Contacts of the helix formed by residues 241 - 252 (chain C) in PDB entry 3GBA
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 241 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C GLN 3.1 15.8 + - - -
239C GLU 3.2 1.4 + - - -
240C GLU* 1.3 77.4 - - - +
242C LYS* 1.3 57.6 + - - +
243C LEU 3.4 2.5 - - - -
244C HIS* 3.4 13.4 + - - +
245C MET* 3.0 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 4.2 18.8 + - - +
237C LEU* 2.9 39.1 + - + +
240C GLU* 3.8 33.4 - - + +
241C GLY* 1.3 76.5 - - - +
243C LEU* 1.3 61.0 + - - +
245C MET* 3.3 18.9 + - + +
246C MET* 2.9 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TYR* 3.9 17.5 + - - +
39C LEU* 4.1 21.8 - - + -
105C PHE* 3.7 37.9 - - + +
234C ILE* 3.9 10.5 - - + +
237C LEU* 3.5 25.1 + - + -
238C GLN* 3.9 36.6 - - + +
241C GLY 3.4 0.4 - - - -
242C LYS* 1.3 76.4 - - - +
244C HIS* 1.3 63.0 - - - +
246C MET* 3.3 11.6 + - - +
247C LYS* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C GLN 5.9 0.4 + - - -
241C GLY* 3.4 16.2 + - - +
242C LYS 3.3 0.2 - - - -
243C LEU* 1.3 78.1 - - - +
245C MET* 1.3 66.2 + - + +
247C LYS* 3.3 6.6 + - - +
248C GLU* 3.0 27.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
240C GLU 5.2 3.1 - - - +
241C GLY 3.0 24.6 + - - +
242C LYS* 3.6 20.9 - - + +
243C LEU 3.3 0.2 - - - -
244C HIS* 1.3 81.2 - - + +
246C MET* 1.3 59.4 + - + +
248C GLU* 3.4 8.0 + - - +
249C LYS* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TYR* 3.6 34.7 - - + +
38C ASP* 3.9 15.0 - - + +
39C LEU* 3.5 43.3 - - + +
42C GLU* 4.6 15.3 - - - +
237C LEU* 5.3 1.1 - - - -
242C LYS* 2.9 29.7 + - + +
243C LEU* 3.7 11.0 - - + +
245C MET* 1.3 75.7 - - + +
247C LYS* 1.3 65.4 + - - +
249C LYS* 3.3 7.8 + - + -
250C TRP* 3.2 32.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TYR* 3.6 11.1 - - + -
106C MET* 4.1 26.4 - - + +
107C THR 5.3 1.6 + - - -
192C THR* 4.4 13.1 - - - +
195C GLU* 3.6 23.4 + - - -
243C LEU 3.0 15.8 + - - +
244C HIS* 3.8 6.1 - - - +
245C MET 3.3 0.2 - - - -
246C MET* 1.3 77.0 - - - +
248C GLU* 1.3 63.7 + - - +
250C TRP 3.3 0.5 + - - -
251C TRP* 3.0 65.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C HIS* 3.0 25.5 + - + +
245C MET* 3.7 7.9 - - - +
247C LYS* 1.3 75.8 - - - +
249C LYS* 1.3 70.1 + - - +
251C TRP* 5.0 2.2 - - - -
252C ARG* 2.9 67.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP* 2.8 33.4 + - - +
245C MET 2.9 18.3 + - - +
246C MET* 3.5 9.9 - - + +
247C LYS 3.2 0.2 - - - -
248C GLU* 1.3 86.3 + - - +
250C TRP* 1.3 86.0 + - + +
252C ARG* 3.9 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PRO* 3.9 10.0 - - + +
18C MET* 3.5 32.3 - - + -
33C GLU* 3.9 22.7 - - + -
34C GLY* 3.5 28.7 - - - -
35C TYR* 3.5 24.6 - + + +
38C ASP* 2.9 27.2 + - - -
196C TYR* 3.4 21.5 + - - -
200C ARG* 4.1 2.3 + - - -
246C MET* 3.2 24.9 + - + +
249C LYS* 1.3 105.0 - - + +
251C TRP* 1.3 80.5 - - + +
252C ARG 4.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C PRO* 3.7 26.5 - - + -
16C TYR* 3.4 44.4 - + - -
35C TYR* 4.0 16.4 - + + -
106C MET* 4.0 4.9 - - + -
192C THR* 3.0 29.2 + - - -
195C GLU* 3.8 29.1 - - + +
196C TYR* 3.7 20.6 - + + +
199C GLN* 5.6 2.3 - - - +
200C ARG* 3.0 18.5 + - - +
247C LYS* 3.0 60.3 + - + +
248C GLU* 4.5 1.8 - - - +
250C TRP* 1.3 88.0 - - + +
252C ARG* 1.3 66.2 + - - +
253C GLY 3.4 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C ARG* 3.2 11.1 + - - -
248C GLU* 2.9 51.1 + - - +
249C LYS* 4.1 9.4 - - - +
250C TRP 3.5 2.5 - - - +
251C TRP* 1.3 76.5 - - - +
253C GLY* 1.3 65.4 + - - +
----------------------------------------------------------
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