Contacts of the helix formed by residues 385 - 396 (chain A) in PDB entry 2XCV
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 LYS 385 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A VAL* 3.1 34.1 + - + +
382A TRP* 3.8 6.0 - - - +
383A THR 3.0 1.6 + - - -
384A ASP* 1.3 98.3 + - - +
386A SER* 1.3 59.4 + - - +
387A SER* 3.4 4.7 - - - -
388A LEU* 3.3 26.0 + - + +
389A PHE* 3.1 26.3 + - - +
430A MET* 5.4 8.0 - - + +
433A CYS* 3.5 35.9 - - - -
434A TYR* 5.8 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A TRP* 3.5 14.7 + - - +
383A THR* 3.1 19.7 + - - -
384A ASP 3.7 0.4 - - - -
385A LYS* 1.3 74.1 - - - +
387A SER* 1.3 54.3 + - - +
388A LEU 3.0 4.3 - - - -
389A PHE* 3.1 7.9 + - - +
390A GLU* 2.7 51.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP 5.8 0.3 - - - -
385A LYS* 4.7 2.8 - - - -
386A SER* 1.3 77.7 + - - +
388A LEU* 1.3 57.5 + - - +
390A GLU* 4.2 10.3 + - - -
391A GLU* 3.3 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LYS* 3.3 36.5 + - + +
386A SER 3.0 0.8 - - - -
387A SER* 1.3 79.7 + - - +
389A PHE* 1.3 64.0 + - - +
391A GLU* 3.6 6.9 + - - +
392A LEU* 3.3 15.2 + - - +
426A VAL* 3.6 37.8 - - + +
429A ASP* 4.0 23.3 - - + +
430A MET* 3.7 19.5 - - + +
433A CYS* 4.8 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A TRP* 3.4 46.7 - + + -
385A LYS 3.1 13.2 + - - +
386A SER* 3.7 7.9 - - - +
388A LEU* 1.3 72.2 - - - +
390A GLU* 1.3 59.4 + - + +
392A LEU* 3.1 13.8 + - + +
393A GLN* 2.8 72.5 + - + +
430A MET* 3.9 28.3 - - + -
442A ARG* 4.0 25.6 - - - -
444A GLY 4.0 5.4 - - - -
445A SER* 4.8 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A SER* 2.7 38.6 + - - +
387A SER* 4.2 7.4 + - - -
389A PHE* 1.3 73.3 - - + +
391A GLU* 1.3 65.0 + - - +
393A GLN* 3.2 19.5 + - - +
394A SER* 3.0 27.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A SER 3.3 21.0 + - - +
388A LEU* 3.7 10.6 - - - +
389A PHE 3.3 0.4 - - - -
390A GLU* 1.3 78.5 - - - +
392A LEU* 1.3 61.9 + - - +
394A SER* 3.3 16.3 + - - -
395A LEU* 3.4 24.0 + - + +
422A ARG* 2.6 42.1 + - - -
426A VAL* 4.0 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU 3.3 4.9 + - - +
389A PHE* 3.1 14.2 + - + +
391A GLU* 1.3 78.5 - - - +
393A GLN* 1.3 57.4 + - - +
394A SER 3.4 0.5 + - - -
395A LEU* 3.5 11.8 + - - +
396A ASP* 2.5 37.0 + - - +
423A ILE* 3.8 35.9 - - + +
426A VAL* 3.5 22.3 - - + +
427A THR* 4.0 12.6 - - - +
430A MET* 4.3 11.9 - - - -
444A GLY* 3.6 39.0 - - - +
445A SER* 3.6 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A PHE* 2.8 53.0 + - + +
390A GLU* 3.3 23.8 - - - +
392A LEU* 1.3 79.7 - - - +
394A SER* 1.3 62.8 + - - +
396A ASP* 3.6 17.4 + - - +
445A SER* 6.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLU 3.0 13.9 + - - -
391A GLU* 3.3 10.2 + - - -
393A GLN* 1.3 74.2 - - - +
395A LEU* 1.3 56.5 + - - +
396A ASP 2.7 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A GLU* 3.4 28.0 + - + +
392A LEU* 3.7 9.6 - - - +
394A SER* 1.3 77.4 - - - +
396A ASP* 1.3 63.6 + - - +
422A ARG* 3.7 28.5 - - + -
423A ILE* 3.9 25.4 - - + +
426A VAL* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU* 2.5 37.6 - - - +
393A GLN* 3.9 11.8 - - - +
394A SER 2.7 18.3 + - - +
395A LEU* 1.3 76.4 - - - +
423A ILE* 3.7 28.7 - - - +
445A SER* 4.6 15.6 + - - -
----------------------------------------------------------
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