Contacts of the helix formed by residues 260 - 278 (chain C) in PDB entry 1GG3
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 SER 260 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C SER* 3.6 12.4 - - - -
258C LEU* 3.2 2.4 + - - +
259C PRO* 1.3 81.6 - - - +
261C TYR* 1.3 67.5 + - - +
262C ARG* 3.0 16.9 + - - +
263C ALA* 2.9 24.8 + - - +
264C ALA* 2.9 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C TYR* 4.3 9.3 - + + -
235C ARG* 3.0 46.5 + - - +
236C SER* 3.9 2.6 - - - +
260C SER* 1.3 75.9 - - - +
262C ARG* 1.3 90.2 + - + +
264C ALA* 3.0 1.6 + - - +
265C LYS* 2.6 55.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C SER* 3.0 12.2 + - - +
261C TYR* 1.3 110.0 + - + +
263C ALA* 1.3 53.2 + - - +
265C LYS* 3.1 5.3 + - - +
266C LYS* 2.8 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C HIS* 5.5 2.4 + - - +
258C LEU* 4.1 10.3 - - + +
259C PRO* 4.1 19.7 - - + -
260C SER* 2.9 27.4 + - - +
262C ARG* 1.3 76.7 - - - +
264C ALA* 1.3 57.1 + - - +
266C LYS* 3.7 12.7 - - - +
267C LEU* 3.4 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C TYR* 4.2 12.2 - - + +
235C ARG 3.9 14.6 - - - +
236C SER 4.0 7.9 - - - -
237C SER 4.5 2.7 - - - +
238C PHE* 4.2 2.7 - - + +
258C LEU* 3.5 28.5 - - + -
260C SER 2.9 14.1 + - - +
261C TYR 3.6 3.1 - - - +
263C ALA* 1.3 75.5 - - - +
265C LYS* 1.3 62.5 + - - +
266C LYS 3.2 0.7 - - - -
267C LEU* 3.7 2.3 - - - +
268C TRP* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C LYS* 5.5 9.0 - - - +
233C TYR* 3.4 38.6 - - + +
261C TYR* 2.6 34.4 + - + +
262C ARG* 3.6 4.5 - - - +
264C ALA* 1.3 71.4 - - - +
266C LYS* 1.3 57.5 + - - +
268C TRP* 3.1 18.4 + - + +
269C LYS* 2.7 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C SER* 3.7 23.4 + - - -
53C LYS 2.8 31.4 + - - -
54C THR* 4.1 24.3 + - + +
192C HIS* 4.9 20.0 - - + +
262C ARG* 2.8 20.3 + - + +
263C ALA* 3.7 11.9 - - - +
265C LYS* 1.3 78.8 - - - +
267C LEU* 1.3 59.0 + - - +
269C LYS* 3.4 6.2 + - - +
270C VAL* 3.0 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C HIS* 3.4 35.4 - - + +
204C LEU* 3.7 27.6 - - + -
206C VAL* 3.9 5.8 - - + -
211C LEU* 5.4 1.3 - - + -
238C PHE* 3.8 19.1 - - + -
258C LEU* 3.4 29.6 - - + -
263C ALA 3.4 14.1 + - - +
264C ALA 3.8 4.3 - - - +
265C LYS 3.2 0.2 - - - -
266C LYS* 1.3 77.0 - - - +
268C TRP* 1.3 67.8 + - - +
270C VAL* 3.2 5.8 + - - +
271C CYS* 3.0 42.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C ILE* 3.1 36.7 + - + -
232C SER* 3.6 17.4 - - - +
233C TYR* 3.8 32.5 - + + -
238C PHE* 3.7 14.4 - - + -
264C ALA 2.9 21.2 + - - +
265C LYS* 3.4 20.9 - - + +
267C LEU* 1.3 77.7 - - - +
269C LYS* 1.3 87.4 + - + +
271C CYS* 3.8 1.4 - - - +
272C VAL* 3.0 51.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 269 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TRP* 5.4 4.2 + - - +
57C ASP* 2.9 39.3 + - - +
60C LYS* 4.0 16.8 - - - +
265C LYS* 2.7 31.0 + - + +
266C LYS* 3.7 6.5 - - - +
268C TRP* 1.3 91.6 - - + +
270C VAL* 1.3 65.5 + - + +
272C VAL* 3.4 5.4 + - - +
273C GLU* 3.0 50.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 270 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TRP* 4.5 22.4 - - + +
78C LYS* 6.4 0.4 - - - -
190C ASP* 3.9 18.2 - - - +
192C HIS* 4.2 16.2 - - + +
206C VAL* 4.0 12.3 - - + -
266C LYS* 3.0 23.5 + - + +
267C LEU 3.2 5.8 + - - +
269C LYS* 1.3 76.5 - - + +
271C CYS* 1.3 64.7 + - - +
273C GLU* 2.9 13.7 + - - +
274C HIS* 2.9 50.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 271 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C VAL* 4.1 17.0 - - - -
211C LEU* 4.5 7.9 - - - -
225C TRP* 3.6 19.4 - - + -
231C ILE* 3.8 21.5 - - + -
238C PHE* 3.7 14.8 - - - -
240C ILE* 5.7 0.4 - - + -
267C LEU* 3.0 40.1 + - - +
268C TRP 3.8 3.6 - - - +
270C VAL* 1.3 79.5 - - - +
272C VAL* 1.3 64.4 + - - +
274C HIS 3.2 1.9 + - - -
275C HIS* 2.8 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 272 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C ILE* 4.0 17.7 - - + +
268C TRP* 3.0 52.3 + - + +
269C LYS* 3.7 5.6 - - - +
271C CYS* 1.3 76.1 - - - +
273C GLU* 1.3 68.2 + - + +
275C HIS* 3.0 7.7 + - + +
276C THR* 2.9 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 273 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TRP* 4.6 7.3 - - - +
57C ASP* 5.7 2.1 - - - -
78C LYS* 3.3 34.1 + - - -
79C PHE* 3.9 18.0 - - + -
269C LYS* 3.0 43.7 + - + +
270C VAL* 2.9 17.9 + - - +
272C VAL* 1.3 77.3 - - + +
274C HIS* 1.3 58.8 + - + +
276C THR* 3.0 9.5 + - - -
277C PHE* 2.8 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 274 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C TRP* 6.0 0.6 + - - -
78C LYS* 4.1 23.5 + - + +
79C PHE* 4.0 16.4 - + - -
80C TYR 5.7 0.7 - - - -
188C GLY 5.0 4.0 - - - -
190C ASP* 5.3 3.9 - - + +
206C VAL* 3.6 10.8 - - + +
207C CYS* 3.7 25.9 + - - -
225C TRP* 3.5 24.5 - - + +
270C VAL* 2.9 50.8 + - + +
271C CYS 3.7 1.3 - - - +
273C GLU* 1.3 72.7 - - + +
275C HIS* 1.3 66.0 + - - +
276C THR 2.8 1.6 + - - -
277C PHE 3.0 0.2 + - - -
278C PHE* 3.0 53.4 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 275 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C TRP* 3.7 48.3 + + + +
226C PRO* 5.5 1.2 - - - +
228C VAL* 3.4 31.7 + - + -
229C LEU* 5.2 6.7 - - + +
231C ILE* 4.3 8.5 - - + -
271C CYS 2.8 16.5 + - - +
272C VAL* 3.4 11.3 + - - +
274C HIS* 1.3 72.9 - - - +
276C THR* 1.3 66.3 + - - +
279C ARG* 3.1 53.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 276 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C VAL* 2.9 23.2 + - - +
273C GLU* 3.3 9.4 - - - -
274C HIS 2.8 1.2 + - - -
275C HIS* 1.3 83.6 + - - +
277C PHE* 1.3 68.1 + - - +
279C ARG* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 277 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TYR* 4.0 22.4 - - + -
42C PHE* 3.8 44.2 - + - -
79C PHE* 3.5 55.2 - + + -
273C GLU 2.8 10.1 + - - +
274C HIS* 3.8 1.6 - - - +
276C THR* 1.3 78.0 - - - +
278C PHE* 1.3 86.8 + + - +
279C ARG* 3.1 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 278 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C PHE* 5.6 1.3 - + - -
79C PHE* 3.7 26.9 - + + -
80C TYR 3.7 25.1 - - - -
81C PRO* 4.8 1.6 - - + -
82C PRO* 4.2 15.0 - - + -
207C CYS 4.4 0.2 - - - -
208C SER* 3.4 37.2 - - - +
225C TRP* 4.4 14.8 - - + +
226C PRO* 5.8 1.4 - - - +
274C HIS* 3.0 46.1 + + + +
275C HIS 4.3 0.4 - - - -
277C PHE* 1.3 97.0 - + - +
279C ARG* 1.3 70.4 + - - +
----------------------------------------------------------
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