Contacts of the helix formed by residues 237 - 252 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C SER* 3.3 8.9 + - - -
236C GLY* 1.3 78.8 - - - +
238C VAL* 1.3 60.2 + - - -
239C ASP 3.8 0.2 - - - -
241C SER* 2.6 34.5 + - - -
397C MET* 5.3 2.2 - - - -
400C ARG* 4.2 9.9 - - - -
526C POP 3.3 24.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C GLY* 1.3 69.4 - - - -
239C ASP* 1.3 68.7 + - - +
241C SER* 3.2 4.6 + - - -
242C VAL* 2.9 23.6 + - - +
381C LYS* 4.0 15.5 - - + -
384C VAL* 3.8 22.0 - - + -
385C ARG* 4.6 10.3 - - + +
397C MET* 4.0 15.5 - - - +
398C LEU* 3.8 38.8 - - + +
400C ARG* 5.2 7.6 - - + +
526C POP 3.0 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 239 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C VAL* 1.3 74.2 - - - +
240C SER* 1.3 53.1 + - - +
242C VAL 3.4 0.3 + - - -
243C THR* 2.7 38.1 + - - -
335C GLY* 3.3 27.7 - - - +
337C ILE* 3.9 20.6 - - - +
340C ASP* 5.3 1.2 - - - +
376C LEU* 3.4 10.2 - - + +
381C LYS* 2.8 35.7 + - - +
384C VAL* 4.0 4.2 - - - +
526C POP 2.9 29.1 + - - +
527C AMP 5.2 0.2 - - - +
530C MG 3.8 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C LEU* 3.9 7.9 - - - +
233C GLY 3.7 18.6 - - - -
234C LEU* 4.3 4.9 - - - +
235C SER* 2.9 21.7 + - - -
236C GLY 4.1 1.6 + - - -
237C GLY 3.9 3.8 + - - -
239C ASP* 1.3 72.9 - - - +
241C SER* 1.3 55.6 + - - +
243C THR* 3.3 8.5 + - - -
244C ALA* 2.7 35.6 + - - +
335C GLY* 5.0 2.2 - - - -
526C POP 2.7 27.7 + - - -
527C AMP 3.3 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C LEU* 4.4 2.3 - - - +
236C GLY* 4.0 6.8 - - - -
237C GLY 2.6 24.2 + - - -
238C VAL* 3.2 5.2 + - - -
240C SER* 1.3 77.2 + - - +
242C VAL* 1.3 64.2 + - - +
244C ALA* 3.3 5.0 + - - +
245C MET* 3.1 27.2 + - - +
277C PHE* 3.4 32.5 - - - -
393C LEU* 4.0 13.7 - - - -
397C MET* 3.9 12.6 - - - -
398C LEU* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C VAL 2.9 19.8 + - - +
239C ASP 4.0 1.1 - - - +
241C SER* 1.3 72.8 - - - +
243C THR* 1.3 66.5 + - - +
245C MET* 3.4 3.9 + - - +
246C LEU* 3.0 22.8 + - + +
376C LEU* 4.1 9.2 - - + -
384C VAL* 3.7 30.3 - - + +
387C ILE* 3.5 36.3 - - + -
388C GLY* 3.8 15.7 - - - +
391C LEU* 4.2 10.0 - - + +
393C LEU* 4.0 10.8 - - + -
398C LEU* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C LEU* 4.1 13.7 - - + -
239C ASP 2.7 24.7 + - - -
240C SER* 3.5 8.7 - - - -
241C SER 3.2 0.2 - - - -
242C VAL* 1.3 78.0 - - - +
244C ALA* 1.3 62.5 + - - +
246C LEU* 3.2 6.3 + - - +
247C LEU* 2.9 43.5 + - + +
333C ALA* 4.3 2.0 - - + -
334C GLN 3.9 12.1 + - - +
335C GLY* 3.3 11.7 - - - -
375C PRO* 3.9 18.8 - - + -
376C LEU* 3.3 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C LEU* 3.6 18.8 - - + +
234C LEU* 4.0 17.5 - - + -
240C SER 2.7 21.0 + - - +
241C SER* 3.4 7.0 - - - +
242C VAL 3.3 0.2 - - - -
243C THR* 1.3 74.5 - - - +
245C MET* 1.3 53.1 + - - +
247C LEU 3.4 0.2 + - - -
248C HIS* 2.8 36.9 + - - +
255C LEU* 3.7 7.1 - - - +
257C CYS* 4.5 2.2 - - - -
277C PHE* 4.5 3.8 - - + -
283C LEU* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C SER 3.1 15.0 + - - +
242C VAL 3.9 0.7 - - - +
244C ALA* 1.3 76.9 - - - +
246C LEU* 1.3 66.4 + - - +
248C HIS* 3.6 11.3 - - + +
249C ARG* 3.1 23.4 + - - +
277C PHE* 4.0 22.0 - - + -
281C PHE* 3.6 42.8 - - + -
283C LEU* 4.6 7.9 - - + -
391C LEU* 3.7 43.4 - - + +
393C LEU* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C ILE* 6.5 0.2 - - + -
214C ILE* 4.0 28.9 - - + -
217C ALA* 4.0 20.0 - - + -
218C VAL* 4.2 13.4 - - + +
221C ILE* 4.6 7.6 - - + -
242C VAL 3.0 16.3 + - - +
243C THR* 3.5 5.6 - - - +
245C MET* 1.3 76.6 - - - +
247C LEU* 1.3 57.1 + - - +
249C ARG* 3.2 7.1 + - + +
250C ALA* 3.0 26.3 + - - +
375C PRO* 4.0 18.8 - - + +
376C LEU* 3.9 27.6 - - + -
379C LEU* 5.9 0.4 - - + -
387C ILE* 4.2 10.5 - - + -
391C LEU* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ILE* 3.8 34.1 - - + -
225C VAL* 5.7 0.2 - - + -
230C VAL* 4.5 6.1 - - + -
232C LEU* 4.1 4.3 - - + -
243C THR* 2.9 31.1 + - + +
244C ALA 3.8 2.7 - - - +
246C LEU* 1.3 74.5 - - - +
248C HIS* 1.3 61.0 + - - +
250C ALA* 4.2 3.8 - - - -
251C ILE* 2.8 49.4 + - + +
255C LEU* 3.9 25.1 - - + -
333C ALA* 3.3 31.0 - - + -
373C VAL* 4.4 13.5 - - + -
375C PRO* 4.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ALA 2.8 23.4 + - - +
245C MET* 3.6 17.3 - - + +
246C LEU 3.3 0.2 - - - -
247C LEU* 1.3 73.0 - - - +
249C ARG* 1.3 62.7 + - + +
252C GLY* 2.9 44.8 + - - +
255C LEU* 3.9 7.5 - - + +
281C PHE* 3.6 23.3 + - + -
282C GLY 3.8 11.9 - - - -
283C LEU* 3.4 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C ILE* 3.7 28.7 - - - +
215C ASP* 3.9 14.1 + - - -
218C VAL* 4.0 16.2 - - + +
222C ARG* 3.3 18.3 + - - +
245C MET 3.1 10.4 + - - +
246C LEU* 3.4 11.0 - - + +
247C LEU 3.1 0.4 - - - -
248C HIS* 1.3 84.6 - - + +
250C ALA* 1.3 59.4 + - - +
252C GLY 4.6 0.6 + - - -
390C GLU 5.3 4.0 + - - -
391C LEU* 3.6 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C VAL* 3.9 16.2 - - + +
221C ILE* 3.6 38.4 - - + -
222C ARG* 3.0 32.8 + - + +
246C LEU 3.0 15.2 + - - +
247C LEU 3.0 2.9 + - - +
249C ARG* 1.3 79.4 - - - +
251C ILE* 1.3 60.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C ILE* 4.4 10.1 - - + -
222C ARG* 4.9 6.3 - - + -
225C VAL* 4.5 9.2 - - + -
226C GLY 4.2 17.9 - - - +
230C VAL* 3.5 37.7 - - + -
247C LEU* 2.8 35.4 + - + +
250C ALA* 1.3 84.2 - - + +
252C GLY* 1.3 63.2 + - - +
253C LYS* 3.0 3.8 + - - +
254C ASN* 3.1 28.6 + - + +
255C LEU* 4.1 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C LEU 3.6 2.6 + - - -
248C HIS* 2.9 41.7 + - - -
249C ARG 4.6 0.2 - - - -
250C ALA 3.8 0.8 - - - -
251C ILE* 1.3 72.4 - - - +
253C LYS* 1.3 61.9 + - - -
254C ASN 3.2 1.0 + - - -
255C LEU* 3.3 21.0 + - - +
284C ASN* 4.9 0.3 + - - -
----------------------------------------------------------
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