Contacts of the helix formed by residues 237 - 252 (chain D) in PDB entry 1GPM
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 237 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D SER* 3.0 8.3 + - - -
236D GLY* 1.3 81.4 - - - +
238D VAL* 1.3 65.3 + - - -
240D SER* 3.2 3.6 + - - -
241D SER* 2.9 24.5 + - - -
397D MET* 5.3 0.4 - - - -
400D ARG* 4.9 3.6 - - - -
526D POP 3.2 27.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D GLY* 1.3 70.1 - - - -
239D ASP* 1.3 59.0 + - - +
241D SER* 3.3 4.7 + - - -
242D VAL* 3.0 39.9 + - + +
381D LYS* 3.9 15.7 - - - -
384D VAL* 3.8 22.0 - - + -
385D ARG* 4.5 9.6 - - + +
397D MET* 3.7 20.8 + - - +
398D LEU* 3.5 34.3 - - + +
400D ARG* 5.1 9.1 - - + +
526D POP 3.2 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D VAL* 1.3 75.7 - - - +
240D SER* 1.3 54.2 + - - +
243D THR* 2.6 38.4 + - - -
335D GLY* 3.4 20.9 - - - +
337D ILE* 3.8 26.9 - - - +
340D ASP* 5.3 1.2 - - - +
376D LEU* 3.4 9.7 - - + +
381D LYS* 3.3 29.5 + - - +
384D VAL* 3.8 7.7 - - - +
526D POP 3.1 30.7 + - - +
527D AMP 5.2 0.4 - - - +
530D MG 3.8 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D LEU* 4.2 5.7 - - - +
233D GLY 3.7 23.8 - - - -
234D LEU* 4.0 5.6 - - - +
235D SER* 2.7 32.1 + - - -
236D GLY 3.8 1.4 + - - -
237D GLY 3.2 3.3 + - - -
239D ASP* 1.3 73.4 - - - +
241D SER* 1.3 58.4 + - - +
243D THR* 3.3 7.7 + - - -
244D ALA* 2.9 31.2 + - - +
335D GLY* 4.8 3.6 - - - -
526D POP 2.7 19.1 + - - -
527D AMP 3.8 11.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D LEU* 4.2 6.3 - - - +
236D GLY* 3.7 16.3 + - - -
237D GLY 2.9 21.4 + - - -
238D VAL 3.7 3.8 - - - -
240D SER* 1.3 78.1 + - - +
242D VAL* 1.3 56.0 + - - +
244D ALA* 3.4 3.2 + - - +
245D MET* 3.1 33.4 + - - +
277D PHE* 3.3 32.4 - - - -
393D LEU* 4.3 2.5 - - - -
397D MET* 3.7 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D VAL* 3.0 17.9 + - + +
239D ASP 4.2 1.8 - - - +
241D SER* 1.3 72.4 - - - +
243D THR* 1.3 60.7 + - - +
245D MET* 3.4 2.9 + - - +
246D LEU* 3.0 28.5 + - + +
376D LEU* 4.1 5.6 - - + -
384D VAL* 3.7 29.4 - - + +
387D ILE* 3.6 37.7 - - + -
388D GLY* 4.1 2.5 - - - -
391D LEU* 4.0 9.1 - - + +
393D LEU* 3.9 20.9 - - + -
398D LEU* 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D LEU* 4.0 15.9 - - + -
239D ASP 2.6 22.8 + - - -
240D SER* 3.5 8.1 - - - -
242D VAL* 1.3 77.0 - - - +
244D ALA* 1.3 57.3 + - - +
246D LEU* 3.3 6.2 + - - +
247D LEU* 2.9 48.1 + - + +
333D ALA* 4.6 0.9 - - + -
334D GLN 4.0 7.4 + - - +
335D GLY* 3.2 15.9 - - - -
375D PRO* 4.0 20.6 - - + -
376D LEU* 3.3 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D LEU* 3.5 21.8 - - + -
234D LEU* 4.4 9.2 - - + -
240D SER 2.9 17.2 + - - +
241D SER* 3.7 5.4 - - - +
242D VAL 3.3 0.2 - - - -
243D THR* 1.3 76.3 - - - +
245D MET* 1.3 52.8 + - - +
247D LEU* 3.3 1.2 + - - -
248D HIS* 2.7 37.5 + - - +
255D LEU* 3.7 6.7 - - - +
257D CYS* 4.1 6.5 - - - -
277D PHE* 5.2 1.1 - - + -
283D LEU* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D SER 3.1 17.4 + - - +
242D VAL* 3.9 1.6 - - - +
243D THR 3.3 0.2 - - - -
244D ALA* 1.3 75.9 - - - +
246D LEU* 1.3 60.6 + - - +
248D HIS* 3.6 12.9 - - + +
249D ARG* 3.1 22.3 + - - +
277D PHE* 4.5 3.6 - - + -
281D PHE* 3.6 48.7 - - + -
283D LEU* 4.3 19.3 - - + -
391D LEU* 3.6 44.2 - - + +
393D LEU* 4.0 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D ILE* 4.1 28.9 - - + -
217D ALA* 4.0 24.2 - - + -
218D VAL* 4.5 7.5 - - + +
221D ILE* 4.4 8.9 - - + +
242D VAL 3.0 16.6 + - - +
243D THR* 3.6 5.2 - - - +
245D MET* 1.3 74.3 - - - +
247D LEU* 1.3 64.9 + - - +
249D ARG* 3.1 6.8 + - - +
250D ALA* 3.0 22.7 + - - +
375D PRO* 4.0 17.7 - - + +
376D LEU* 3.7 28.7 - - + -
379D LEU* 6.0 0.2 - - + -
387D ILE* 4.3 9.0 - - + -
391D LEU* 3.9 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D ILE* 3.8 34.8 - - + -
230D VAL* 4.4 5.8 - - + -
232D LEU* 4.3 3.8 - - + -
243D THR* 2.9 30.0 + - + +
244D ALA 3.8 2.7 - - - +
246D LEU* 1.3 77.7 - - - +
248D HIS* 1.3 62.8 + - - +
250D ALA* 4.3 3.1 - - - +
251D ILE* 2.9 45.7 + - + +
255D LEU* 3.9 26.5 - - + -
333D ALA* 3.4 30.7 - - + -
373D VAL* 4.3 13.0 - - + -
375D PRO* 4.5 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D ALA 2.7 21.2 + - - +
245D MET* 3.6 18.8 - - + +
246D LEU 3.2 0.2 - - - -
247D LEU* 1.3 72.5 - - - +
249D ARG* 1.3 62.7 + - + +
252D GLY* 3.0 42.3 + - - +
255D LEU* 4.0 8.1 - - + +
281D PHE 4.1 8.2 + - - -
282D GLY 3.9 20.1 + - - -
283D LEU* 3.8 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D ILE* 3.7 26.3 - - - +
215D ASP* 3.5 23.0 + - - -
218D VAL* 3.9 20.4 - - + +
222D ARG* 3.4 14.1 + - - +
245D MET 3.1 12.2 + - - +
246D LEU* 3.4 9.6 - - - +
248D HIS* 1.3 86.4 - - + +
250D ALA* 1.3 59.0 + - - +
252D GLY 4.8 0.3 + - - -
390D GLU 6.0 0.4 + - - -
391D LEU* 4.2 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D VAL* 3.6 26.2 - - + +
221D ILE* 3.7 35.4 - - + -
222D ARG* 2.8 25.5 + - + +
246D LEU 3.0 15.1 + - - +
247D LEU 3.1 2.6 + - - +
249D ARG* 1.3 79.3 - - - +
251D ILE* 1.3 63.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D ILE* 4.0 19.3 - - + -
222D ARG* 4.9 4.9 - - + -
225D VAL* 4.4 13.2 - - + -
226D GLY 4.5 9.9 - - - +
228D ASP 4.7 1.1 - - - +
230D VAL* 3.7 33.2 - - + -
247D LEU* 2.9 30.0 + - + +
250D ALA* 1.3 79.1 - - - +
252D GLY* 1.3 73.0 + - - +
253D LYS 3.3 0.7 + - - -
254D ASN* 3.2 47.3 + - + +
255D LEU* 4.1 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D LEU 3.8 0.6 + - - +
248D HIS* 3.0 36.4 + - - -
249D ARG 4.7 0.8 + - - -
250D ALA 3.8 0.4 - - - -
251D ILE* 1.3 77.9 - - - +
253D LYS* 1.3 53.2 + - - -
254D ASN 2.7 14.0 + - - -
255D LEU* 3.1 19.8 + - - +
----------------------------------------------------------
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