Contacts of the helix formed by residues 429 - 443 (chain D) in PDB entry 6PUO
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 VAL 429 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D ILE* 3.6 39.0 - - + +
190D PHE* 4.0 21.1 - - + +
193D GLY* 3.8 19.8 - - - -
194D LEU* 4.6 3.8 - - + +
419D PHE* 4.0 19.5 - - + -
428D ASP* 1.3 77.0 - - - +
430D ASP* 1.3 65.6 + - - +
431D VAL 3.4 0.2 - - - -
432D ALA* 3.1 5.8 + - + +
433D ILE* 3.1 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 430 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D GLY* 3.9 11.2 + - - +
196D LYS* 3.3 26.8 + - - +
197D VAL* 3.7 32.5 - - + +
428D ASP* 3.3 21.2 - - - +
429D VAL* 1.3 74.6 - - - +
431D VAL* 1.3 73.3 + - - +
433D ILE* 3.2 6.1 + - - +
434D LEU* 3.0 38.3 + - + +
464D ARG* 3.8 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 431 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427D GLN* 3.8 29.4 - - + -
428D ASP* 3.9 13.0 - - + +
430D ASP* 1.3 95.4 + - - +
432D ALA* 1.3 59.8 + - - +
434D LEU* 4.1 6.5 - - + +
435D GLN* 2.9 46.2 + - - +
464D ARG* 4.8 8.7 - - - +
466D ASP* 4.9 3.8 - - - +
467D ILE* 4.6 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 432 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D VAL* 4.9 6.7 - - + +
417D THR* 5.4 5.3 - - + +
419D PHE* 4.1 20.9 - - + -
428D ASP 3.8 12.3 - - - +
429D VAL 3.1 10.4 + - - +
431D VAL* 1.3 83.6 - - + +
433D ILE* 1.3 59.1 + - + +
435D GLN* 3.8 7.5 - - - +
436D ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 433 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D LEU* 5.7 3.1 - - + -
171D ILE* 5.5 7.4 - - + -
194D LEU* 5.0 9.9 - - + -
197D VAL* 4.5 24.2 - - + -
326D VAL* 4.1 33.5 - - + +
328D VAL* 5.4 15.0 - - + -
351D VAL* 4.7 18.2 - - + -
429D VAL* 3.1 32.6 + - + +
430D ASP* 3.2 5.8 + - - +
432D ALA* 1.3 76.2 - - + +
434D LEU* 1.3 62.8 + - + +
436D ALA* 3.3 6.8 + - - +
437D LEU* 2.9 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D LEU* 4.7 9.9 - - + -
197D VAL* 4.4 21.3 - - + -
201D THR* 5.1 3.4 - - - +
430D ASP* 3.0 23.5 + - + +
431D VAL* 4.1 6.5 - - - +
433D ILE* 1.3 79.6 - - + +
435D GLN* 1.3 57.5 + - - +
437D LEU* 3.3 6.3 + - + +
438D LEU* 2.9 34.8 + - - +
462D TRP* 3.6 41.6 - - + -
464D ARG* 3.7 36.3 - - - +
467D ILE* 4.7 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 435 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431D VAL* 2.9 34.9 + - + +
432D ALA* 3.9 6.5 - - - +
434D LEU* 1.3 73.7 - - - +
436D ALA* 1.3 62.0 + - - +
438D LEU* 3.4 5.8 + - - +
439D LYS* 2.9 31.8 + - - +
442D ARG* 4.9 1.4 + - - -
467D ILE* 5.4 10.4 - - + +
470D SER* 4.9 10.3 + - - -
471D GLU* 5.0 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 436 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D VAL* 5.8 0.7 - - + -
349D PRO* 4.6 8.8 - - + +
350D CYS 5.6 0.4 - - - +
351D VAL* 3.9 24.2 - - + -
414D GLN 5.5 0.2 - - - +
415D LEU 5.6 1.2 - - - +
417D THR* 4.0 19.5 - - + +
432D ALA 2.9 18.3 + - - +
433D ILE 3.6 4.3 - - - +
434D LEU 3.3 0.2 - - - -
435D GLN* 1.3 77.0 - - - +
437D LEU* 1.3 57.5 + - - +
439D LYS* 3.4 13.2 + - - +
440D ALA* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 437 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D LEU* 3.8 28.3 - - + -
324D PRO* 3.8 22.7 - - + -
325D ILE 4.4 7.6 - - - +
326D VAL* 4.9 11.2 - - + +
349D PRO* 3.8 25.8 - - + -
433D ILE* 2.9 17.9 + - + +
434D LEU* 3.7 7.6 - - + +
435D GLN 3.3 0.2 - - - -
436D ALA* 1.3 77.7 - - - +
438D LEU* 1.3 57.0 + - - +
440D ALA* 3.4 1.5 + - + +
441D SER* 3.0 29.0 + - - +
458D LEU* 5.6 4.5 - - + -
462D TRP* 3.7 28.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
434D LEU 2.9 21.2 + - - +
435D GLN* 3.9 5.6 - - - +
437D LEU* 1.3 75.9 - - + +
439D LYS* 1.3 59.8 + - - +
441D SER* 3.3 4.1 + - - +
442D ARG* 2.9 38.5 + - - +
455D GLN* 3.8 46.6 - - + +
458D LEU* 4.9 13.9 - - + -
459D ALA* 5.4 2.5 - - + -
462D TRP* 4.7 17.3 - - + -
467D ILE* 3.7 18.4 - - + -
471D GLU* 3.3 26.9 - - - +
472D ILE* 4.9 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 439 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D ARG 4.3 5.9 + - - -
414D GLN* 3.3 40.7 + - - +
416D LEU 4.2 4.4 + - - -
417D THR* 3.2 27.2 + - - +
435D GLN 2.9 16.6 + - - +
436D ALA* 3.8 11.7 - - - +
438D LEU* 1.3 76.2 - - - +
440D ALA* 1.3 61.1 + - - +
442D ARG* 3.2 25.4 + - - +
443D SER* 3.2 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 440 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D GLY 5.3 1.6 - - - +
349D PRO* 3.7 29.2 - - + -
414D GLN 5.2 3.6 - - - +
415D LEU* 4.0 28.9 - - + +
436D ALA 2.9 16.6 + - - +
437D LEU* 3.7 2.2 - - + +
438D LEU 3.3 0.2 - - - -
439D LYS* 1.3 79.9 - - - +
441D SER* 1.3 59.8 + - - +
442D ARG 3.5 0.3 + - - -
443D SER* 3.7 6.7 + - - -
444D GLN* 3.6 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 441 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437D LEU* 3.0 18.7 + - - -
438D LEU* 3.8 7.4 - - - -
439D LYS 3.3 0.2 - - - -
440D ALA* 1.3 76.3 - - - +
442D ARG* 1.3 61.7 + - - +
443D SER 3.4 0.2 - - - -
444D GLN* 3.6 10.7 - - - +
451D ASN* 2.8 21.5 + - - -
454D HIS* 3.7 24.6 + - - -
455D GLN* 4.1 11.1 - - - +
458D LEU* 4.7 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 442 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435D GLN 4.9 1.6 + - - -
438D LEU* 2.9 19.6 + - - +
439D LYS* 3.5 37.2 + - - +
440D ALA 3.2 0.4 - - - -
441D SER* 1.3 79.6 - - - +
443D SER* 1.3 62.4 + - - +
444D GLN 3.1 9.5 + - - +
446D HIS* 4.3 6.8 + - - -
451D ASN* 3.4 14.6 + - - +
452D TRP* 4.9 21.9 - - + +
455D GLN* 3.4 33.1 + - - +
471D GLU* 3.7 22.6 + - - -
472D ILE* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 443 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D GLN* 3.6 43.7 - - - +
415D LEU* 4.9 4.0 - - - +
439D LYS 3.2 5.7 + - - -
440D ALA* 3.7 8.7 + - - -
441D SER 3.4 0.2 - - - -
442D ARG* 1.3 77.5 - - - +
444D GLN* 1.3 64.7 + - - +
445D ASP* 3.7 1.6 + - - -
----------------------------------------------------------
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