Contacts of the helix formed by residues 435 - 447 (chain D) in PDB entry 2QMR
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 TYR 435 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D LEU* 5.0 0.4 - - + -
399D LEU* 3.6 38.4 - - + +
403D LYS* 4.0 25.6 - - - +
431D GLY 3.5 24.9 - - - -
432D MET* 2.8 17.8 + - + +
434D PRO* 1.3 83.8 - - + +
436D LEU* 1.3 65.1 + - - +
437D PRO* 3.5 2.0 - - - -
438D GLU* 3.5 18.4 + - + +
439D LEU* 3.2 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429D MET* 4.9 4.5 - - - -
432D MET* 3.4 16.2 - - + +
433D ILE* 3.5 20.6 - - + +
435D TYR* 1.3 79.5 - - - +
437D PRO* 1.4 66.1 - - + +
438D GLU 3.0 0.3 + - - -
439D LEU* 4.4 10.5 - - + +
440D ILE* 2.8 41.1 + - + +
465D TYR* 3.0 44.9 - - + -
468D TRP* 3.5 52.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 437 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D ILE 3.4 13.5 - - - +
434D PRO 3.8 9.6 - - - +
435D TYR 3.5 3.1 - - - -
436D LEU* 1.4 91.6 - - + +
438D GLU* 1.3 57.0 + - + +
441D PRO* 3.2 20.9 - - - +
468D TRP* 3.8 16.8 - - + -
472D GLN* 5.9 0.2 - - - +
477D TYR* 3.6 23.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 438 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C VAL* 4.2 22.5 - - - +
295C ARG* 5.4 14.7 + - - +
403D LYS* 4.6 11.1 + - - -
407D PHE* 5.5 5.8 - - - -
434D PRO 5.6 0.7 - - - +
435D TYR* 3.6 23.1 - - + +
436D LEU 3.1 0.2 - - - -
437D PRO* 1.3 77.8 - - + +
439D LEU* 1.3 71.6 + - + +
440D ILE 3.5 0.4 - - - -
441D PRO* 3.9 4.8 - - - +
442D HIS* 3.4 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 439 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399D LEU* 6.1 0.2 - - + -
402D LEU* 5.5 1.1 - - + -
403D LYS* 4.8 12.1 - - - +
406D LEU* 3.7 27.1 - - + -
407D PHE* 4.3 19.3 - - + -
421D LEU* 4.1 21.8 - - + -
432D MET* 3.7 31.2 - - + -
435D TYR* 3.2 25.7 + - + +
436D LEU* 3.1 10.2 + - + +
438D GLU* 1.3 82.8 - - + +
440D ILE* 1.3 55.2 + - - +
442D HIS* 3.1 7.6 + - - +
443D LEU* 2.7 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 440 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D LEU* 2.8 28.3 + - + +
439D LEU* 1.3 74.7 - - - +
441D PRO* 1.4 64.1 - - + +
443D LEU* 3.0 11.4 + - + +
444D ILE* 2.8 48.8 + - + +
462D LEU* 4.3 17.7 - - + -
465D TYR* 4.1 18.8 - - + -
468D TRP* 3.4 33.0 - - + -
469D VAL* 3.7 19.1 - - + -
477D TYR* 4.0 18.8 - - + -
481D LEU* 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 441 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D LEU 3.8 1.8 - - - +
437D PRO 3.2 28.5 - - - +
438D GLU* 3.9 4.7 - - - +
439D LEU 3.9 0.7 - - - -
440D ILE* 1.4 96.0 - - + +
442D HIS* 1.3 56.7 + - - +
444D ILE* 3.5 13.9 + - + +
445D GLN* 3.0 30.0 + - - +
477D TYR* 3.9 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 442 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C ARG* 4.9 9.2 - - - +
406D LEU* 3.5 33.0 + - + +
407D PHE* 3.7 35.6 - + + -
414D LYS* 5.1 2.6 - - + +
418D ILE* 5.9 0.4 - - + -
438D GLU 3.4 16.6 + - - +
439D LEU* 3.1 11.5 + - - +
441D PRO* 1.3 77.2 - - - +
443D LEU* 1.3 70.4 + - + +
445D GLN* 3.3 13.1 + - + +
446D CYS* 3.1 44.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 443 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406D LEU* 5.4 1.3 - - + -
418D ILE* 3.9 34.1 - - + -
421D LEU* 3.7 27.4 - - + -
439D LEU* 2.7 26.4 + - + +
440D ILE* 3.5 10.5 - - + +
442D HIS* 1.3 75.0 - - - +
444D ILE* 1.3 60.0 + - - +
446D CYS* 2.8 21.4 + - - -
447D LEU* 3.0 9.7 + - - +
458D THR* 3.2 25.5 - - + +
461D THR* 3.9 15.5 - - + +
462D LEU* 3.8 26.7 - - + +
465D TYR* 5.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 444 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D ILE* 2.8 41.0 + - + +
441D PRO* 3.6 11.9 - - + +
442D HIS 3.4 0.2 - - - -
443D LEU* 1.3 71.5 - - - +
445D GLN* 1.3 67.7 + - - +
447D LEU* 3.1 23.5 - - - +
448D SER* 4.2 4.9 + - - -
462D LEU* 4.2 12.5 - - + +
477D TYR* 4.0 22.2 - - + +
480D PRO* 4.2 18.6 - - + +
481D LEU* 4.1 16.2 - - + +
484D GLU* 3.8 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 445 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D PRO 3.0 17.4 + - - +
442D HIS* 3.3 18.8 - - + +
443D LEU 3.0 0.8 - - - -
444D ILE* 1.3 80.1 + - - +
446D CYS* 1.3 64.1 + - - +
447D LEU 3.1 1.8 - - - -
448D SER* 3.1 25.8 + - - -
449D ASP 4.1 1.2 + - - -
484D GLU* 5.2 5.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 446 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D LYS* 4.8 9.9 - - - -
418D ILE* 4.1 15.0 - - + -
442D HIS* 3.1 52.3 + - - -
443D LEU* 2.8 14.8 + - - +
445D GLN* 1.3 66.3 - - - +
447D LEU* 1.3 55.2 + - - +
448D SER 2.9 6.1 - - - -
449D ASP* 2.8 37.0 + - + +
454D VAL* 4.2 11.9 - - + +
455D ARG* 4.2 3.6 - - - +
458D THR* 3.7 19.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 447 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443D LEU 3.0 4.6 + - - -
444D ILE* 3.1 20.9 - - + +
446D CYS* 1.3 75.4 - - - +
448D SER* 1.3 57.7 + - - +
449D ASP 3.5 0.2 - - - -
455D ARG* 3.1 10.9 - - - +
458D THR* 3.8 22.4 - - + +
459D CYS* 3.8 32.8 - - - +
462D LEU* 3.7 22.0 - - + -
481D LEU* 4.4 5.4 - - + -
484D GLU* 3.6 29.2 - - + +
485D LEU* 4.1 14.4 - - + +
488D ARG* 3.0 43.0 + - + -
----------------------------------------------------------
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