Contacts of the helix formed by residues 240 - 257 (chain A) in PDB entry 2KTY
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 ARG 240 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 6.1 1.1 - - - -
169A HIS* 3.5 24.3 + - + +
204A TYR* 3.9 10.8 + - - -
210A HIS* 5.5 9.3 - - - -
238A PRO 2.7 10.9 + - - -
239A SER* 1.3 93.6 + - - +
241A ARG* 1.3 64.0 + - - +
242A GLY 3.1 1.4 + - - -
243A ASP* 3.1 7.7 + - - +
244A LEU* 2.9 33.9 + - + +
312A THR* 4.3 10.3 + - - +
313A GLU 3.5 21.6 + - - -
314A LYS* 4.7 10.1 - - - +
315A PRO* 3.5 53.6 - - + +
317A TYR* 5.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ILE* 5.5 1.8 - - - +
231A ASP* 5.2 4.2 + - - +
239A SER 2.6 13.0 + - - +
240A ARG* 1.3 72.5 - - - +
242A GLY* 1.3 59.0 + - - +
244A LEU* 4.4 7.1 - - - +
245A GLU* 2.8 63.3 + - - +
279A ARG* 3.3 26.1 - - - +
306A VAL* 3.4 23.7 - - - +
307A LYS* 3.1 37.0 + - - +
309A LEU* 5.1 5.4 - - + -
310A ASP 2.9 24.7 + - - +
311A TYR* 3.0 44.7 - - - +
312A THR* 4.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ASP* 3.0 38.5 + - - -
238A PRO* 3.6 8.8 - - - -
239A SER 4.4 0.4 - - - +
240A ARG 3.1 0.8 - - - -
241A ARG* 1.3 77.5 - - - +
243A ASP* 1.3 66.1 + - - +
245A GLU* 3.1 2.4 + - - +
246A ILE* 2.9 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 3.2 51.6 - - + +
169A HIS* 3.4 22.7 + - - -
174A VAL* 3.5 17.1 - - - +
175A HIS 5.0 5.7 - - - +
176A GLY* 5.0 1.0 - - - -
178A ILE* 5.8 0.5 - - - +
238A PRO* 3.5 23.4 - - - +
240A ARG* 3.1 9.9 + - - +
242A GLY* 1.3 74.2 - - - +
244A LEU* 1.3 64.6 + - + +
246A ILE* 3.3 12.6 + - - +
247A LEU* 3.1 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 3.8 20.9 - - + -
165A LEU* 5.7 2.9 - - + -
240A ARG* 2.9 28.5 + - + +
241A ARG* 4.0 4.9 - - - +
243A ASP* 1.3 76.8 - - + +
245A GLU* 1.3 64.5 + - - +
247A LEU* 3.1 4.2 + - - -
248A GLY 3.0 18.7 + - - -
302A TYR* 3.1 23.7 + - - +
306A VAL* 3.2 30.1 - - + -
309A LEU* 5.4 5.4 - - + -
315A PRO* 4.5 18.8 - - + -
316A LEU 4.5 0.9 - - - +
317A TYR* 4.9 9.4 - - + -
320A LEU* 3.2 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A SER* 5.0 2.2 - - - +
230A ILE* 5.4 5.9 - - + +
231A ASP* 4.7 6.3 - - - +
241A ARG* 2.8 58.8 + - - +
242A GLY* 3.1 6.9 + - - +
244A LEU* 1.3 76.6 - - - +
246A ILE* 1.3 64.5 + - + +
248A GLY* 3.0 12.3 + - - -
249A TYR* 3.0 40.3 + - + +
279A ARG* 4.3 10.0 - - - +
302A TYR* 5.4 0.7 - - - -
303A MET* 3.2 35.6 - - - +
306A VAL* 3.8 12.6 - - - +
307A LYS* 4.4 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A HIS 5.6 0.4 - - - +
176A GLY* 3.9 20.4 - - - +
178A ILE* 3.2 35.9 - - + -
227A PHE* 3.3 18.1 - - + +
228A THR 4.7 3.1 - - - +
229A SER* 3.2 31.6 - - - +
231A ASP* 5.0 3.1 - - + -
238A PRO* 4.5 7.6 - - + -
242A GLY* 2.9 33.9 + - - +
243A ASP* 3.5 16.8 - - - +
245A GLU* 1.3 74.5 - - - +
247A LEU* 1.3 63.5 + - - +
249A TYR* 3.1 6.6 + - + +
250A CYS* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A SER* 3.3 32.8 - - - +
161A ILE* 4.2 9.0 - - + -
162A LEU* 3.2 46.0 - - + +
165A LEU* 6.0 3.1 - - + -
178A ILE* 3.8 26.0 - - + +
243A ASP 3.1 8.9 + - - +
244A LEU* 3.1 10.6 + - - +
246A ILE* 1.3 80.0 - - - +
248A GLY* 1.3 56.5 + - - +
250A CYS* 3.0 12.9 - - - -
251A MET* 2.9 39.9 + - + +
254A TRP* 5.0 3.4 - - + -
302A TYR* 3.8 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU 3.0 10.3 + - - -
245A GLU 3.0 4.4 + - - -
247A LEU* 1.3 75.6 - - - +
249A TYR* 1.3 64.9 + - - +
251A MET* 3.2 6.9 + - - +
252A ILE* 3.1 24.4 + - - +
299A ILE* 3.6 6.2 - - - +
302A TYR* 3.8 20.8 - - - -
303A MET* 4.0 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLU 5.9 1.8 - - - +
227A PHE* 5.5 3.1 - - + -
229A SER* 3.4 19.7 - - - +
230A ILE* 5.4 0.6 - - + +
245A GLU* 3.0 39.8 + - + -
246A ILE* 3.5 5.8 - - + +
248A GLY* 1.3 75.3 - - - +
250A CYS* 1.3 60.0 + - - +
252A ILE* 2.8 25.1 - - + +
253A GLN* 3.1 10.9 + - - +
259A LEU* 5.4 0.4 - - - -
261A TRP* 3.3 40.0 - + + -
275A LYS* 3.2 42.8 + - + +
278A TYR* 5.3 7.2 - + + +
279A ARG* 3.9 23.4 + - - +
282A ILE* 5.6 0.2 - - - +
286A MET* 5.9 2.2 - - + -
303A MET* 3.4 27.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ILE* 3.8 16.6 - - + -
227A PHE* 3.5 32.5 - - + -
246A ILE 3.1 4.1 + - - +
247A LEU* 3.0 42.8 - - - -
249A TYR* 1.3 79.2 - - - +
251A MET* 1.3 57.1 + - - +
253A GLN* 3.4 3.9 + - - +
254A TRP* 3.0 67.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A VAL* 3.5 31.1 - - + +
155A LEU* 5.1 4.3 - - + -
158A SER* 3.4 30.5 - - - +
247A LEU* 2.9 36.1 + - + +
248A GLY* 3.4 9.9 - - - +
249A TYR 3.2 0.4 - - - -
250A CYS* 1.3 80.5 - - - +
252A ILE* 1.3 63.1 + - - +
254A TRP* 3.1 10.0 + - + +
255A LEU* 3.1 19.6 + - - +
299A ILE* 3.9 24.7 - - + -
302A TYR* 4.6 7.6 - - + -
324A LEU* 3.6 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLY 3.1 9.1 + - - +
249A TYR* 2.8 30.1 - - + +
251A MET* 1.3 78.6 - - - +
253A GLN* 1.3 52.8 + - - +
255A LEU* 3.7 4.4 - - + +
256A THR* 2.6 59.3 + - + +
259A LEU* 4.7 12.6 - - + -
261A TRP* 4.8 5.4 - - + -
285A LEU 5.0 0.2 - - - +
286A MET* 3.4 50.5 - - + +
289A CYS* 4.7 9.9 - - + -
290A PHE* 5.8 0.7 - - + -
299A ILE* 3.6 23.7 - - + +
303A MET* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 4.5 7.5 - - - -
147A LYS* 3.4 33.8 - - + +
226A GLU* 4.2 7.3 + - - -
227A PHE* 3.5 27.9 - - - -
249A TYR 3.1 18.4 + - - +
250A CYS* 3.4 4.7 - - - +
251A MET 3.2 0.2 - - - -
252A ILE* 1.3 78.0 - - - +
254A TRP* 1.3 85.4 + - - +
256A THR* 3.3 6.7 + - - -
257A GLY* 2.7 30.7 + - - -
258A HIS 3.7 1.7 + - - -
259A LEU* 3.5 36.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.0 28.9 - - + +
142A TYR* 5.3 4.1 - - + +
147A LYS* 2.6 29.3 - - + +
149A PHE* 3.5 43.9 + + + -
154A VAL* 4.2 20.6 - - + -
157A LEU* 4.7 17.5 - - + -
158A SER 5.5 0.4 - - - -
161A ILE* 6.0 2.2 - - + -
178A ILE* 4.5 16.2 - - + -
180A ALA* 4.8 11.5 - - + +
183A LEU* 4.7 8.1 - - + -
227A PHE* 4.8 5.6 - + - -
247A LEU* 5.0 4.9 - - + -
250A CYS* 3.0 53.2 + - + +
251A MET* 3.1 15.0 + - + +
253A GLN* 1.3 105.2 + - - +
255A LEU* 1.3 59.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ARG* 6.0 0.6 - - - -
149A PHE 4.1 17.9 - - - +
150A SER* 4.5 1.3 - - - -
151A ARG* 4.3 35.0 - - + +
154A VAL* 4.2 7.4 - - + +
251A MET 3.1 15.5 + - - +
252A ILE* 3.9 6.3 - - + +
254A TRP* 1.3 78.3 - - - +
256A THR* 1.3 60.2 + - + +
290A PHE* 3.1 30.7 - - + -
294A ASN* 3.6 23.7 + - - +
295A LYS 5.4 0.7 - - - +
296A PRO* 5.3 6.3 - - + -
299A ILE* 3.5 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LYS 4.5 0.2 - - - -
148A ARG* 5.9 1.6 - - - -
252A ILE* 2.6 43.5 + - + +
253A GLN* 3.3 6.1 + - - -
255A LEU* 1.3 80.3 - - - +
257A GLY* 1.3 58.1 + - - +
258A HIS* 2.8 33.9 + - - +
259A LEU* 4.9 0.5 - - - +
289A CYS* 3.6 26.0 - - + -
290A PHE* 3.2 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA* 3.7 8.8 - - - +
147A LYS* 2.9 56.6 + - - +
148A ARG* 5.1 3.8 - - - -
253A GLN 2.7 15.3 + - - -
256A THR* 1.3 72.3 - - - +
258A HIS* 1.3 67.2 + - - +
----------------------------------------------------------
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