Contacts of the helix formed by residues 430 - 442 (chain D) in PDB entry 4L28
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 THR 430 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C GLN* 6.2 1.3 - - - -
428D THR 3.6 1.7 + - - -
429D ILE* 1.3 76.5 - - - +
431D CYS* 1.3 59.0 + - - +
433D HIS* 3.1 30.4 - - + +
434D THR* 2.8 29.5 + - - -
475D PRO 2.8 24.9 + - - +
476D SER* 3.0 16.8 + - - -
477D ASP 2.9 13.1 + - - -
478D GLN* 4.3 2.9 - - - +
479D VAL* 4.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 431 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D THR* 1.3 76.0 + - - +
432D GLY* 1.3 60.1 + - - +
434D THR* 3.2 3.5 + - - -
435D ILE* 2.9 36.0 + - + +
464D MET* 4.0 28.9 - - + +
468D LEU* 5.1 5.2 - - + -
473D VAL* 4.9 11.0 - - - -
474D GLN 4.0 10.5 - - - +
475D PRO* 3.7 7.0 - - + +
477D ASP* 3.0 21.0 + - - +
478D GLN 3.8 16.4 - - - -
479D VAL* 4.1 3.1 - - - -
482D VAL* 4.4 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 432 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431D CYS* 1.3 77.3 - - - +
433D HIS* 1.3 61.6 + - - +
435D ILE* 3.3 14.0 + - - +
436D GLU* 3.0 35.7 + - - +
468D LEU* 5.6 0.2 - - - -
475D PRO* 3.0 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 433 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429D ILE* 3.4 25.9 - - + +
430D THR* 3.1 32.6 - - + +
432D GLY* 1.3 78.6 - - - +
434D THR* 1.3 56.2 + - - +
436D GLU* 3.2 12.5 + - - +
437D ILE* 3.0 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 434 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425D VAL* 4.4 22.7 - - + -
429D ILE* 3.3 26.3 - - + +
430D THR 2.8 15.5 + - - -
431D CYS 3.2 6.7 + - - -
433D HIS* 1.3 73.7 - - - +
435D ILE* 1.3 66.1 + - - +
437D ILE* 3.3 4.7 + - + +
438D LEU* 2.9 43.3 + - + +
446D ALA* 5.2 1.3 - - + -
459D VAL* 4.9 5.6 - - + -
464D MET* 3.8 18.4 - - + -
479D VAL* 3.5 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 435 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431D CYS* 2.9 19.4 + - + +
432D GLY* 3.5 14.6 - - - +
434D THR* 1.3 76.4 - - - +
436D GLU* 1.3 70.1 + - + +
438D LEU* 3.9 1.0 - - - +
439D ARG* 3.0 48.6 + - - +
461D LEU* 4.0 19.3 - - + -
464D MET* 3.9 22.4 - - + -
465D LEU* 4.2 18.4 - - + -
468D LEU* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 436 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D GLY* 3.0 21.8 + - - +
433D HIS* 3.2 13.1 + - - +
435D ILE* 1.3 81.4 - - + +
437D ILE* 1.3 64.2 + - + +
439D ARG* 4.0 4.0 - - - +
440D GLU* 2.9 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 437 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D LEU* 3.7 30.7 - - + -
425D VAL* 6.1 4.0 - - + -
429D ILE* 5.0 4.5 - - + -
433D HIS* 3.0 41.5 + - + +
434D THR* 3.8 7.9 - - + +
436D GLU* 1.3 76.4 - - + +
438D LEU* 1.3 66.4 + - + +
440D GLU* 3.2 10.1 + - - +
441D LYS* 3.0 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 438 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D LEU* 5.4 7.6 - - + -
425D VAL* 6.0 0.9 - - + -
434D THR* 2.9 37.9 + - + +
435D ILE* 3.9 2.9 - - - +
437D ILE* 1.3 81.2 - - + +
439D ARG* 1.3 59.4 + - - +
441D LYS* 3.2 3.0 + - + -
442D GLY 2.8 6.8 + - - -
443D PHE* 2.8 60.1 + - + +
444D ASN 4.4 4.0 - - - +
445D GLN* 3.6 35.9 - - - +
446D ALA* 4.0 11.9 - - + +
459D VAL* 4.9 4.0 - - + +
460D THR 5.0 0.9 - - - -
461D LEU* 4.5 20.4 - - + +
464D MET* 5.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 439 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435D ILE* 3.0 38.5 + - - +
436D GLU* 4.1 3.8 - - - +
438D LEU* 1.3 71.4 - - - +
440D GLU* 1.3 66.1 + - - +
441D LYS 3.0 1.8 - - - -
442D GLY* 2.9 15.4 + - - +
443D PHE 4.7 2.5 - - - -
461D LEU* 3.8 32.9 - - + +
465D LEU* 5.1 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 440 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436D GLU* 2.9 23.5 + - - +
437D ILE* 3.7 9.9 - - - +
439D ARG* 1.3 77.1 - - - +
441D LYS* 1.3 62.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 441 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D LEU* 3.6 35.4 - - + -
437D ILE* 3.0 20.8 + - + +
438D LEU* 3.9 2.5 - - + +
439D ARG 3.0 0.4 - - - -
440D GLU* 1.3 82.2 - - + +
442D GLY* 1.3 58.4 + - - +
443D PHE* 3.1 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 442 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438D LEU 2.8 5.1 + - - -
439D ARG* 2.9 13.2 + - - -
440D GLU 3.5 0.2 - - - -
441D LYS* 1.3 78.4 - - - +
443D PHE* 1.3 63.6 + - - +
444D ASN* 4.0 0.9 + - - +
----------------------------------------------------------
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