Contacts of the helix formed by residues 436 - 445 (chain A) in PDB entry 2O8C
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 PHE 436 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A LEU* 3.6 41.3 - - + -
366A PHE* 6.3 3.6 - + - -
421A LEU* 5.0 6.3 - - + -
432A LEU 4.1 12.3 - - - -
433A LEU* 3.7 17.2 + - + +
434A ALA 3.5 0.2 - - - -
435A VAL* 1.3 95.7 - - + +
437A VAL* 1.3 66.7 + - + +
439A PRO* 3.6 4.9 - - - +
440A LEU* 3.4 31.3 - - - +
598A VAL* 4.7 9.0 - - + -
601A GLN* 4.3 18.2 - - + -
602A LEU* 3.7 52.9 - - + -
605A VAL* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ILE* 4.8 6.6 - - + +
421A LEU* 4.3 35.2 - - + +
422A GLU* 4.2 27.6 - - + +
424A HIS* 5.3 5.2 - - + +
430A LYS* 6.2 1.8 - - + -
433A LEU* 3.2 27.6 + - + +
436A PHE* 1.3 81.1 - - + +
438A THR* 1.3 69.6 + - + +
440A LEU* 4.0 2.0 - - - +
441A THR* 3.2 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A LEU 4.5 0.4 + - - -
434A ALA* 2.5 40.1 + - + +
437A VAL* 1.3 78.7 - - + +
439A PRO* 1.4 67.8 - - - +
441A THR* 3.3 21.2 - - + +
442A ASP* 3.3 18.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A ALA 4.7 0.2 - - - +
435A VAL* 3.4 25.8 - - + +
436A PHE 3.6 14.6 - - - +
438A THR* 1.4 96.2 - - - +
440A LEU* 1.3 51.9 + - - +
442A ASP* 3.0 9.2 + - + +
443A LEU* 2.8 43.1 + - + +
598A VAL* 4.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 3.9 21.1 - - + +
417A VAL* 4.7 5.6 - - + -
418A ILE* 3.9 19.6 - - + +
421A LEU* 4.2 12.8 - - + -
436A PHE* 3.4 20.6 - - - +
437A VAL 3.5 0.6 + - - +
438A THR 3.4 0.6 - - - -
439A PRO* 1.3 80.3 - - - +
441A THR* 1.3 57.6 + - - +
443A LEU* 3.8 7.3 - - + +
444A ARG* 3.2 23.0 + - - +
595A LEU* 3.9 28.0 - - + -
598A VAL* 3.9 23.3 - - + -
599A LEU* 4.2 10.1 - - + -
602A LEU* 3.9 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ILE* 4.0 22.6 - - - +
422A GLU* 5.3 6.0 + - - +
437A VAL* 3.2 18.4 + - + +
438A THR* 3.3 22.4 - - + +
440A LEU* 1.3 76.7 - - - +
442A ASP* 1.3 68.2 + - - +
443A LEU 3.5 0.2 - - - -
444A ARG* 3.4 18.6 - - - +
445A SER* 3.7 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A THR* 3.3 17.1 + - - +
439A PRO* 3.0 11.8 + - + +
441A THR* 1.3 84.3 - - - +
443A LEU* 1.3 58.8 + - + +
444A ARG 3.1 1.8 - - - -
445A SER* 2.9 21.9 + - - +
446A ASP* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 4.4 4.1 - - + +
439A PRO* 2.8 22.8 + - + +
440A LEU* 4.1 15.3 - - + +
442A ASP* 1.3 74.3 - - + +
444A ARG* 1.3 62.9 + - - +
446A ASP* 3.2 19.2 + - + +
447A PHE* 3.2 34.0 + - + +
591A PRO* 4.3 14.8 - - + +
594A THR* 3.5 25.6 - - - +
595A LEU* 3.7 41.5 - - + +
598A VAL* 4.7 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ILE* 5.2 6.9 - - - +
414A LEU* 4.4 10.7 - - + +
415A PRO* 3.5 43.9 - - + +
418A ILE* 5.0 8.1 - - + -
440A LEU 3.2 15.8 + - - +
441A THR* 3.4 17.9 - - - +
443A LEU* 1.3 79.4 - - - +
445A SER* 1.3 60.7 + - - +
446A ASP 3.6 0.2 + - - -
447A PHE* 3.7 4.1 + - - +
448A SER* 3.6 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A THR 3.7 6.2 + - - -
442A ASP* 2.9 27.7 + - - +
444A ARG* 1.3 78.9 - - - +
446A ASP* 1.3 63.4 + - - +
447A PHE 3.4 0.7 - - - -
448A SER* 3.0 27.2 + - - -
----------------------------------------------------------
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