Contacts of the helix formed by residues 245 - 264 (chain C) in PDB entry 4HH3
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 245 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 3.6 18.8 - - - -
239C LEU* 3.8 5.8 - - - -
244C ILE* 1.3 74.7 - - - +
246C ARG* 1.3 65.4 + - - +
247C MET* 3.5 14.6 + - - +
248C GLN* 2.9 44.3 + - - +
249C VAL* 3.1 16.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
65A GLU* 6.3 1.4 - - - +
87A GLU* 3.0 23.9 + - - +
89A ASN* 5.7 6.3 - - - +
127A GLN* 3.6 17.9 - - - +
239C LEU* 3.7 31.8 - - + +
245C SER* 1.3 69.2 - - - +
247C MET* 1.3 67.0 + - - +
249C VAL* 3.1 23.5 + - - +
250C THR* 2.9 35.1 + - - +
334C LEU* 2.8 31.9 + - - +
335C GLU* 4.4 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 4.9 1.4 + - - +
123A ILE* 4.0 11.9 - - + -
127A GLN* 3.2 24.7 - - - +
126B VAL* 3.5 45.1 - - + +
129B GLN* 4.4 13.5 - - - +
130B LEU* 4.0 16.8 - - + -
245C SER* 3.2 15.8 + - - +
246C ARG* 1.3 77.8 - - - +
248C GLN* 1.3 72.7 + - + +
250C THR* 3.1 5.9 + - - -
251C LEU* 3.0 43.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C LEU 4.3 4.3 - - - +
200C SER* 3.3 27.9 + - - +
201C THR* 5.0 5.9 + - - +
203C PRO* 5.0 0.5 - - - +
243C ARG 4.5 1.7 + - - +
244C ILE* 3.2 22.6 - - + +
245C SER* 2.9 41.4 + - - +
247C MET* 1.3 91.8 - - + +
249C VAL* 1.3 62.9 + - - +
251C LEU* 3.3 9.9 + - + +
252C ALA* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C LEU* 4.8 11.0 - - + +
239C LEU* 4.4 14.8 - - + -
244C ILE* 3.7 25.1 - - + -
245C SER 3.1 14.4 + - - +
246C ARG* 3.1 35.4 + - - +
248C GLN* 1.3 74.4 - - - +
250C THR* 1.3 58.3 + - - +
252C ALA* 3.3 7.6 + - - +
253C TYR* 2.9 28.8 + - + +
334C LEU* 3.9 31.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
127A GLN* 3.5 28.2 + - + +
130A LEU* 3.8 21.5 - - + -
131A VAL* 4.3 22.2 - - + -
134A GLN* 4.2 2.5 - - - +
130B LEU* 4.4 1.6 - - + -
246C ARG* 2.9 21.4 + - - -
247C MET* 3.3 11.7 - - - -
249C VAL* 1.3 78.3 - - - +
251C LEU* 1.3 61.0 + - - +
253C TYR* 3.3 7.5 + - + +
254C SER* 3.1 26.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
130A LEU* 4.5 1.1 - - + -
129B GLN* 3.7 30.3 - - + +
130B LEU* 4.0 17.7 - - + -
133B ALA* 3.6 30.3 - - + -
203C PRO* 3.9 18.4 - - + -
204C LEU* 3.6 16.9 - - + +
247C MET* 3.0 39.7 + - + +
248C GLN* 3.6 11.9 - - + +
250C THR* 1.3 73.0 - - - +
252C ALA* 1.3 65.8 + - - +
254C SER* 3.3 4.9 + - - -
255C ALA* 3.0 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C LEU* 3.4 39.5 - - + +
203C PRO* 4.0 9.3 - - - +
235C LEU* 4.3 15.5 - - + -
248C GLN 3.0 10.3 + - - +
249C VAL* 3.4 12.3 - - - +
251C LEU* 1.3 77.0 - - - +
253C TYR* 1.3 59.1 + - - +
255C ALA* 3.2 3.1 + - - +
256C LEU* 2.9 33.7 + - + +
334C LEU* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A VAL* 6.2 2.0 - - + -
134A GLN* 3.5 27.6 - - - -
228C PHE* 4.2 7.9 - + - -
249C VAL* 2.9 17.6 + - + +
250C THR* 3.6 7.6 - - + +
251C LEU 3.2 0.2 - - - -
252C ALA* 1.3 78.4 - - - +
254C SER* 1.3 60.3 + - - +
256C LEU* 3.4 7.9 + - - +
257C GLN* 3.1 23.5 + - - +
285C LYS 3.5 12.3 + - - -
286C PRO* 3.7 0.3 - - - +
287C ILE* 3.0 16.2 + - + -
288C LEU* 2.9 41.9 + - + +
289C GLU* 2.6 34.0 + - - -
334C LEU* 3.6 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 3.4 24.7 - - - +
134A GLN* 2.7 35.2 + - - +
133B ALA* 5.2 6.5 - - - -
137B MET* 4.4 10.1 - - - +
204C LEU* 5.2 2.0 - - - -
250C THR 3.1 11.6 + - - -
251C LEU* 3.3 8.5 + - - -
253C TYR* 1.3 75.5 - - - +
255C ALA* 1.3 62.5 + - - +
257C GLN* 3.3 4.3 + - - +
258C MET* 3.0 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C LEU* 4.6 5.4 - - + -
203C PRO* 3.7 34.3 - - + +
204C LEU* 4.2 6.3 - - + +
207C LEU* 3.4 20.8 - - + +
210C VAL* 5.3 2.0 - - + -
251C LEU 3.0 12.7 + - - +
252C ALA 3.6 7.9 - - - +
254C SER* 1.3 78.4 - - - +
256C LEU* 1.3 57.1 + - - +
258C MET* 3.3 8.3 + - - +
259C ALA* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 256 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C LEU* 4.7 8.3 - - + -
199C LEU* 3.9 34.3 - - + -
210C VAL* 4.9 1.1 - - + -
214C LEU* 4.3 21.5 - - + -
224C PHE* 3.9 13.1 - - + -
228C PHE* 3.7 36.8 - - + -
231C CYS* 5.9 0.2 - - + -
235C LEU* 5.4 4.7 - - + -
252C ALA* 2.9 24.8 + - + +
253C TYR* 3.6 9.0 - - + +
254C SER 3.3 0.2 - - - -
255C ALA* 1.3 73.5 - - - +
257C GLN* 1.3 60.4 + - - +
259C ALA* 3.7 3.7 - - - +
260C LEU* 2.8 31.0 + - - +
288C LEU* 3.8 13.9 - - + -
334C LEU* 5.6 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 257 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLN* 2.8 64.1 + - - +
138A GLU* 3.4 11.6 - - + +
137B MET* 4.3 3.9 - - - -
141B TYR* 2.7 34.9 + - + +
253C TYR* 3.1 13.5 + - - +
254C SER 3.3 8.9 + - - +
256C LEU* 1.3 75.9 - - - +
258C MET* 1.3 62.3 + - + +
260C LEU* 3.4 5.0 + - + +
261C ARG* 3.1 23.4 + - + +
287C ILE* 3.6 17.3 - - + +
288C LEU* 4.0 19.9 + - + +
291C ALA* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 258 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA* 3.4 35.0 - - + +
137B MET* 3.7 30.5 - - + -
140B ASP* 3.7 27.7 - - + +
141B TYR* 5.2 4.0 - - + -
204C LEU* 3.8 24.2 - - + -
207C LEU* 3.6 25.4 - - + -
254C SER* 3.0 20.3 + - - +
255C ALA* 3.3 6.3 + - - +
257C GLN* 1.3 76.1 - - - +
259C ALA* 1.3 62.3 + - - +
261C ARG* 3.2 7.6 + - - +
262C ARG* 3.1 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C LEU* 4.4 6.0 - - + +
210C VAL* 4.0 13.0 - - + -
211C GLU* 4.5 10.3 - - - -
214C LEU* 3.7 26.0 - - + -
224C PHE* 4.4 0.2 - - - -
255C ALA 2.9 17.1 + - - +
256C LEU* 3.7 4.7 - - - +
258C MET* 1.3 72.4 - - - +
260C LEU* 1.3 68.6 + - - +
262C ARG* 3.2 18.8 + - - +
263C ILE* 3.4 20.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
138A GLU* 5.8 0.2 - - - +
224C PHE* 3.6 27.2 - - + -
256C LEU 2.8 21.7 + - - +
257C GLN* 3.6 7.4 - - + +
259C ALA* 1.3 72.3 - - - +
261C ARG* 1.3 71.1 + - + +
263C ILE* 3.1 3.3 + - - +
264C HIS* 2.8 56.3 + - + +
288C LEU* 3.8 21.1 - - + -
291C ALA* 3.9 25.4 - - + +
292C LEU* 3.8 30.1 - - + +
295C GLU* 4.8 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 261 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLU* 2.9 34.0 + - - +
141A TYR* 3.4 40.6 + - + -
142A GLU* 5.0 1.4 + - - -
141B TYR* 3.6 33.2 - - + +
144B GLN* 5.8 8.4 - - + +
257C GLN* 3.1 12.6 + - + +
258C MET* 3.2 5.6 + - - +
260C LEU* 1.3 89.0 - - + +
262C ARG* 1.3 59.2 + - - +
263C ILE 3.2 0.9 - - - -
264C HIS 3.0 18.0 + - - -
265C HIS* 3.5 18.6 - - - +
291C ALA* 3.5 17.6 + - - +
294C ALA* 5.9 1.8 - - - +
295C GLU* 3.0 31.3 + - - +
298C ARG* 5.8 0.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
140B ASP* 2.7 39.8 + - - +
207C LEU* 3.5 39.7 + - - +
208C THR* 4.8 5.9 + - - +
211C GLU* 3.0 40.9 + - + +
215C ARG* 2.9 21.2 + - - +
258C MET* 3.1 17.7 + - - +
259C ALA* 3.2 10.9 + - - +
261C ARG* 1.3 77.1 - - - +
263C ILE* 1.3 58.2 - - - +
265C HIS* 4.7 6.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C GLU* 3.9 11.9 - - + +
214C LEU* 3.7 31.2 - - + -
215C ARG* 3.8 42.2 + - + +
218C ALA 4.5 5.2 - - - +
224C PHE* 4.5 4.7 - - + -
259C ALA 3.4 17.7 - - - +
260C LEU* 3.1 4.6 + - - +
261C ARG 3.2 0.6 - - - -
262C ARG* 1.3 86.9 - - + +
264C HIS* 1.3 91.8 + - + +
265C HIS* 4.1 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 264 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C ALA 2.9 21.7 + - - -
219C PRO 3.4 27.1 - - - -
220C THR* 3.5 13.8 + - - -
221C ALA* 4.1 16.2 + - + +
224C PHE* 4.0 21.7 - + - -
260C LEU* 2.8 32.0 + - + +
261C ARG* 3.0 20.6 + - - -
263C ILE* 1.3 94.1 + - + +
265C HIS* 1.3 64.5 + - - +
266C LEU* 6.1 1.7 - - + +
295C GLU* 3.9 15.7 - - + +
----------------------------------------------------------
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