Contacts of the helix formed by residues 438 - 443 (chain A) in PDB entry 2O1X
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 438 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A GLN* 3.5 19.3 - - - +
432A ALA 5.4 2.0 - - - -
435A ASN 4.0 8.3 - - - -
436A GLY 3.5 0.6 - - - -
437A VAL* 1.3 106.6 - - + +
439A ASP* 1.3 59.2 + - - +
440A LEU 3.4 2.5 - - - -
441A SER* 2.8 22.1 + - - -
442A PHE* 3.0 19.4 + - + -
562A ASN* 3.5 2.5 - - - -
563A THR* 4.2 14.6 - - + -
593A GLU 6.5 0.2 - - - -
594A PHE* 3.6 29.6 - + - -
403B TYR* 3.7 17.7 - - - +
407B LEU* 3.5 25.4 - - + -
445B SER* 3.7 17.9 - - - -
447B PRO* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A SER* 2.9 34.1 + - - +
399A LEU* 5.4 2.7 - - + -
421A ILE* 4.5 8.4 - - + +
424A ALA* 4.1 0.5 - - - +
436A GLY 3.4 3.8 - - - +
438A PHE* 1.3 74.1 - - - +
440A LEU* 1.3 62.0 + - - +
441A SER 3.0 4.9 - - - -
442A PHE* 3.4 23.2 - - + -
443A LEU* 3.0 36.9 + - + +
451A ILE* 5.5 1.6 - - - +
477A ARG* 2.3 57.7 + - - +
562A ASN* 3.4 1.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
439A ASP* 1.3 78.0 - - - +
441A SER* 1.3 57.0 + - - +
444A ARG* 3.2 31.5 + - - +
451A ILE* 3.7 27.8 - - + +
453A LEU* 3.8 16.2 - - + -
477A ARG* 3.3 39.9 - - - +
538A VAL* 4.0 19.7 - - + +
560A GLU* 4.1 19.7 - - + +
561A ASP 5.2 0.4 - - - +
562A ASN* 2.9 37.0 + - + +
566A GLY 4.0 0.5 - - - +
567A GLY* 4.2 4.4 - - - -
568A PHE* 4.7 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A PHE 2.8 11.2 + - - -
440A LEU* 1.3 79.1 - - - +
442A PHE* 1.3 64.6 + - - -
444A ARG* 3.3 15.9 + - - +
445A SER* 3.6 8.7 + - - -
562A ASN* 3.2 17.3 + - - -
563A THR* 3.5 1.9 - - - +
565A VAL 2.9 18.0 + - - -
566A GLY* 3.2 20.1 + - - +
441B SER* 6.1 0.2 - - - -
445B SER* 3.1 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A SER* 4.6 1.3 - - - -
399A LEU* 4.3 20.2 - - + -
400A GLN* 3.8 38.8 - - + -
403A TYR* 3.4 46.2 - + + -
406A VAL* 6.3 0.2 - - + -
438A PHE* 3.0 24.5 + - + -
439A ASP* 3.4 29.2 - - + -
441A SER* 1.3 76.3 - - - +
443A LEU* 1.3 83.8 + - + +
445A SER* 3.9 6.9 + - - -
446A ILE* 3.5 7.3 - - - +
403B TYR* 3.1 37.5 - + + +
442B PHE* 4.9 7.4 - - + +
445B SER* 5.8 2.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
399A LEU* 4.4 10.5 - - + -
403A TYR* 5.5 0.2 - - + -
406A VAL* 4.2 17.0 - - + -
419A PHE* 6.0 1.6 - - + -
421A ILE* 4.2 13.7 - - + -
439A ASP* 3.0 25.2 + - + +
442A PHE* 1.3 92.4 - - + +
444A ARG* 1.3 66.4 + - - +
445A SER 3.1 2.5 - - - -
446A ILE* 3.0 42.4 + - + +
449A VAL* 4.1 15.0 - - + +
451A ILE* 3.4 19.7 - - + -
475A ALA* 3.6 31.2 - - + -
----------------------------------------------------------
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