Contacts of the helix formed by residues 241 - 259 (chain I) in PDB entry 3KC3
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 ASP 241 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183I ALA* 3.7 21.7 - - + +
185I ARG* 3.6 24.9 + - - +
212I LYS* 2.8 34.2 + - - +
213I GLU 5.7 0.4 - - - -
214I THR* 4.6 13.6 + - - +
239I LYS* 4.7 6.2 + - - +
240I TYR* 1.3 83.2 + - - +
242I LYS* 1.3 58.9 + - - +
243I SER 3.1 0.9 - - - -
244I CYS* 2.8 45.7 + - - +
245I ASP* 3.8 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ARG* 5.0 9.3 + - - +
281C MET* 3.5 30.0 - - - +
178I HIS* 3.2 72.4 + - + +
181I ASN* 4.4 12.3 - - - +
182I ILE 4.8 6.1 - - - +
183I ALA* 4.2 8.5 - - + -
214I THR* 5.1 6.1 - - - +
238I GLU* 3.4 37.2 + - - +
240I TYR 2.4 24.5 + - - +
241I ASP* 1.3 70.2 - - + +
243I SER* 1.3 56.0 + - - +
245I ASP* 3.2 16.8 + - - +
246I MET* 3.8 2.0 - - - +
316I ILE* 5.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 243 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240I TYR* 3.6 18.2 + - - +
242I LYS* 1.3 75.7 - - - +
244I CYS* 1.3 61.6 + - - +
245I ASP 3.2 2.5 - - - -
246I MET* 3.6 9.3 - - - +
247I TRP 3.4 5.5 + - - -
310I PRO* 3.4 38.4 - - - +
313I ARG* 3.0 31.6 + - - -
314I MET 5.9 1.3 - - - -
316I ILE* 6.5 0.2 - - - -
233L GLU* 4.0 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 244 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I ARG* 4.1 24.0 - - - -
241I ASP* 2.8 30.9 + - - +
243I SER* 1.3 75.2 + - - +
245I ASP* 1.3 74.1 + - - +
246I MET 3.2 0.9 - - - -
247I TRP* 3.8 6.0 + - - +
248I SER* 3.4 15.6 + - - -
313I ARG* 3.8 6.1 - - - +
229L TYR 5.6 0.3 - - - +
231L ALA* 4.0 13.5 - - + +
233L GLU* 3.6 18.2 - - - +
234L VAL* 4.6 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 245 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I ILE* 4.4 12.8 - - + +
177I LEU* 5.7 0.3 - - - +
178I HIS* 3.2 24.5 + - + +
183I ALA* 3.6 2.5 - - - -
184I HIS* 2.9 29.0 + - - +
185I ARG* 2.8 32.1 + - - -
187I VAL* 4.3 7.8 + - + +
241I ASP 4.5 3.4 - - - -
242I LYS 3.5 10.1 - - - +
243I SER 3.2 0.2 - - - -
244I CYS* 1.3 82.0 - - - +
246I MET* 1.3 61.7 + - + +
248I SER* 2.8 25.4 - - - -
249I LEU* 3.0 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 246 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174I ILE* 3.8 9.4 - - + -
178I HIS* 3.2 34.8 - - + -
242I LYS 3.8 2.5 - - - +
243I SER* 3.6 16.4 - - - +
245I ASP* 1.3 77.6 - - - +
247I TRP* 1.3 64.5 + - - +
248I SER 3.0 1.3 - - - -
249I LEU* 3.2 17.6 + - + +
250I GLY* 3.0 18.5 + - - -
305I LEU* 3.7 23.2 - - + +
313I ARG* 4.7 4.0 - - - -
314I MET 3.0 26.9 - - - +
315I THR* 4.0 1.8 - - - +
316I ILE* 3.6 40.4 - - + -
319I PHE* 4.9 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 247 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243I SER 3.4 4.2 + - - -
244I CYS 3.9 7.9 - - - +
246I MET* 1.3 76.7 - - - +
248I SER* 1.3 57.6 + - - +
250I GLY* 3.1 3.8 + - - -
251I VAL* 2.8 38.5 + - + +
263I PHE* 3.4 37.7 - + - -
279I ILE* 3.9 14.8 - - + -
282I GLY* 5.3 1.3 - - - -
305I LEU 3.5 12.6 - - - -
306I LEU* 3.1 47.2 - - + +
307I LYS 3.6 17.0 - - - -
308I THR* 4.2 1.3 - - - -
313I ARG* 3.8 21.4 - - - +
228L TYR 5.0 1.0 + - - -
229L TYR 3.4 23.5 + - - -
230L VAL 3.8 7.7 + - - -
231L ALA* 3.7 12.1 - - + -
232L PRO* 3.6 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 248 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187I VAL* 2.3 47.9 + - - +
244I CYS 3.4 9.3 + - - -
245I ASP* 2.8 19.0 + - - -
246I MET 3.0 0.2 - - - -
247I TRP* 1.3 84.5 - - - +
249I LEU* 1.3 49.6 + - - +
251I VAL* 2.9 7.4 + - - +
252I ILE* 2.8 38.4 + - - +
229L TYR* 4.1 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I MET* 4.6 8.2 - - - +
170I ILE* 3.5 29.6 - - + -
171I GLY* 4.3 11.9 - - - -
174I ILE* 4.0 21.1 - - + -
187I VAL* 4.4 8.1 - - + -
245I ASP 3.0 12.6 + - - +
246I MET* 3.2 21.3 + - - +
248I SER* 1.3 70.2 - - - +
250I GLY* 1.3 56.0 + - - +
252I ILE* 3.0 7.1 + - + +
253I MET* 2.6 37.4 + - - +
305I LEU* 4.3 10.5 - - + -
316I ILE* 5.1 1.1 - - + -
319I PHE* 3.5 40.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 250 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246I MET 3.0 11.1 + - - -
247I TRP 3.3 4.3 - - - -
249I LEU* 1.3 76.4 - - - +
251I VAL* 1.3 62.0 + - - +
253I MET* 3.8 2.9 - - - +
254I TYR* 3.1 23.7 + - - +
302I ILE* 4.4 3.6 - - - +
305I LEU* 3.5 31.1 - - - +
306I LEU* 3.8 14.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I PRO* 5.9 0.4 - - + -
247I TRP* 2.8 42.1 + - + +
248I SER 2.9 6.9 + - - +
250I GLY* 1.3 71.2 - - - -
252I ILE* 1.3 69.5 + - + +
254I TYR* 3.1 11.4 + - - +
255I ILE* 3.2 25.4 + - + +
262I PRO* 4.0 27.8 - - + -
263I PHE* 4.8 2.5 - - + -
306I LEU* 4.0 9.2 - - + -
228L TYR* 4.2 27.6 - - + +
229L TYR* 4.2 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146I LEU* 4.7 2.2 - - + -
147I PHE* 4.7 7.4 - - + -
167I MET* 3.0 23.3 - - + -
170I ILE* 3.9 15.5 - - + -
187I VAL* 3.8 26.7 - - + +
189I PRO* 3.9 29.2 - - + -
192I LEU* 3.5 28.0 - - + -
248I SER 2.8 18.6 + - - +
249I LEU* 3.8 8.5 - - + +
251I VAL* 1.3 72.5 - - + +
253I MET* 1.3 65.5 + - - +
255I ILE* 3.0 11.4 + - - +
256I LEU* 3.0 25.6 + - + +
229L TYR* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 253 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167I MET* 3.3 27.9 - - + +
249I LEU 2.6 18.7 + - - +
250I GLY* 3.8 4.7 - - - +
252I ILE* 1.3 71.0 - - - +
254I TYR* 1.3 63.4 + - - +
256I LEU* 2.8 14.3 + - + +
257I LEU* 3.1 26.5 + - + +
298I VAL* 4.7 3.6 - - - +
301I LEU* 3.9 17.9 - - + -
302I ILE* 3.7 25.4 - - + -
305I LEU* 3.6 10.3 - - + -
319I PHE* 3.2 41.5 - - + -
324I TRP* 4.2 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 254 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250I GLY 3.1 12.8 + - - +
251I VAL 3.4 9.0 - - - +
252I ILE 3.0 0.2 + - - -
253I MET* 1.3 75.0 - - - +
255I ILE* 1.3 63.4 + - - +
257I LEU* 3.1 12.5 + - - -
258I CYS* 3.4 20.9 + - - -
260I TYR* 3.1 29.9 - + - -
261I PRO 3.7 3.3 + - - -
262I PRO* 3.5 43.3 - - + +
284I TYR* 4.1 6.2 - + + +
285I GLU 2.7 29.5 + - - -
286I PHE* 4.0 14.6 - + - -
287I PRO* 3.7 13.0 - - - +
291I TRP* 3.6 23.9 + + - -
302I ILE* 3.9 21.0 - - + +
306I LEU* 4.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 255 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147I PHE* 3.8 31.9 - - + -
189I PRO* 4.8 1.8 - - + -
251I VAL* 3.5 18.4 - - + +
252I ILE* 3.0 6.8 + - - +
254I TYR* 1.3 76.5 - - - +
256I LEU* 1.3 59.8 + - - +
259I GLY* 3.0 42.7 + - - +
260I TYR* 3.6 7.6 - - - +
261I PRO* 3.4 39.0 - - + -
338I THR* 3.4 6.6 - - - +
342I LEU* 4.5 8.1 - - + -
348I ARG* 4.0 10.3 - - - +
228L TYR* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146I LEU* 4.9 2.9 - - + -
147I PHE* 3.8 28.3 - - + -
150I ILE* 4.4 10.5 - - + -
158I PHE* 3.4 28.8 - - + -
163I ALA* 4.3 14.1 - - + +
166I ILE* 3.7 30.5 - - + -
167I MET* 3.0 35.0 - - + -
252I ILE* 3.0 10.7 + - + +
253I MET* 2.8 11.6 + - - +
255I ILE* 1.3 78.5 - - - +
257I LEU* 1.3 55.9 + - + +
336I LEU* 4.2 1.0 - - - +
338I THR* 2.6 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I GLU* 4.1 16.8 - - + -
163I ALA* 4.0 16.4 - - + -
253I MET* 3.1 30.9 + - + +
254I TYR 3.1 2.4 + - - +
256I LEU* 1.3 81.4 - - - +
258I CYS* 1.3 57.6 + - - +
290I GLU 4.4 6.6 - - - +
291I TRP* 3.9 21.1 - - + -
294I VAL* 4.7 9.6 - - + +
298I VAL* 3.8 26.0 - - + -
302I ILE* 4.0 11.4 - - + -
324I TRP* 4.3 6.7 - - + -
336I LEU* 3.8 40.7 - - + +
337I HIS 4.7 1.2 + - - -
338I THR* 3.4 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 258 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254I TYR* 3.4 25.3 + - - -
256I LEU 3.4 0.2 - - - -
257I LEU* 1.3 79.4 - - - +
259I GLY* 1.3 61.4 + - - +
260I TYR* 3.1 54.9 - - - -
290I GLU* 3.8 24.5 - - + +
291I TRP* 3.3 24.2 - - + +
337I HIS* 4.2 1.9 - - - -
338I THR* 4.0 9.6 - - - +
341I VAL* 4.0 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 259 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255I ILE* 3.0 21.8 + - - +
258I CYS* 1.3 79.1 - - - +
260I TYR* 1.3 61.2 + - - +
338I THR* 3.8 24.8 - - - +
341I VAL* 3.9 12.9 - - - +
342I LEU* 3.1 23.4 - - - +
345I ASP* 5.9 0.9 - - - -
348I ARG* 4.8 2.3 + - - -
----------------------------------------------------------
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