Contacts of the helix formed by residues 231 - 241 (chain A) in PDB entry 4GQG
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 ASP 231 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A TYR* 2.7 38.6 + - - +
227A SER 3.2 5.0 + - - +
228A LEU 3.1 15.2 + - - +
229A LEU 3.6 0.2 - - - -
230A GLU* 1.3 75.0 - - - +
232A PRO* 1.4 72.1 - - - +
233A LYS* 2.9 23.0 + - - +
234A ILE* 3.2 22.6 + - + +
235A LYS* 3.1 21.5 + - - +
292A PHE* 4.3 8.3 - - - -
294A ARG* 4.4 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLU 3.1 10.1 - - - +
231A ASP* 1.4 88.3 - - - +
233A LYS* 1.3 56.2 + - + +
235A LYS* 3.4 10.2 + - + +
236A GLU* 3.0 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASP* 2.9 12.8 + - - +
232A PRO* 1.3 73.9 - - + +
234A ILE* 1.3 65.1 + - - +
236A GLU* 3.8 13.4 - - - +
237A ILE* 3.3 29.1 + - - +
288A THR* 5.8 1.1 - - + -
292A PHE* 3.4 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PRO* 4.3 2.5 - - + -
228A LEU* 4.2 10.8 - - + +
231A ASP* 3.2 23.0 + - + +
233A LYS* 1.3 77.8 - - - +
235A LYS* 1.3 57.4 + - - +
237A ILE* 3.3 5.7 + - - +
238A ALA* 3.0 25.5 + - - +
245A ALA* 3.7 35.2 - - + +
248A VAL* 4.3 9.7 - - + +
249A LEU* 4.1 27.1 - - + -
289A ILE* 4.0 28.3 - - + -
292A PHE* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU 3.2 23.3 - - - -
230A GLU* 3.6 19.9 - - - +
231A ASP 3.1 18.8 + - - +
232A PRO* 3.7 9.6 - - + +
234A ILE* 1.3 74.8 - - - +
236A GLU* 1.3 59.7 + - - +
238A ALA* 3.3 8.1 - - + +
239A ALA* 2.8 29.6 + - - +
245A ALA* 4.1 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A PRO* 3.0 27.2 + - + +
233A LYS* 3.8 12.0 - - - +
235A LYS* 1.3 73.3 - - - +
237A ILE* 1.3 66.5 + - + +
239A ALA* 3.4 7.2 + - - +
240A LYS* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LYS 3.3 17.3 + - - +
234A ILE* 3.8 6.3 - - - +
236A GLU* 1.3 78.5 - - + +
238A ALA* 1.3 64.3 + - - +
240A LYS* 3.2 14.7 + - - +
241A HIS* 3.4 14.8 - - + -
248A VAL* 4.4 7.0 - - + -
281A LEU* 3.6 30.5 - - + -
285A GLU* 3.8 34.3 - - + +
288A THR* 4.5 15.3 - - + -
289A ILE* 3.6 31.0 - - + -
292A PHE* 5.3 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE 3.0 14.1 + - - +
235A LYS* 3.3 12.1 - - + +
236A GLU 3.2 0.2 - - - -
237A ILE* 1.3 74.3 - - - +
239A ALA* 1.3 65.8 + - - +
241A HIS* 2.9 13.3 + - - -
243A LYS* 3.0 36.5 + - - +
244A THR 3.7 21.8 - - - +
245A ALA 3.8 3.6 - - - +
248A VAL* 3.5 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LYS 2.8 19.2 + - - +
236A GLU* 3.7 8.5 - - - +
238A ALA* 1.3 72.3 - - - +
240A LYS* 1.3 64.6 + - - +
241A HIS 3.0 1.4 + - - -
242A LYS* 3.0 17.8 + - - +
243A LYS 4.2 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLU 3.1 13.7 + - - +
237A ILE* 3.2 11.2 + - - +
239A ALA* 1.3 75.6 - - - +
241A HIS* 1.3 68.2 + - - +
242A LYS* 3.8 3.3 + - - +
282A SER* 5.8 2.6 + - - -
285A GLU* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 3.4 21.7 + - + +
238A ALA* 2.9 7.3 + - - +
240A LYS* 1.3 88.0 + - + +
242A LYS* 1.3 75.7 + - - +
243A LYS* 3.6 12.6 - - + +
248A VAL* 5.5 0.2 - - + -
279A PHE* 3.7 30.5 - + + +
280A LYS 3.0 27.8 + - - -
281A LEU* 4.0 15.9 - - + +
282A SER* 4.9 0.7 - - - -
285A GLU* 2.8 33.4 + - - -
----------------------------------------------------------
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