Contacts of the helix formed by residues 326 - 332 (chain D) in PDB entry 6RI7
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 SER 326 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D LEU* 4.3 10.7 - - - +
268D LEU* 4.7 3.1 - - - -
305D ALA 4.2 2.9 - - - -
306D LEU 4.0 6.5 - - - -
307D LEU 3.7 5.1 + - - -
308D ASP* 4.2 0.3 + - - -
309D ASN* 3.8 31.0 + - - -
325D LYS* 1.3 81.2 - - - +
327D LEU* 1.3 60.2 + - - +
328D ALA* 3.4 9.4 + - - +
329D ASP* 3.2 26.5 + - - +
330D MET* 2.8 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1329C GLU* 6.0 2.9 - - + -
1332C SER* 4.0 19.1 - - - +
1333C LEU* 3.8 32.1 - - + +
245D LEU* 4.8 11.4 - - + -
265D LEU* 3.5 32.7 - - + +
269D TYR* 4.6 11.4 - - + +
306D LEU* 3.6 35.4 + - + +
307D LEU* 3.8 4.6 + - + +
326D SER* 1.3 72.3 - - - +
328D ALA* 1.3 67.8 + - - +
330D MET* 2.8 23.2 + - - +
331D ILE* 3.0 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1333C LEU* 5.2 1.2 - - - +
115D TRP* 4.3 22.9 - - + +
307D LEU 3.3 16.1 + - - +
308D ASP* 4.1 22.0 - - + +
326D SER* 3.7 5.4 - - - +
327D LEU* 1.3 76.4 - - - +
329D ASP* 1.3 57.5 + - - +
331D ILE* 2.7 22.7 + - - +
332D LYS* 2.8 31.7 + - + +
1329D THR* 5.2 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D ASN* 5.3 4.1 - - - +
323D PRO 5.5 0.3 - - - +
324D LEU 4.0 4.3 - - - +
325D LYS* 3.4 26.1 - - + +
326D SER* 3.2 28.9 + - - +
328D ALA* 1.3 77.9 - - - +
330D MET* 1.3 63.0 + - - +
331D ILE 3.0 1.4 + - - -
332D LYS* 3.2 37.4 - - - +
335D GLN 4.7 1.7 - - - +
336D GLY* 3.8 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 330 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1329C GLU* 3.1 32.3 - - + +
245D LEU* 4.9 5.8 - - - -
249D LEU 4.7 7.6 - - - +
263D SER* 5.6 1.6 - - - +
265D LEU* 3.6 32.1 - - + -
325D LYS* 4.1 29.8 - - - +
326D SER 2.8 11.9 + - - +
327D LEU* 2.8 19.2 + - + +
329D ASP* 1.3 76.7 - - - +
331D ILE* 1.3 57.3 + - + +
335D GLN 5.6 0.7 - - - -
336D GLY* 3.6 2.5 - - - -
337D ARG* 3.0 54.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 331 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1326C LEU* 4.8 9.9 - - + -
1329C GLU* 4.6 13.7 - - + +
1330C ILE* 3.7 27.1 - - + +
1333C LEU* 3.6 30.1 - - + -
115D TRP* 4.8 7.0 - - + -
327D LEU* 3.0 8.2 + - + +
328D ALA* 2.7 8.5 + - - +
330D MET* 1.3 80.5 - - - +
332D LYS* 1.3 68.1 + - - +
333D GLY 4.6 0.3 - - - +
336D GLY* 3.2 11.8 - - - -
337D ARG* 3.4 6.4 + - - +
338D PHE* 4.1 27.1 + - + +
1328D THR* 3.5 25.9 + - + +
1332D LEU* 4.8 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D ASP* 4.9 7.9 + - - -
311D ARG* 4.1 18.5 - - - +
328D ALA* 2.8 27.7 + - + +
329D ASP* 3.2 32.2 - - - +
331D ILE* 1.3 79.4 - - - +
333D GLY* 1.3 72.4 + - - +
336D GLY* 3.1 12.5 + - - -
1327D GLU* 5.4 0.4 - - - -
1328D THR* 3.3 33.4 - - - +
1329D THR* 5.0 9.2 - - - +
14T C 5.1 5.7 + - - -
15T C 5.3 9.0 - - - +
----------------------------------------------------------
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