Contacts of the helix formed by residues 239 - 264 (chain C) in PDB entry 3GTL
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 PRO 239 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LYS* 4.7 7.4 - - + +
73C GLN* 4.6 4.3 - - - +
75C MET* 4.5 28.7 - - + -
234C SER* 4.8 1.6 - - - +
236C GLY* 4.1 6.3 - - - +
237C SER 4.2 4.7 - - - +
238C ILE* 1.4 87.5 - - + +
240C VAL* 1.3 71.9 + - + +
241C ASP* 2.9 8.2 + - - +
242C GLN* 2.9 32.5 + - + +
243C VAL* 5.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C SER 3.4 13.5 - - - +
15C LYS* 3.3 25.3 + - - +
16C ASP* 3.1 37.2 - - - +
17C ASN 3.3 1.3 - - - +
18C VAL* 3.1 27.8 - - + +
232C VAL* 3.5 5.7 - - + +
234C SER* 3.8 16.0 + - - -
238C ILE 3.8 3.0 + - - -
239C PRO* 1.3 72.4 - - + +
241C ASP* 1.3 69.0 + - - +
243C VAL* 3.0 19.1 + - - +
244C VAL* 3.3 14.1 - - - +
109K TRP* 3.8 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C PRO* 2.9 13.1 + - - +
240C VAL* 1.3 78.8 - - - +
242C GLN* 1.3 85.9 + - - +
244C VAL* 3.3 11.0 - - - +
245C VAL* 3.0 34.8 + - - +
105K PHE* 3.7 4.2 - - + -
106K GLU* 5.0 3.6 - - - +
109K TRP* 3.1 58.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 242 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C MET* 4.8 9.4 - - + +
238C ILE* 3.1 23.6 - - + -
239C PRO* 2.9 15.5 + - + +
241C ASP* 1.3 94.3 + - - +
243C VAL* 1.3 54.6 + - - +
245C VAL* 3.1 25.0 + - - +
246C ARG* 2.5 68.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C MET* 3.8 19.7 - - + -
41C ILE* 3.7 18.6 - - + +
172C PRO* 3.5 27.8 - - + +
173C ALA* 4.9 3.4 - - + -
232C VAL* 3.7 29.2 - - + -
233C GLU 5.4 0.4 - - - +
234C SER* 5.1 6.5 - - - -
238C ILE* 3.4 24.1 - - + +
240C VAL* 3.0 13.6 + - - +
242C GLN* 1.3 82.5 - - - +
244C VAL* 1.3 65.7 + - - +
246C ARG* 3.6 1.1 - - - +
247C GLY* 2.8 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 244 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C VAL* 4.6 11.4 - - + -
20C PHE* 4.9 9.9 - - + -
33C LEU* 6.2 3.1 - - + -
37C MET* 4.2 11.5 - - + +
232C VAL* 4.7 14.6 - - + -
240C VAL 3.3 12.1 - - - +
241C ASP* 3.3 13.9 - - - +
243C VAL* 1.3 77.9 - - + +
245C VAL* 1.3 51.0 + - - +
247C GLY* 3.1 0.9 + - - -
248C ILE* 2.9 57.8 + - + +
101K LEU* 5.9 0.2 - - + -
105K PHE* 3.3 42.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 245 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C ASP* 3.0 24.9 + - - +
242C GLN* 3.2 24.0 - - - +
243C VAL 2.9 0.8 + - - -
244C VAL* 1.3 72.9 - - - +
246C ARG* 1.3 66.1 + - + +
247C GLY 3.0 1.1 - - - -
248C ILE* 3.3 9.6 + - + +
249C ASP* 2.9 30.8 + - - +
102K LYS* 4.1 16.6 - - + +
105K PHE* 3.6 25.6 - - + -
106K GLU* 4.2 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ILE* 3.4 17.5 - - + -
42C PRO 5.4 0.4 + - - -
74C SER 3.8 2.8 + - - -
75C MET* 3.1 37.4 + - - +
77C ILE* 4.5 3.0 - - - +
78C GLU* 3.0 50.7 + - - +
238C ILE* 3.5 34.3 - - - +
242C GLN* 2.5 62.5 + - - +
243C VAL* 3.8 2.0 - - - +
245C VAL* 1.3 76.7 - - + +
247C GLY* 1.3 53.0 + - - +
249C ASP* 3.4 9.8 - - + +
250C THR* 2.4 38.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 4.8 1.6 - - - -
36C VAL* 3.7 11.5 - - - +
37C MET* 3.9 17.0 - - - -
41C ILE* 3.8 12.5 - - - +
243C VAL 2.8 12.4 + - - -
244C VAL 3.5 3.8 - - - -
246C ARG* 1.3 74.8 - - - +
248C ILE* 1.3 65.6 + - - +
249C ASP 3.0 1.1 + - - -
250C THR 3.2 0.2 + - - -
251C LEU* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 3.7 17.0 - - + +
244C VAL* 2.9 43.5 + - + +
245C VAL* 3.6 8.3 - - - +
247C GLY* 1.3 76.3 - - - +
249C ASP* 1.3 61.6 + - - +
251C LEU* 4.0 3.9 - - - +
252C GLN* 3.3 21.6 + - + +
98K LEU* 3.4 31.6 - - + +
101K LEU* 3.5 41.1 - - + -
102K LYS* 3.8 24.5 - - + +
105K PHE* 4.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLU* 5.5 3.7 - - - +
245C VAL* 2.9 20.7 + - - +
246C ARG* 3.4 14.8 - - + +
248C ILE* 1.3 77.9 - - - +
250C THR* 1.3 57.8 + - - +
252C GLN* 3.1 20.3 + - - +
253C LYS* 2.9 55.0 + - - +
102K LYS* 3.9 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL* 4.4 10.3 - - + -
40C GLU* 3.9 24.5 - - + +
41C ILE* 2.9 17.1 - - - +
42C PRO* 4.8 6.8 - - + +
78C GLU* 5.5 0.9 + - - -
246C ARG* 2.4 29.8 + - - +
247C GLY 3.2 2.0 + - - -
249C ASP* 1.3 69.1 - - - +
251C LEU* 1.3 58.1 + - - +
252C GLN 3.0 1.3 - - - -
253C LYS* 2.8 20.7 + - + +
254C LYS* 2.8 38.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C MET 4.7 1.3 - - - +
32C SER 3.4 27.8 - - - +
33C LEU* 3.7 25.8 - - + +
36C VAL* 3.7 18.1 - - + +
247C GLY 3.1 14.3 + - - +
248C ILE 4.0 2.9 - - - +
250C THR* 1.3 77.6 - - - +
252C GLN* 1.3 56.1 + - - +
254C LYS* 3.8 7.5 + - + +
255C VAL* 3.0 38.3 + - + +
41K THR* 4.1 15.3 - - + +
42K LEU* 5.7 1.8 - - + -
45K LEU* 4.2 18.6 - - + -
98K LEU* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ILE* 3.3 12.5 + - - +
249C ASP* 3.1 18.6 + - - +
250C THR 3.0 0.8 - - - -
251C LEU* 1.3 75.2 - - - +
253C LYS* 1.3 61.1 + - + +
255C VAL* 3.4 6.4 + - - +
256C ALA* 3.0 27.2 + - - +
95K ILE* 3.5 36.9 + - + +
98K LEU* 3.8 14.8 - - + +
99K GLY* 3.4 32.7 - - - +
102K LYS* 3.2 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLU* 5.5 12.1 - - - +
249C ASP* 2.9 44.7 + - + +
250C THR* 2.8 22.0 + - + +
252C GLN* 1.3 78.0 - - + +
254C LYS* 1.3 56.9 + - - +
255C VAL 3.1 0.2 - - - -
256C ALA* 2.9 9.7 + - - +
257C SER* 2.9 26.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C VAL* 4.8 1.3 - - + -
40C GLU* 2.7 35.4 - - - +
165C LYS* 5.5 4.8 - - - +
250C THR* 2.8 25.3 + - + +
251C LEU* 3.9 12.8 - - + +
253C LYS* 1.3 72.7 - - + +
255C VAL* 1.3 59.7 + - - +
257C SER* 3.3 20.0 + - - +
258C ILE* 3.6 5.5 - - - +
10K PHE* 5.8 5.9 - - - +
37K LYS 4.4 4.0 + - - -
38K GLU* 2.8 32.4 + - - +
41K THR* 5.3 3.1 - - + -
42K LEU* 3.2 41.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C LEU* 3.0 33.7 + - + +
252C GLN* 3.7 7.6 - - - +
253C LYS 3.1 0.8 - - - -
254C LYS* 1.3 79.8 - - - +
256C ALA* 1.3 62.6 + - - +
258C ILE* 3.3 24.3 - - - +
259C LEU* 3.6 5.0 + - - +
42K LEU* 4.9 13.0 - - + -
45K LEU* 5.4 3.4 - - + -
46K ILE* 5.9 4.5 - - + -
91K CYS* 3.9 21.8 - - + +
94K ILE* 4.1 26.2 - - + -
95K ILE* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C GLN* 3.0 13.5 + - + +
253C LYS* 2.9 10.6 + - - +
255C VAL* 1.3 74.4 - - - +
257C SER* 1.3 51.1 + - - +
258C ILE 2.9 5.2 - - - -
259C LEU* 2.8 12.8 + - + +
260C LEU* 2.8 35.4 + - - +
95K ILE* 4.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C LYS 2.9 12.3 + - - -
254C LYS* 3.3 22.1 + - - +
256C ALA* 1.3 74.9 - - - +
258C ILE* 1.3 56.9 + - - +
260C LEU* 3.9 14.0 - - - +
261C ALA* 3.2 24.1 + - - +
18K LYS* 4.7 17.2 - - - +
38K GLU* 5.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C LYS 3.6 17.9 - - - +
255C VAL* 3.3 9.8 + - - +
256C ALA 2.9 0.8 - - - -
257C SER* 1.3 76.9 + - - +
259C LEU* 1.3 69.3 + - - +
260C LEU 3.0 1.3 - - - -
261C ALA* 2.7 17.2 + - - +
262C LEU* 2.9 24.4 + - + +
18K LYS* 4.7 13.2 - - + -
19K LEU* 4.6 12.6 - - + -
35K PHE* 4.0 25.6 - - + -
38K GLU* 5.1 0.2 - - - +
42K LEU* 3.3 35.9 - - + -
46K ILE* 4.3 3.6 - - + -
87K LEU* 5.0 2.7 - - + -
91K CYS* 3.7 25.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C VAL 3.6 2.1 + - - +
256C ALA* 2.8 18.7 + - + +
258C ILE* 1.3 80.5 - - - +
260C LEU* 1.3 61.2 + - - +
262C LEU* 3.3 16.2 + - + +
263C THR* 3.0 18.7 + - - -
88K LYS* 4.4 11.4 - - + +
91K CYS* 3.3 35.0 - - + -
92K ASN* 3.8 37.5 - - - +
95K ILE* 4.6 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C ALA 2.8 14.6 + - - +
257C SER* 3.9 11.9 - - - +
259C LEU* 1.3 78.0 - - - +
261C ALA* 1.3 60.8 + - - +
263C THR* 3.3 22.8 + - + -
264C GLN* 2.9 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C SER 3.2 17.1 + - - +
258C ILE* 2.7 15.5 + - - +
260C LEU* 1.3 73.7 - - - +
262C LEU* 1.3 62.1 + - - +
264C GLN* 3.3 21.5 + - - +
265C MET* 3.8 14.6 + - - +
18K LYS* 4.4 22.9 - - + -
19K LEU* 4.4 15.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C ILE* 2.9 21.3 + - + +
259C LEU* 3.6 11.7 - - + +
261C ALA* 1.3 73.9 - - - +
263C THR* 1.3 64.0 + - - +
265C MET* 3.3 15.5 + - + +
266C ASP* 3.1 20.8 - - - +
19K LEU* 3.7 25.4 - - + -
21K ILE* 5.3 5.8 - - + -
84K LYS* 4.7 16.8 - - + +
87K LEU* 3.8 29.6 - - + -
88K LYS* 3.8 40.8 - - + +
91K CYS* 5.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C LEU 3.0 14.8 + - - -
260C LEU* 3.5 18.5 - - + +
262C LEU* 1.3 77.6 - - - +
264C GLN* 1.3 61.7 + - + +
265C MET 3.6 0.5 + - - -
266C ASP* 4.2 16.1 + - - +
267C GLN* 4.8 7.8 + - - -
88K LYS* 5.7 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C LEU* 2.9 38.1 + - + +
261C ALA* 3.3 17.3 - - - +
262C LEU 3.2 0.8 - - - -
263C THR* 1.3 78.4 - - + +
265C MET* 1.3 59.8 + - - +
267C GLN* 3.9 20.1 - - - +
268C ASP 5.2 0.2 + - - -
----------------------------------------------------------
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