -
423A PHE* 3.6 9.5 - - - +
424A GLN* 1.3 83.0 - - - +
426A PRO* 1.3 79.4 - - - +
427A LEU 3.8 0.2 + - - -
463A LYS 5.4 0.9 + - - -
464A SER* 3.1 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A GLU* 6.0 0.7 - - - +
304A TYR* 3.8 23.1 - - + +
384A LEU* 4.2 25.6 - - + -
385A VAL 3.1 16.6 - - - +
386A HIS* 3.6 26.0 - - + +
425A SER* 1.3 95.0 - - - +
427A LEU* 1.3 65.1 + - - +
428A PHE 4.4 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A GLY 3.5 0.2 - - - +
384A LEU* 4.4 2.7 - - - -
385A VAL* 2.9 43.3 + - + +
423A PHE* 4.6 9.0 - - + -
425A SER 4.0 0.9 - - - +
426A PRO* 1.3 84.1 - - - +
428A PHE* 1.3 64.0 + - - +
435A LEU* 3.8 23.3 - - + -
455A ALA* 3.6 29.4 - - + +
457A VAL* 4.0 12.6 - - + -
462A SER* 3.8 16.2 - - - +
463A LYS 3.3 34.3 - - - +
464A SER* 3.7 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A SER* 4.7 5.4 - - - -
383A GLY* 3.5 22.2 - - - -
384A LEU* 4.0 18.2 - - + +
426A PRO 4.3 0.4 - - - -
427A LEU* 1.3 73.3 - - - +
429A ALA* 1.3 76.6 + - - +
430A LYS* 3.4 40.4 - - + -
433A ASP* 5.0 0.2 - - - +
457A VAL* 3.4 21.5 - - - +
460A THR* 4.8 10.6 + - + +
462A SER* 5.2 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A MET* 5.0 0.2 - - + -
379A MET* 4.0 27.6 - - + -
381A HIS 3.9 0.4 - - - +
382A SER* 3.1 2.8 - - - -
383A GLY 2.7 37.5 + - - +
385A VAL* 4.1 19.1 - - + -
427A LEU 3.5 0.2 + - - -
428A PHE* 1.3 85.0 - - - +
430A LYS* 1.3 60.0 + - - +
433A ASP* 4.0 7.0 - - - +
435A LEU* 5.6 1.8 - - + -
457A VAL* 4.5 12.8 - - + -
----------------------------------------------------------
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