Contacts of the helix formed by residues 443 - 460 (chain A) in PDB entry 1YHV
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 PRO 443 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A HIS* 3.2 52.9 + - + +
386A ILE* 3.5 18.3 - - + -
414A ILE* 3.9 26.2 - - + -
419A SER 4.8 2.0 - - - +
420A LYS* 5.6 2.5 - - - +
442A GLY* 1.3 83.1 - - - +
444A LYS* 1.3 60.6 + - + +
445A VAL* 3.0 6.9 + - - -
446A ASP* 3.0 13.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLU* 4.5 0.7 - - - +
442A GLY 3.1 2.9 + - - +
443A PRO* 1.3 78.0 - - + +
445A VAL* 1.3 63.4 + - - +
446A ASP 3.1 0.4 - - - -
447A ILE* 3.2 11.7 + - + +
448A TRP 3.1 13.0 + - - -
506A VAL* 3.1 39.7 + - + +
507A GLU* 3.5 15.6 + - - +
509A ARG* 2.9 58.2 + - + +
510A GLY 3.9 15.7 - - - +
511A SER* 3.9 21.7 - - - +
514A GLU* 5.0 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ILE* 3.8 18.6 - - + -
388A ARG* 4.8 7.0 - - + -
432A ALA* 3.9 15.1 + - + +
434A GLU* 3.5 17.9 - - - +
435A VAL* 3.7 17.0 - - + -
441A TYR* 3.6 34.3 - - + -
442A GLY 3.2 19.0 + - - +
444A LYS* 1.3 77.7 - - - +
446A ASP* 1.3 65.4 + - - +
448A TRP* 3.4 3.5 + - - +
449A SER* 3.1 30.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU* 3.9 18.4 - - + +
381A HIS* 2.9 27.9 + - + +
386A ILE* 3.4 7.7 - - - +
387A HIS* 2.9 30.3 + - - +
388A ARG* 2.8 29.2 + - - -
390A ILE* 3.8 12.1 - - + +
443A PRO 3.0 8.9 + - - +
445A VAL* 1.3 78.2 - - - +
447A ILE* 1.3 58.4 + - - +
449A SER* 3.4 7.5 + - - -
450A LEU* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU* 3.8 24.9 - - + -
377A LEU* 4.1 10.8 - - + -
381A HIS* 4.7 6.3 - - + -
444A LYS* 3.2 19.2 + - + +
446A ASP* 1.3 75.4 - - - +
448A TRP* 1.3 65.5 + - - +
450A LEU* 3.2 7.0 + - + +
451A GLY 3.0 17.3 + - - -
501A CYS* 3.8 24.5 - - + +
509A ARG* 4.0 4.7 - - + -
510A GLY 3.4 26.5 - - - +
511A SER* 4.2 2.2 - - - -
512A ALA* 3.8 28.7 - - + +
515A LEU* 3.6 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A TYR 5.3 0.4 + - - -
430A TRP 3.4 19.3 - - - -
431A MET 3.3 10.9 + - - -
432A ALA* 3.6 19.5 - - + -
433A PRO* 3.5 38.4 - - + -
444A LYS 3.1 5.7 + - - -
445A VAL 3.6 7.9 - - - +
447A ILE* 1.3 76.3 - - - +
449A SER* 1.3 61.4 - - - +
451A GLY* 2.9 13.0 + - - -
452A ILE* 3.1 26.5 + - + +
476A ILE* 4.3 10.4 - - + +
480A GLY 3.8 23.3 - - - -
481A THR* 4.0 3.1 - - - -
482A PRO* 4.1 18.2 - - + -
501A CYS 3.5 10.9 + - - -
502A LEU* 3.3 42.8 - - + +
503A ASP 3.9 5.4 - - - -
504A MET* 4.1 5.2 - - - -
509A ARG* 3.7 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ARG 5.6 2.6 + - - -
390A ILE* 3.5 39.8 + - - -
430A TRP* 2.8 30.6 + - - +
431A MET* 4.8 1.2 - - - -
445A VAL 3.1 13.2 + - - -
446A ASP* 3.7 5.6 + - - -
447A ILE 3.3 0.2 - - - -
448A TRP* 1.3 78.4 - - - +
450A LEU* 1.3 57.8 + - - +
452A ILE* 3.1 6.2 + - - +
453A MET* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A CYS* 4.5 17.9 - - - +
373A CYS* 3.9 27.1 - - + -
374A LEU* 3.5 43.5 - - + +
377A LEU* 4.5 10.5 - - + -
390A ILE* 4.0 7.8 - - + +
446A ASP 3.0 15.1 + - - +
447A ILE* 3.4 10.8 - - + +
448A TRP 3.2 0.2 - - - -
449A SER* 1.3 76.0 - - - +
451A GLY* 1.3 59.8 + - - +
453A MET* 3.0 15.8 + - + +
454A ALA* 2.9 25.5 + - - +
457A MET* 5.6 2.0 - - + -
497A PHE* 4.5 12.3 - - + -
501A CYS* 4.6 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ILE 3.0 6.9 + - - -
448A TRP 2.9 9.2 + - - -
450A LEU* 1.3 79.1 - - - +
452A ILE* 1.3 59.2 + - - +
454A ALA* 3.2 10.8 + - - +
455A ILE* 3.1 23.7 + - - +
498A LEU* 4.2 2.5 - - - +
501A CYS* 3.8 23.1 - - - +
502A LEU* 3.9 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A TYR 3.7 14.1 - - - +
430A TRP* 3.5 19.1 - - + -
448A TRP* 3.1 38.5 + - + +
449A SER 3.1 6.9 + - - +
451A GLY* 1.3 74.5 - - - +
453A MET* 1.3 65.1 + - - +
455A ILE* 3.0 9.3 + - + +
456A GLU* 3.0 20.1 + - - +
462A PRO* 3.5 30.5 - - + -
463A PRO* 3.9 11.9 - - + -
482A PRO* 4.0 20.6 - - + -
502A LEU* 3.7 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 3.7 21.1 - - + -
373A CYS* 5.0 7.0 - - - -
390A ILE* 3.0 22.9 - - + +
391A LYS* 2.7 45.1 - - - +
392A SER* 3.4 10.8 - - - -
395A ILE* 3.5 26.2 - - + -
430A TRP* 4.2 0.2 - - - -
449A SER 2.9 7.9 + - - +
450A LEU* 3.0 15.9 + - + +
452A ILE* 1.3 78.7 - - - +
454A ALA* 1.3 61.1 + - - +
456A GLU* 3.1 22.8 + - - +
457A MET* 3.0 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ILE* 5.1 0.4 - - - -
370A CYS* 4.4 17.7 - - - -
450A LEU 2.9 11.2 + - - +
451A GLY* 3.4 11.7 - - - +
452A ILE 3.2 0.2 - - - -
453A MET* 1.3 73.2 - - - +
455A ILE* 1.3 65.6 + - - +
457A MET* 3.1 16.3 + - + +
458A ILE* 3.1 27.6 + - - +
494A PHE* 4.5 7.9 - - + -
497A PHE* 5.1 4.0 - - + -
498A LEU* 3.5 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A GLY 3.1 10.6 + - - +
452A ILE* 3.0 13.2 + - + +
454A ALA* 1.3 78.5 - - - +
456A GLU* 1.3 53.0 + - - +
458A ILE* 3.1 6.6 + - + +
459A GLU* 2.7 58.3 + - - +
461A GLU 3.8 12.1 - - - +
463A PRO* 4.0 19.1 - - + -
482A PRO* 4.0 25.8 - - + +
483A GLU 6.1 0.4 - - - +
484A LEU* 4.2 18.2 - - + -
498A LEU* 4.8 6.1 - - + -
502A LEU* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A THR* 5.2 1.9 - - - +
356A VAL* 3.6 23.8 - - + +
392A SER* 2.6 41.2 + - - -
430A TRP* 2.7 38.2 + - - +
452A ILE 3.0 16.4 + - - +
453A MET* 3.1 14.8 + - + +
455A ILE* 1.3 76.4 - - - +
457A MET* 1.3 59.2 + - - +
460A GLY* 2.7 28.1 + - - +
461A GLU* 3.9 11.0 - - - +
462A PRO* 3.9 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 457 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU* 4.2 10.5 - - + -
356A VAL* 3.7 25.0 - - + +
360A CYS* 5.8 0.3 - - - -
361A MET* 3.7 42.9 + - - +
366A ILE* 3.9 29.9 - - + +
369A VAL* 3.9 26.2 - - + -
370A CYS* 3.7 29.8 - - - -
450A LEU* 5.5 2.7 - - + +
453A MET* 3.0 26.8 + - + +
454A ALA* 3.1 13.4 + - - +
456A GLU* 1.3 75.0 - - - +
458A ILE* 1.3 61.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A CYS* 6.1 1.2 - - - -
366A ILE* 4.3 4.7 - - + -
454A ALA 3.1 17.6 + - - +
455A ILE* 3.6 7.9 - - - +
457A MET* 1.3 82.8 - - - +
459A GLU* 1.3 73.9 + - + +
460A GLY 3.7 0.4 - - - -
484A LEU* 4.4 8.5 - - + -
490A LEU* 3.7 35.2 - - + -
494A PHE* 3.5 36.3 - - + -
498A LEU* 3.8 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A ILE* 2.7 29.0 + - + +
458A ILE* 1.3 89.5 - - + +
460A GLY* 1.3 57.2 + - - +
461A GLU* 3.4 14.6 + - + +
463A PRO* 5.7 2.3 - - - +
483A GLU 5.1 1.9 - - - +
484A LEU* 3.4 21.5 - - - +
485A GLN* 2.8 55.5 + - + +
486A ASN 4.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 460 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A VAL* 3.8 21.9 - - - +
357A THR* 4.0 21.6 - - - +
456A GLU* 2.7 25.6 + - - +
457A MET 4.7 0.2 - - - -
458A ILE 3.7 0.6 - - - -
459A GLU* 1.3 71.2 - - - +
461A GLU* 1.3 64.7 + - - +
----------------------------------------------------------
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