Contacts of the helix formed by residues 415 - 429 (chain P) in PDB entry 5A31
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 415 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410P GLU* 5.9 0.2 - - - -
413P LYS 3.3 10.8 - - - +
414P MET* 1.4 84.0 - - + +
416P PHE* 1.3 77.2 + - + +
417P TYR* 3.2 2.2 - - + -
418P CYS* 2.9 31.6 - - - -
419P LEU* 3.1 7.8 + - - +
442P CYS* 5.2 1.0 - - - +
445P LYS* 6.0 6.1 - - + -
446P LEU* 4.0 26.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 416 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523J ILE* 4.5 14.9 - - + +
524J ALA* 4.0 39.5 - - + -
527J ILE* 4.1 31.3 - - + +
415P PRO* 1.3 91.0 - - + +
417P TYR* 1.3 59.6 + - + +
419P LEU* 3.1 9.3 + - + +
420P TYR* 2.7 34.9 + - - +
446P LEU* 4.8 21.1 - - + -
448P GLN* 5.6 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 417 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ILE* 4.3 9.1 - - + +
55D GLY* 3.9 27.6 + - - -
503J HIS* 5.3 0.2 - + - -
516J VAL* 4.4 6.6 + - - +
519J LEU* 4.1 27.3 - - + +
520J GLY* 4.0 23.1 + - - -
523J ILE* 4.1 18.8 - - + -
409P TYR* 3.6 27.8 - + + -
414P MET* 4.1 23.1 - - + +
415P PRO* 3.2 0.8 - - + -
416P PHE* 1.3 80.2 - - + +
418P CYS* 1.3 64.5 + - - +
420P TYR* 3.1 6.1 + - - +
421P TYR* 2.9 50.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 418 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406P GLY* 3.5 14.1 - - - +
409P TYR* 3.8 6.4 - - - +
410P GLU* 3.2 42.0 - - + +
414P MET 4.4 1.5 + - - +
415P PRO* 2.9 34.1 + - - -
416P PHE 3.3 0.4 - - - -
417P TYR* 1.3 79.3 - - - +
419P LEU* 1.3 62.5 + - - +
421P TYR 3.5 0.2 + - - -
422P TYR* 2.9 32.7 + - + -
442P CYS* 4.0 24.2 - - - -
445P LYS* 6.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 419 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527J ILE* 3.6 42.6 - - + -
415P PRO 3.1 13.0 + - - +
416P PHE* 3.1 12.1 + - + +
418P CYS* 1.3 75.7 - - - +
420P TYR* 1.3 65.8 + - - +
422P TYR* 3.4 5.1 + - - +
423P ARG* 3.0 21.3 + - + +
439P LEU* 3.4 27.6 - - + -
442P CYS* 4.5 15.3 - - + -
443P TYR* 3.9 22.7 - - + +
446P LEU* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 420 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496J GLU* 4.8 11.0 + - + +
499J VAL* 3.8 28.5 - - + +
500J ASP* 5.1 3.3 + - - +
503J HIS* 4.3 6.2 - + - -
523J ILE* 3.1 42.6 - - + -
526J TYR* 3.8 35.9 - + - -
527J ILE* 4.9 6.5 - - + +
402P TRP* 4.0 13.5 - + - -
416P PHE 2.7 12.8 + - - +
417P TYR 3.6 5.2 - - - +
419P LEU* 1.3 75.9 - - - +
421P TYR* 1.3 77.8 + + - +
423P ARG* 3.4 4.1 + - + +
424P ARG* 2.8 55.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 421 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ILE* 5.2 0.5 - - - +
503J HIS* 3.2 30.4 - + - -
389P ARG* 2.7 34.9 + - - -
392P ILE* 5.4 0.2 - - + -
402P TRP* 3.5 32.2 - + + +
405P LEU* 3.8 28.5 - - + -
406P GLY* 3.4 20.0 - - - +
409P TYR* 3.6 22.9 - + - -
417P TYR* 2.9 47.5 + + + -
420P TYR* 1.3 80.1 - + - +
422P TYR* 1.3 68.1 + - - +
424P ARG* 3.1 5.4 + - - +
425P ALA* 2.9 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 422 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403P TYR* 3.2 54.9 + + - -
406P GLY* 3.4 7.2 - - - -
407P GLN* 2.8 34.2 - - - +
410P GLU* 3.0 25.5 + - - -
418P CYS* 2.9 28.8 + - + +
419P LEU* 3.9 3.6 - - - +
420P TYR 3.3 0.2 - - - -
421P TYR* 1.3 75.3 - - - +
423P ARG* 1.3 58.0 + - - +
425P ALA* 3.1 5.6 + - + +
426P HIS* 2.8 30.2 + - - +
435P MET* 4.7 5.5 - - + +
438P ALA* 3.8 15.5 - - + +
439P LEU* 4.1 18.4 - - + +
442P CYS* 3.4 23.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 423 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526J TYR* 3.8 29.3 + - + -
527J ILE* 4.2 20.4 - - + -
530J SER* 4.1 14.5 - - - +
531J GLU* 4.6 9.7 - - - +
532J ALA* 3.8 33.8 - - - +
533J TYR* 4.6 17.4 - - - -
419P LEU* 3.0 16.3 + - + +
420P TYR* 3.6 7.2 - - - +
422P TYR* 1.3 76.1 - - - +
424P ARG* 1.3 57.8 + - - +
426P HIS* 3.1 11.1 + - + +
427P GLN* 2.9 45.2 + - - +
439P LEU* 4.2 21.0 - - + +
443P TYR* 5.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 424 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496J GLU* 5.2 7.0 + - - +
396P LYS* 4.6 18.4 + - - +
402P TRP* 3.1 50.8 - - + +
420P TYR* 2.8 42.6 + - + +
421P TYR 3.3 8.7 - - - +
423P ARG* 1.3 82.0 - - - +
425P ALA* 1.3 59.8 + - - +
427P GLN* 3.6 31.5 + - - +
428P LEU* 3.5 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 425 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399P TYR* 4.2 7.9 - - - +
402P TRP* 3.7 23.0 - - + +
403P TYR* 3.8 18.4 - - + +
421P TYR 2.9 12.6 + - - +
422P TYR* 3.3 9.4 - - - +
424P ARG* 1.3 74.6 - - - +
426P HIS* 1.3 64.0 + - - +
428P LEU* 3.1 22.2 + - - +
429P ARG* 3.2 8.1 + - - +
435P MET* 4.1 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 426 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532J ALA* 5.6 0.4 - - - -
533J TYR* 3.5 45.5 + + + -
422P TYR 2.8 19.5 + - - +
423P ARG* 3.5 9.8 + - - +
425P ALA* 1.3 74.5 - - - +
427P GLN* 1.3 63.7 + - - +
429P ARG 2.6 34.4 - - - +
430P PRO* 3.5 25.3 + - + +
432P ASP 4.5 1.3 - - - -
435P MET* 4.0 19.0 - - + +
436P LEU* 3.3 33.3 - - + +
439P LEU* 4.0 17.2 - - + +
458P ARG* 3.7 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 427 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496J GLU* 3.3 24.2 + - - -
533J TYR* 5.7 8.5 - - + -
215P ASP* 4.2 14.6 - - - +
242P GLN* 5.8 0.7 - - - +
397P ARG* 4.8 8.8 + - - +
423P ARG* 2.9 28.2 + - - +
424P ARG* 3.7 30.0 + - - +
425P ALA 3.3 0.2 - - - -
426P HIS* 1.3 79.0 + - - +
428P LEU* 1.3 63.2 + - - +
429P ARG* 3.4 1.7 + - - -
430P PRO* 4.6 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 428 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240P GLU 5.8 0.7 - - - +
242P GLN* 2.7 30.7 + - - +
396P LYS 3.4 20.2 - - - +
397P ARG* 3.1 70.2 + - - +
399P TYR* 3.7 12.6 - - + -
402P TRP* 3.5 23.6 - - + +
424P ARG* 3.5 12.2 + - - +
425P ALA 3.1 12.0 + - - +
427P GLN* 1.3 81.8 - - - +
429P ARG* 1.3 63.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 429 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240P GLU 5.2 7.3 + - - -
241P LEU 5.4 0.2 + - - -
242P GLN* 3.4 30.5 + - - +
244P ILE* 6.1 0.4 - - - +
275P ASN* 3.7 32.8 + - - +
277P ARG* 5.8 1.1 - - - +
397P ARG 4.6 3.4 + - - -
399P TYR* 3.3 48.4 - - + +
425P ALA 3.2 5.6 + - - +
426P HIS* 2.6 27.2 + - - +
428P LEU* 1.3 90.3 - - + +
430P PRO* 1.4 64.7 - - + +
431P ASN* 3.5 2.6 + - + +
432P ASP* 3.0 46.3 + - - +
----------------------------------------------------------
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