Contacts of the helix formed by residues 235 - 244 (chain A) in PDB entry 2GL7
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 GLY 235 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A VAL* 3.6 10.3 - - - +
203A GLN* 5.3 2.4 - - - +
232A PHE 3.3 10.2 + - - -
233A LYS 3.4 2.2 + - - -
234A SER* 1.3 78.8 - - - +
236A GLY* 1.3 61.9 + - - +
237A ILE 3.4 2.2 - - - -
238A PRO* 3.6 21.4 - - - +
239A ALA* 3.8 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A VAL* 3.9 22.4 - - - -
202A MET* 4.9 0.2 - - - +
218A LEU* 5.7 0.9 - - - -
231A ILE* 3.0 22.6 + - - -
232A PHE 4.3 0.4 + - - -
234A SER 3.2 1.2 - - - -
235A GLY* 1.3 76.7 - - - +
237A ILE* 1.3 60.1 + - - +
239A ALA* 3.5 2.0 + - - +
240A LEU* 3.0 39.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
231A ILE 4.3 1.2 + - - -
232A PHE* 3.7 27.1 + - + +
235A GLY 3.4 0.2 - - - -
236A GLY* 1.3 73.9 - - - +
238A PRO* 1.3 72.9 - - + +
239A ALA 3.2 0.3 + - - -
240A LEU* 3.2 7.0 + - - +
241A VAL* 3.1 24.8 + - + +
259A LEU* 4.4 4.2 - - + +
262A LEU* 4.1 24.9 - - + -
269A ALA* 3.6 38.1 - - + +
272A ALA* 3.7 16.2 - - + +
273A VAL* 3.6 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLN* 4.4 8.2 + - - +
235A GLY* 3.6 20.9 - - - +
237A ILE* 1.3 95.8 - - + +
239A ALA* 1.3 59.5 + - - +
241A VAL* 3.6 3.5 + - - +
242A LYS* 3.3 20.1 + - - +
272A ALA* 5.5 3.6 - - + +
276A ALA* 4.2 22.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
199A VAL* 3.9 20.6 - - + -
202A MET* 3.7 17.9 - - + -
203A GLN* 3.3 34.7 - - + +
235A GLY 3.8 2.9 + - - +
236A GLY 3.5 6.5 + - - +
237A ILE 3.2 0.6 - - - -
238A PRO* 1.3 77.0 - - - +
240A LEU* 1.3 65.9 + - - +
242A LYS* 3.2 6.8 + - - +
243A MET* 3.2 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A MET* 3.8 25.1 - - + -
215A ALA* 5.7 3.4 - - + +
218A LEU* 4.5 9.4 - - + -
231A ILE* 4.3 6.7 - - + -
236A GLY 3.0 24.2 + - - +
237A ILE 3.2 4.2 + - - +
239A ALA* 1.3 76.3 - - - +
241A VAL* 1.3 62.8 + - - +
243A MET* 3.1 15.1 + - + +
244A LEU* 3.3 14.6 + - - +
254A TYR 5.0 0.4 - - - +
255A ALA* 3.8 26.8 - - + +
258A THR* 3.7 32.3 - - + +
259A LEU* 4.0 18.8 - - + -
262A LEU* 3.9 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ILE* 3.1 26.7 + - + +
238A PRO 3.7 5.6 - - - +
239A ALA 3.2 0.2 - - - -
240A LEU* 1.3 74.1 - - - +
242A LYS* 1.3 64.6 + - - +
244A LEU* 3.3 15.0 + - + +
259A LEU* 4.4 13.9 - - + -
273A VAL* 4.6 7.4 - - + +
276A ALA* 3.6 39.7 - - + +
277A GLY 4.3 0.2 - - - -
278A GLY* 3.9 25.8 - - - +
281A LYS* 3.3 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLN* 2.7 39.3 + - - +
205A THR 5.8 0.6 + - - -
238A PRO 3.3 10.1 + - - +
239A ALA* 3.2 12.0 + - - +
241A VAL* 1.3 78.7 - - - +
243A MET* 1.3 80.5 + - + +
245A GLY* 3.0 22.0 + - - -
246A SER 4.2 0.2 + - - -
281A LYS* 4.7 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A MET* 3.2 54.1 - - + +
203A GLN* 3.7 10.8 - - - +
211A ALA* 5.7 4.5 - - - -
239A ALA 3.4 13.9 - - - +
240A LEU* 3.1 9.9 + - - +
242A LYS* 1.3 107.0 - - + +
244A LEU* 1.3 56.4 + - - +
245A GLY 3.0 5.2 - - - -
246A SER* 3.1 28.6 + - - +
251A VAL* 4.0 22.1 - - + +
252A LEU* 4.3 7.3 - - - -
255A ALA* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU 3.3 10.4 + - - +
241A VAL* 3.4 21.1 - - + +
242A LYS 3.1 0.8 - - - -
243A MET* 1.3 75.9 - - - +
245A GLY* 1.3 55.7 + - - +
246A SER 3.4 1.1 - - - +
252A LEU* 4.0 17.6 - - + +
255A ALA* 4.1 6.5 - - + -
256A ILE* 3.8 40.2 - - + +
259A LEU* 3.8 20.4 - - + -
278A GLY 4.5 2.0 - - - +
281A LYS* 4.2 20.8 - - + +
282A MET* 4.3 23.8 - - + -
285A LEU* 3.7 31.9 - - + +
----------------------------------------------------------
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