Contacts of the helix formed by residues 428 - 441 (chain P) in PDB entry 1HI0
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 ASP 428 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125P LEU* 3.8 15.6 - - - +
426P ILE 3.8 0.4 - - - -
427P LYS* 1.3 90.0 - - - +
429P MET* 1.3 65.6 + - - +
430P PRO* 3.0 18.1 - - + +
431P SER* 2.6 36.7 + - - -
432P ALA* 2.9 23.6 + - - +
434P ARG* 4.5 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 429 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125P LEU* 3.5 35.2 - - + +
128P ARG* 3.7 32.3 - - + +
129P ALA* 3.8 7.4 - - - +
132P ARG* 3.2 38.1 - - + +
343P GLU* 4.0 5.2 - - - +
428P ASP* 1.3 74.1 - - - +
430P PRO* 1.3 64.3 - - + +
432P ALA* 2.9 3.7 + - - +
433P CYS* 2.6 43.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 430 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428P ASP* 3.0 17.3 - - + +
429P MET* 1.3 92.4 - - + +
431P SER* 1.3 63.7 + - - +
433P CYS* 3.1 6.3 + - + +
434P ARG* 2.8 47.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 431 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425P ARG 3.2 23.9 - - - +
427P LYS* 2.8 34.3 + - - -
428P ASP* 2.6 32.2 + - - -
430P PRO* 1.3 73.4 - - - +
432P ALA* 1.3 54.5 + - - +
434P ARG* 3.3 27.5 + - - +
435P PHE* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 432 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125P LEU* 4.2 12.3 - - + +
126P LEU* 4.9 2.8 - - + +
129P ALA* 4.1 16.6 - - + -
426P ILE* 3.8 25.1 - - + -
428P ASP 2.9 20.5 + - - +
429P MET* 3.1 7.2 - - - +
431P SER* 1.3 75.0 + - - +
433P CYS* 1.3 68.5 + - - +
435P PHE* 2.9 4.8 + - - +
436P LEU* 2.8 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 433 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129P ALA* 4.0 18.1 - - - +
132P ARG* 4.2 18.2 - - - -
133P LEU* 3.9 15.7 - - + +
429P MET* 2.6 46.7 + - - +
430P PRO* 3.6 5.6 - - + +
432P ALA* 1.3 71.6 - - - +
434P ARG* 1.3 58.5 + - + +
436P LEU* 3.8 2.4 - - - +
437P ASP* 2.8 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 434 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425P ARG 5.5 0.2 + - - -
428P ASP* 4.5 2.0 + - - -
430P PRO* 2.8 27.9 + - - +
431P SER* 3.3 46.0 + - - +
433P CYS* 1.3 77.6 - - + +
435P PHE* 1.3 63.3 + - - +
437P ASP* 3.6 5.6 - - - +
438P SER* 3.0 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 435 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P LEU* 4.4 7.2 - - + -
411P LEU* 4.0 31.9 - - + -
415P LEU* 4.5 12.1 - - + -
422P LEU* 4.2 18.8 - - + -
425P ARG* 3.5 37.0 - - + +
426P ILE* 3.8 34.8 - - + -
431P SER 2.9 17.9 + - - +
432P ALA 2.9 2.9 + - - +
434P ARG* 1.3 76.1 - - - +
436P LEU* 1.3 55.7 + - - +
438P SER* 3.0 7.6 + - - -
439P TYR* 2.8 41.0 + - + +
444P GLU* 3.9 27.4 - - + -
446P ILE* 4.7 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P LEU* 3.9 9.6 - - + +
129P ALA* 3.7 11.7 - - + -
130P ALA* 3.3 41.7 - - + +
133P LEU* 3.7 13.2 - - + -
408P ILE* 3.9 14.8 - - + -
411P LEU* 4.0 16.8 - - + -
432P ALA 2.8 18.3 + - - +
433P CYS 3.8 3.1 - - - +
435P PHE* 1.3 76.2 - - - +
437P ASP* 1.3 57.6 + - - +
439P TYR* 3.1 6.8 + - + +
440P TRP* 2.8 60.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 437 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133P LEU* 3.4 18.8 - - + +
297P LYS* 3.4 18.7 + - - -
298P TYR* 2.8 25.6 + - - -
433P CYS 2.8 19.5 + - - +
434P ARG* 3.6 6.2 - - - +
436P LEU* 1.3 78.6 - - - +
438P SER* 1.3 67.1 + - - +
440P TRP 3.3 0.5 + - - -
441P GLN* 2.8 39.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 438 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425P ARG* 4.7 3.9 + - - -
434P ARG 3.0 12.6 + - - -
435P PHE* 3.0 10.2 + - - -
437P ASP* 1.3 81.7 + - - +
439P TYR* 1.3 62.6 + - - +
441P GLN* 3.2 7.2 + - - +
442P GLY 3.5 0.2 + - - -
443P HIS* 3.2 43.3 + - - +
444P GLU* 2.4 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 439 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301P THR* 4.1 4.7 - - + +
407P SER 4.9 0.2 - - - -
410P TYR 4.8 0.2 - - - -
411P LEU* 3.7 39.2 + - + -
414P GLN* 2.7 27.1 + - - -
435P PHE* 2.8 18.7 + + + +
436P LEU* 3.4 18.6 - - + +
438P SER* 1.3 76.9 - - - +
440P TRP* 1.3 76.1 + + - +
442P GLY* 2.9 22.2 + - - -
443P HIS 4.9 0.2 - - - +
444P GLU* 3.8 16.7 + - + +
446P ILE* 3.1 37.7 - - + +
447P ARG* 3.9 5.1 - - - -
448P GLN* 3.4 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 440 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130P ALA* 3.8 29.6 - - + -
133P LEU* 3.7 39.5 - - + -
134P MET* 3.9 25.1 - - + -
298P TYR* 3.5 40.3 - + + +
300P TYR* 3.7 1.4 - - - +
301P THR* 3.0 47.1 + - - +
302P PHE* 3.6 19.7 - + - -
404P LEU* 5.9 1.6 - - - -
407P SER* 2.9 26.8 + - - -
408P ILE* 4.4 4.6 - - + +
436P LEU* 2.8 35.7 + - + +
437P ASP 3.3 0.2 + - - -
439P TYR* 1.3 91.0 - + - +
441P GLN* 1.3 57.4 + - - +
442P GLY 3.1 0.9 - - - -
448P GLN* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 441 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297P LYS* 3.9 29.5 - - - +
298P TYR* 4.0 7.1 - - + +
300P TYR* 3.5 18.1 - - - +
437P ASP* 2.8 39.9 + - - +
438P SER* 3.7 8.9 - - - +
439P TYR 3.1 1.8 - - - -
440P TRP* 1.3 76.3 - - - +
442P GLY* 1.3 61.7 + - - +
443P HIS* 3.4 37.7 + - + +
----------------------------------------------------------
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