Contacts of the helix formed by residues 441 - 453 (chain D) in PDB entry 1JIQ
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 SER 441 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ARG* 4.7 6.0 - - - +
440D LYS* 1.3 76.0 - - - +
442D THR* 1.3 64.9 + - - +
443D GLU* 3.3 11.5 + - - +
444D GLU* 2.9 38.7 + - - +
445D ALA* 2.9 21.0 + - - +
467D VAL* 4.3 4.7 - - - -
468D PHE 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 442 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D SER* 1.3 73.2 - - - +
443D GLU* 1.3 53.0 + - - +
445D ALA* 4.4 0.4 - - - -
446D ARG* 2.6 40.7 + - + +
463D LEU* 3.3 34.1 - - + -
464D PRO* 6.2 0.4 - - + -
467D VAL* 3.7 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 443 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441D SER* 3.2 10.6 + - - +
442D THR* 1.3 79.4 - - - +
444D GLU* 1.3 60.5 + - + +
446D ARG* 3.5 12.1 + - - +
447D LYS* 2.9 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 444 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ARG* 2.9 34.6 + - - -
438D ARG* 4.7 3.5 + - - -
439D GLY 4.1 0.9 - - - +
440D LYS* 3.3 21.5 - - + +
441D SER* 2.9 39.4 + - - +
443D GLU* 1.3 79.5 - - + +
445D ALA* 1.3 63.3 + - - +
447D LYS* 3.3 8.7 + - - +
448D GLU* 3.1 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 445 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D LYS* 4.1 12.1 - - + +
441D SER 2.9 16.8 + - - +
442D THR 3.7 2.2 - - - +
444D GLU* 1.3 73.4 - - - +
446D ARG* 1.3 65.8 + - - +
448D GLU* 2.9 8.0 + - - +
449D LEU* 2.8 27.5 + - - +
463D LEU* 4.0 13.5 - - + -
466D LYS* 4.0 32.1 - - + +
467D VAL* 4.3 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 446 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442D THR* 2.6 25.3 + - + +
443D GLU* 3.7 10.1 + - - +
445D ALA* 1.3 71.3 - - - +
447D LYS* 1.3 78.4 + - - +
449D LEU* 3.3 4.9 + - - +
450D GLN* 2.8 66.7 + - - +
459D LEU* 4.0 25.4 - - + +
463D LEU* 3.4 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 447 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443D GLU* 2.9 19.2 + - + +
444D GLU* 3.5 7.9 - - - +
445D ALA 3.1 0.2 - - - -
446D ARG* 1.3 92.6 - - - +
448D GLU* 1.3 67.2 + - + +
450D GLN* 3.7 1.9 + - - +
451D ALA* 3.1 24.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 448 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C GLU* 6.1 0.2 - - - -
520C GLN* 3.0 25.0 + - - -
440D LYS* 2.7 37.4 + - - +
444D GLU* 3.1 14.8 + - - +
445D ALA* 2.9 7.8 + - - +
447D LYS* 1.3 75.9 - - + +
449D LEU* 1.3 67.2 + - + +
451D ALA* 3.2 6.5 + - - +
452D ALA* 2.9 23.3 + - - +
466D LYS* 5.7 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 449 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445D ALA 2.8 14.8 + - - +
446D ARG 3.6 3.8 - - - +
448D GLU* 1.3 76.9 - - + +
450D GLN* 1.3 64.6 + - - +
452D ALA* 2.8 22.4 + - + +
453D GLY 3.3 3.8 + - - -
454D LYS* 3.5 35.1 + - + +
458D ASP 5.1 0.7 - - - +
459D LEU* 3.9 22.2 - - + +
462D LEU* 4.2 14.1 - - + -
463D LEU* 3.7 49.8 - - + +
466D LYS* 4.3 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 450 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446D ARG* 2.8 60.3 + - - +
447D LYS 4.0 3.1 - - - +
449D LEU* 1.3 75.7 - - - +
451D ALA* 1.3 62.1 + - - +
453D GLY* 3.2 15.2 + - - -
454D LYS 4.2 6.3 + - - +
459D LEU* 3.7 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 451 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447D LYS* 3.1 23.1 + - + +
448D GLU* 3.5 8.3 - - - +
449D LEU 3.2 0.2 - - - -
450D GLN* 1.3 74.8 - - - +
452D ALA* 1.3 63.8 + - - +
453D GLY 3.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 452 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448D GLU 2.9 10.7 + - - +
449D LEU* 2.8 14.6 + - + +
451D ALA* 1.3 79.6 - - - +
453D GLY* 1.3 58.2 + - - +
454D LYS* 4.2 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 453 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450D GLN 3.2 11.6 + - - -
451D ALA 4.5 0.2 - - - -
452D ALA* 1.3 78.8 - - - +
454D LYS* 1.3 67.4 + - - +
455D SER 3.7 1.0 + - - -
----------------------------------------------------------
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