Contacts of the helix formed by residues 234 - 255 (chain P) in PDB entry 4G7Z
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 LYS 234 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96P LEU* 4.8 21.8 - - + +
99P GLU* 3.5 22.4 - - - +
227P PHE* 4.3 1.0 - - - -
232P ARG 3.5 3.9 + - - +
233P PHE* 1.3 77.4 - - - +
235P PHE* 1.3 64.7 + - - +
236P SER* 3.2 2.5 - - - +
237P THR* 3.2 17.4 + - - +
238P TYR 3.8 2.8 + - - -
4R A 3.0 27.2 + - - +
5R A 2.9 44.7 + - - +
6R T 3.7 13.5 + - - +
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Residues in contact with PHE 235 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99P GLU* 2.9 31.4 + - + +
187P LEU* 4.8 8.1 - - + -
191P ASN* 3.6 31.0 - - + -
220P LEU* 3.6 16.8 - - + -
223P ALA* 3.2 35.0 - - + -
224P VAL* 3.6 27.1 - - + -
227P PHE* 3.6 38.0 - + + -
233P PHE 3.7 1.4 + - - -
234P LYS* 1.3 71.8 - - - +
236P SER* 1.3 56.7 + - - +
238P TYR* 3.1 2.3 + + - -
239P ALA* 2.8 49.4 + - + +
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Residues in contact with SER 236 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194P LEU* 4.0 14.7 - - - +
234P LYS* 4.3 0.4 - - - +
235P PHE* 1.3 79.1 - - - +
237P THR* 1.3 59.9 + - - +
239P ALA 4.1 0.2 - - - -
240P THR* 2.7 33.6 + - - -
4R A 3.7 5.9 - - - +
5R A 2.4 52.0 + - - +
6R T 3.6 27.3 + - - -
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Residues in contact with THR 237 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233P PHE* 4.8 1.8 - - + -
234P LYS 3.2 5.6 + - - -
235P PHE 3.1 0.6 - - - -
236P SER* 1.3 79.3 + - - +
238P TYR* 1.3 63.6 - - - +
240P THR* 4.0 8.0 + - - -
241P TRP* 4.2 4.9 + - - +
2R A 3.6 35.7 - - - +
3R T 3.7 20.6 - - - +
4R A 3.0 56.8 + - + +
5R A 3.5 13.0 + - - +
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Residues in contact with TYR 238 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223P ALA 3.6 14.6 - - - -
226P LYS* 3.4 8.6 - - + +
227P PHE* 3.3 62.8 - + + -
233P PHE* 5.7 0.4 - - + +
234P LYS 3.8 0.8 + - - -
235P PHE* 3.1 4.0 + + - +
237P THR* 1.3 78.9 - - - +
239P ALA* 1.3 65.2 + - - +
241P TRP* 3.4 9.8 + - + +
242P TRP* 3.0 45.0 + + - -
1R T 3.2 39.3 - - - +
2R A 3.3 53.4 + + - +
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Residues in contact with ALA 239 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194P LEU* 3.8 17.5 - - + -
220P LEU* 4.0 7.4 - - + -
223P ALA* 3.5 14.3 - - + +
235P PHE* 2.8 45.1 + - + +
238P TYR* 1.3 75.9 - - - +
240P THR* 1.3 66.4 + - - +
242P TRP* 3.0 6.1 + - - +
243P ILE* 2.9 26.4 + - + +
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Residues in contact with THR 240 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194P LEU* 4.0 7.8 - - - +
198P ILE* 3.9 22.9 - - + +
236P SER 2.7 21.7 + - - -
237P THR 4.1 4.3 - - - -
238P TYR 3.3 0.2 - - - -
239P ALA* 1.3 77.7 - - - +
241P TRP* 1.3 64.1 + - - +
243P ILE* 3.4 1.2 + - - +
244P ARG* 3.1 58.4 + - - +
5R A 3.8 33.7 + - + +
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Residues in contact with TRP 241 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237P THR 4.2 6.1 + - - +
238P TYR* 3.4 10.3 + - + +
239P ALA 3.1 0.8 - - - -
240P THR* 1.3 80.4 - - - +
242P TRP* 1.3 115.4 + + + +
244P ARG* 3.5 6.2 + - - +
245P GLN* 3.1 58.4 + - + +
1R T 3.8 50.3 + - - +
2R A 5.2 8.0 + - - -
5R A 5.8 0.2 - - - +
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Residues in contact with TRP 242 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219P GLY* 3.4 27.2 - - - +
222P ARG* 3.7 28.5 - - + -
223P ALA* 3.9 14.6 - - + -
226P LYS* 3.8 31.6 - - + -
238P TYR* 3.0 61.9 - + - -
239P ALA 3.0 5.6 + - - +
241P TRP* 1.3 109.2 - + - +
243P ILE* 1.3 61.4 + - - +
245P GLN* 3.3 7.2 + - + +
246P ALA* 3.1 18.7 + - - +
1R T 4.1 12.5 - + - -
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Residues in contact with ILE 243 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194P LEU* 3.8 22.2 - - + -
195P VAL* 3.6 23.3 - - + +
198P ILE* 3.6 41.3 - - + -
216P GLY* 3.9 27.3 - - - +
219P GLY* 4.5 0.2 - - - -
220P LEU* 4.1 13.2 - - + +
239P ALA* 2.9 24.9 + - + +
240P THR 3.7 4.5 - - - +
241P TRP 3.2 0.2 - - - -
242P TRP* 1.3 73.4 - - - +
244P ARG* 1.3 65.0 + - - +
245P GLN 3.0 2.0 + - - -
246P ALA* 3.4 1.9 + - - +
247P ILE* 3.1 38.3 + - + +
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Residues in contact with ARG 244 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361M MET* 5.3 7.4 - - - +
198P ILE* 4.1 16.0 - - + +
201P LYS* 3.0 31.9 - - - +
202P TYR* 3.4 25.3 + - - +
240P THR* 3.1 40.0 + - - +
241P TRP* 3.9 6.5 - - + +
243P ILE* 1.3 75.3 - - - +
245P GLN* 1.3 63.7 + - - +
246P ALA 3.5 0.2 - - - -
247P ILE* 4.1 5.9 - - - +
248P ASN* 3.2 31.9 + - - +
5R A 3.6 30.9 + - - +
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Residues in contact with GLN 245 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241P TRP* 3.1 54.2 + - + +
242P TRP* 3.5 14.4 - - + +
243P ILE 3.0 0.4 - - - -
244P ARG* 1.3 80.9 - - - +
246P ALA* 1.3 58.4 + - - +
248P ASN* 3.6 3.9 + - - +
249P ARG* 2.9 30.0 + - + +
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Residues in contact with ALA 246 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215P GLU* 3.1 33.9 - - - +
218P GLN* 4.6 3.8 - - + -
219P GLY* 3.8 13.5 - - - +
242P TRP 3.1 16.1 + - - +
243P ILE 4.2 1.1 - - - +
245P GLN* 1.3 73.9 - - - +
247P ILE* 1.3 64.2 + - - +
249P ARG* 4.0 9.6 + - - +
250P ALA* 3.1 24.4 + - - +
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Residues in contact with ILE 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198P ILE* 3.9 20.0 - - + -
199P ALA* 3.8 31.9 - - + -
202P TYR* 3.5 34.1 - - + -
212P LEU* 4.0 16.4 - - + +
215P GLU* 4.6 6.5 - - - -
216P GLY* 3.8 18.4 - - - +
243P ILE* 3.1 24.4 + - + +
244P ARG* 4.2 4.3 - - - +
246P ALA* 1.3 77.0 - - - +
248P ASN* 1.3 57.9 + - - +
250P ALA* 3.2 3.5 + - - +
251P ILE* 2.8 35.3 + - + +
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Residues in contact with ASN 248 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202P TYR* 3.2 33.9 + - - -
205P ARG* 4.2 8.0 + - - +
244P ARG* 3.2 22.0 + - - +
245P GLN* 4.0 3.8 + - - +
247P ILE* 1.3 77.9 - - - +
249P ARG* 1.3 59.7 + - - +
251P ILE* 3.8 9.4 - - - +
252P ALA* 3.0 31.7 + - - +
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Residues in contact with ARG 249 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215P GLU* 3.4 33.3 + - - -
218P GLN* 5.3 1.4 - - - +
245P GLN* 2.9 21.0 + - + +
246P ALA* 4.0 8.5 + - - +
247P ILE 3.4 0.2 - - - -
248P ASN* 1.3 75.8 - - - +
250P ALA* 1.3 70.7 + - - +
252P ALA* 3.9 5.0 - - - +
253P ASP* 3.2 51.1 + - - +
254P GLN* 3.9 6.7 - - - +
262P VAL* 4.9 12.7 - - + +
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Residues in contact with ALA 250 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207P LEU* 3.9 9.6 - - + +
215P GLU* 3.4 36.3 - - + -
246P ALA 3.1 20.2 + - - +
247P ILE 3.6 2.9 - - - +
249P ARG* 1.3 82.1 - - - +
251P ILE* 1.3 63.6 + - - +
252P ALA 3.1 1.8 - - - -
253P ASP* 4.4 0.7 - - - -
254P GLN* 3.0 38.0 + - - +
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Residues in contact with ILE 251 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202P TYR* 3.6 33.7 - - + -
205P ARG* 3.9 40.4 - - + +
207P LEU* 4.0 11.6 - - + +
212P LEU* 3.6 28.5 - - + -
247P ILE* 2.8 21.1 + - + +
248P ASN* 3.8 12.3 - - - +
250P ALA* 1.3 72.4 - - - +
252P ALA* 1.3 60.4 + - - +
255P ALA* 3.2 27.1 - - + +
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Residues in contact with ALA 252 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248P ASN 3.0 18.6 + - - +
249P ARG* 3.9 4.5 - - - +
251P ILE* 1.3 80.0 - - + +
253P ASP* 1.3 65.7 + - - +
255P ALA 4.4 2.1 + - - -
256P ARG* 4.9 6.8 - - - +
260P ILE 4.3 3.6 - - - +
262P VAL* 4.0 22.7 - - + +
265P VAL* 3.8 41.1 - - + +
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Residues in contact with ASP 253 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N PRO* 6.0 2.8 - - - +
30N GLU* 5.4 0.2 - - - +
249P ARG* 3.2 40.7 + - - +
250P ALA* 3.2 3.6 + - - +
252P ALA* 1.3 83.0 - - - +
254P GLN* 1.3 71.0 + - + +
255P ALA 3.7 0.3 + - - -
256P ARG* 4.5 4.0 + - - +
259P ARG* 2.8 54.9 + - - +
260P ILE 5.2 1.5 + - - -
262P VAL* 5.6 4.0 - - + -
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Residues in contact with GLN 254 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N PRO* 5.9 4.0 - - + -
545N ARG* 2.9 31.2 + - - +
549N ASN* 3.8 41.0 + - - +
553N ARG* 4.3 8.5 + - - +
207P LEU* 3.4 28.5 - - + +
211P ASP* 4.7 0.7 - - - +
215P GLU* 3.4 26.5 + - - +
249P ARG* 3.9 6.3 - - - +
250P ALA* 3.0 26.4 + - - +
253P ASP* 1.3 85.2 - - + +
255P ALA* 1.3 62.0 + - - +
256P ARG 3.0 4.6 + - - -
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Residues in contact with ALA 255 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545N ARG* 4.3 6.5 + - - -
593N ASN* 5.7 1.0 - - - +
205P ARG 4.0 20.0 - - - +
206P GLY* 4.3 19.6 - - - +
207P LEU* 5.3 2.2 - - + +
250P ALA 4.4 0.8 + - - -
251P ILE* 3.2 24.7 + - + +
252P ALA 4.4 0.8 + - - +
253P ASP 3.5 2.2 - - - -
254P GLN* 1.3 77.0 - - - +
256P ARG* 1.3 65.1 + - + +
257P THR* 4.0 1.0 + - - -
313P GLU* 3.6 10.3 - - - +
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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) + - + + + + + -
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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