Contacts of the helix formed by residues 202 - 216 (chain B) in PDB entry 1USK
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 TYR 202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.9 35.0 - - + -
18B TRP* 4.3 4.7 - - - -
78B CYS* 4.0 10.2 - - - +
79B SER 4.6 0.2 + - - -
80B SER 5.7 0.2 + - - -
146B ASP* 3.8 14.3 + - - -
148B GLN* 3.8 21.8 - - + -
150B TYR* 3.3 33.5 - + + +
151B GLY 5.7 0.2 - - - -
199B TYR* 3.8 7.2 + - - -
201B GLY* 1.3 77.0 - - - -
203B TYR* 1.3 66.3 + - - +
204B PRO* 3.3 13.8 - - + -
205B GLU* 3.5 10.6 + - - +
206B MET 3.4 14.7 + - - -
227B GLY* 3.5 18.2 - - - +
228B VAL* 3.8 5.7 - - - +
1347B LEU* 2.6 42.9 + - + -
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Residues in contact with TYR 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PRO 3.5 9.2 + - - -
15B ILE* 3.3 22.3 - - + -
16B ALA 4.2 0.2 + - - -
17B GLN* 3.2 22.3 + - + +
18B TRP* 3.4 36.8 - + - -
202B TYR* 1.3 71.2 - - - +
204B PRO* 1.3 92.4 - - + +
205B GLU 3.2 0.2 - - - -
206B MET* 3.9 5.6 - - - -
207B GLY* 3.0 21.8 + - - -
227B GLY 3.3 5.5 + - - -
228B VAL* 3.6 25.4 - - - +
230B ASN* 3.7 26.9 - - + -
232B SER* 3.5 27.4 - - - -
233B LEU* 4.2 10.1 - - + +
236B ILE* 4.0 12.7 - - + +
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Residues in contact with PRO 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO* 3.4 34.3 - - + +
15B ILE* 4.1 5.2 - - + -
202B TYR* 3.3 15.3 - - + -
203B TYR* 1.3 108.5 - - + +
205B GLU* 1.3 75.4 + - - +
208B GLN* 3.2 28.8 + - - +
236B ILE* 4.3 11.5 - - + +
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Residues in contact with GLU 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO* 5.9 1.6 - - - +
146B ASP* 4.7 3.3 - - - +
175B ILE* 3.7 20.2 - - + -
176B THR 4.6 0.4 - - - +
177B ALA* 4.1 15.0 - - + +
178B GLY* 3.1 26.7 + - - +
179B GLU 4.6 4.1 + - - +
182B PHE* 3.8 16.8 - - + -
199B TYR* 3.0 32.3 + - + +
202B TYR* 3.5 14.7 + - - +
203B TYR 3.2 0.2 - - - -
204B PRO* 1.3 93.1 - - - +
206B MET* 1.3 67.5 + - - +
207B GLY 3.4 0.2 + - - -
208B GLN* 3.4 1.4 + - - -
209B MET* 3.0 24.7 + - - +
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Residues in contact with MET 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TYR* 3.9 31.5 - - + -
202B TYR 3.4 6.9 + - - +
203B TYR 4.0 1.3 - - - +
205B GLU* 1.3 79.2 - - - +
207B GLY* 1.3 61.6 + - - +
209B MET* 3.2 9.4 + - - +
210B LEU* 3.0 65.4 + - + +
222B PHE* 3.6 22.9 - - + -
223B MET 4.8 0.4 - - - +
228B VAL* 3.7 24.2 - - + -
233B LEU* 3.7 19.3 - - + -
244B MET* 3.4 30.1 - - + -
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Residues in contact with GLY 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B TYR 3.0 13.6 + - - -
206B MET* 1.3 76.7 - - - +
208B GLN* 1.3 60.1 + - - +
211B ARG* 3.3 18.5 + - - +
233B LEU* 3.7 14.1 - - - +
236B ILE* 3.5 22.8 - - - +
237B ALA* 3.3 23.2 - - - +
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Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B GLU 4.8 5.4 - - - +
180B LYS* 4.0 30.7 - - - +
182B PHE* 3.7 23.8 - - + -
204B PRO 3.2 17.2 + - - +
205B GLU 3.4 2.4 + - - +
206B MET 3.3 0.2 - - - -
207B GLY* 1.3 72.7 - - - +
209B MET* 1.3 65.7 + - - +
211B ARG* 3.4 10.5 + - - +
212B GLN* 3.2 43.9 + - - +
236B ILE* 3.6 16.3 - - + +
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Residues in contact with MET 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ILE* 4.3 4.7 - - + -
182B PHE* 3.7 33.6 - - + -
185B LEU* 3.5 33.9 - - + -
186B ILE* 4.0 7.4 - - + +
197B VAL* 4.9 5.2 - - - -
199B TYR* 3.8 37.9 - - + -
205B GLU 3.0 15.2 + - - +
206B MET* 3.4 12.3 - - + +
208B GLN* 1.3 79.1 - - - +
210B LEU* 1.3 61.8 + - - +
212B GLN* 4.1 0.3 - - - +
213B ALA* 3.1 25.5 + - - +
222B PHE* 3.8 31.6 - - + -
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B MET* 3.0 52.5 + - + +
207B GLY 3.8 3.6 - - - +
208B GLN 3.3 0.2 - - - -
209B MET* 1.3 74.3 - - - +
211B ARG* 1.3 65.9 + - - +
213B ALA* 3.2 6.2 + - - +
214B ARG* 3.2 25.2 + - - +
222B PHE* 3.6 29.6 - - + -
233B LEU* 4.2 9.9 - - + -
237B ALA* 4.0 15.9 - - + -
240B ALA* 3.3 35.7 - - + +
241B ALA* 4.4 4.3 - - - -
244B MET* 4.2 16.6 - - + -
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Residues in contact with ARG 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B GLY 3.3 13.7 + - - +
208B GLN* 3.9 11.4 - - - +
209B MET 3.4 0.2 - - - -
210B LEU* 1.3 79.9 - - - +
212B GLN* 1.3 67.1 + - + +
214B ARG* 3.4 2.9 + - - +
215B SER* 3.2 22.1 + - - -
235B ASN 3.8 6.7 + - - -
236B ILE 2.9 26.1 + - - +
237B ALA 3.6 12.2 + - - +
238B GLY* 3.5 8.5 - - - +
239B ASP 5.5 0.2 - - - +
240B ALA* 3.8 10.9 - - + +
11C MET* 3.4 31.8 + - - +
12C SER* 4.6 6.1 - - - +
13C GLY 5.8 0.2 - - - +
16C ALA* 3.7 24.6 + - - +
17C GLN 4.6 0.2 - - - +
20C ASP* 2.9 40.0 + - - -
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Residues in contact with GLN 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B LYS 2.7 28.1 + - - -
181B ASP* 4.1 3.8 - - - +
182B PHE* 2.9 34.4 + - + +
183B SER* 3.9 3.2 + - - -
186B ILE* 4.5 11.8 - - + +
208B GLN* 3.2 33.5 + - - +
209B MET 4.2 2.2 - - - +
211B ARG* 1.3 81.7 - - + +
213B ALA* 1.3 60.3 + - - +
215B SER* 2.7 24.0 + - - +
216B VAL* 3.6 12.8 + - - +
12C SER* 6.3 3.1 - - - -
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ILE* 3.6 21.9 - - + +
209B MET 3.1 19.8 + - - +
210B LEU 3.5 4.9 - - - +
211B ARG 3.2 0.2 - - - -
212B GLN* 1.3 78.2 - - - +
214B ARG* 1.3 63.5 + - - +
216B VAL* 3.5 5.2 + - - +
217B GLY 3.4 4.0 + - - -
218B LEU* 3.1 41.3 + - + +
222B PHE* 4.1 19.3 - - + -
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Residues in contact with ARG 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B LEU* 3.2 10.4 + - - +
211B ARG 4.1 3.8 - - - +
213B ALA* 1.3 81.3 - - - +
215B SER* 1.3 63.8 + - - +
216B VAL 3.2 0.2 - - - -
217B GLY* 3.2 14.4 + - - +
218B LEU 3.1 28.5 + - - +
219B LYS 4.9 2.0 + - - -
220B THR 3.0 27.6 + - - -
221B GLN* 4.9 3.2 - - - +
222B PHE* 4.0 22.7 - - - +
240B ALA* 3.5 42.9 + - + +
242B GLU 4.7 9.7 + - - -
243B GLY 6.2 0.8 - - - -
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Residues in contact with SER 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ARG* 3.2 13.5 + - - -
212B GLN* 2.7 28.4 + - - +
213B ALA 3.3 0.2 - - - -
214B ARG* 1.3 78.3 - - - +
216B VAL* 1.3 63.9 + - - +
217B GLY 3.5 0.4 + - - -
11C MET* 5.2 23.8 - - - +
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ILE* 3.5 32.1 - - + -
190B LYS* 2.6 46.5 + - + +
212B GLN 4.0 4.3 - - - +
213B ALA 3.5 8.7 + - - +
214B ARG 3.2 0.2 - - - -
215B SER* 1.3 87.0 + - - +
217B GLY* 1.3 52.7 + - - +
218B LEU* 4.6 0.9 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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