Contacts of the helix formed by residues 202 - 216 (chain C) in PDB entry 4U2M
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 ASN 202 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200C GLU 3.4 4.4 + - - +
201C ILE* 1.3 80.5 - - - +
203C PRO* 1.3 71.2 - - - +
204C GLU* 2.9 34.9 + - - +
205C GLY* 3.0 12.2 + - - +
206C PHE* 3.1 16.1 + - - +
227C ALA* 4.1 27.2 - - + +
231C THR* 4.3 5.2 + - - +
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Residues in contact with PRO 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C VAL* 3.8 30.7 - - + +
162C SER* 4.8 8.5 - - - +
163C ARG* 5.6 0.4 - - + +
164C GLU* 3.8 35.2 - - + +
166C PHE* 3.8 4.5 - - + -
201C ILE 3.4 8.7 - - - +
202C ASN* 1.3 89.6 - - - +
204C GLU* 1.3 63.7 + - - +
206C PHE* 3.1 4.4 + - + +
207C CYS* 2.9 24.5 + - - +
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Residues in contact with GLU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C GLU* 5.1 1.9 + - - -
202C ASN* 2.9 11.4 + - - +
203C PRO* 1.3 79.7 - - - +
205C GLY* 1.3 63.6 + - - +
207C CYS* 3.3 8.8 + - + +
208C ILE* 3.1 48.9 + - + +
223C GLY 5.4 0.9 - - - +
224C ASN* 3.9 21.5 + - - +
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Residues in contact with GLY 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ASN* 3.0 16.6 + - - -
204C GLU* 1.3 77.9 - - - +
206C PHE* 1.3 62.6 + - - +
208C ILE* 3.4 3.2 + - - +
209C LEU* 3.1 27.4 + - - +
224C ASN* 6.2 0.9 - - - +
227C ALA* 4.5 5.4 - - - +
228C VAL* 4.2 20.9 - - - +
231C THR* 4.1 15.7 - - - -
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Residues in contact with PHE 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ILE* 3.7 24.7 - - + -
161C VAL* 4.0 14.4 - - + -
166C PHE* 3.5 42.0 - + + -
173C LEU* 5.3 0.2 - - + -
180C PHE* 4.0 16.2 - + - -
197C LEU* 3.9 23.3 - - + -
201C ILE* 4.7 2.5 - - + -
202C ASN 3.1 10.7 + - - +
203C PRO 3.1 8.1 + - - +
205C GLY* 1.3 77.1 - - - +
207C CYS* 1.3 59.7 + - - +
209C LEU* 3.0 4.7 + - - +
210C LEU* 2.8 49.0 + - + +
213C MET* 5.4 2.0 - - + -
231C THR* 4.0 12.0 - - + +
235C LEU* 4.0 26.2 - - + -
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Residues in contact with CYS 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C GLU* 5.5 1.1 - - - +
166C PHE* 3.7 28.3 - - + -
203C PRO 2.9 11.5 + - - +
204C GLU* 3.5 14.1 - - + +
206C PHE* 1.3 79.6 - - - +
208C ILE* 1.3 59.4 + - + +
210C LEU* 3.7 5.4 - - - +
211C ASP* 2.9 48.5 + - - +
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Residues in contact with ILE 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C GLU* 3.1 32.8 + - + +
205C GLY 3.7 4.3 - - - +
206C PHE 3.2 0.2 - - - -
207C CYS* 1.3 84.5 - - + +
209C LEU* 1.3 57.0 + - - +
211C ASP* 3.7 8.1 - - - +
212C PHE* 3.0 25.5 + - - +
217C ARG 4.7 1.7 - - - +
218C LEU* 4.1 18.6 - - + -
219C ASN* 3.9 27.8 + - + +
224C ASN* 3.3 35.7 - - + +
228C VAL* 3.9 20.0 - - + -
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Residues in contact with LEU 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C GLY 3.1 7.7 + - - +
206C PHE 3.0 8.1 + - - +
208C ILE* 1.3 74.3 - - - +
210C LEU* 1.3 60.6 + - - +
212C PHE* 3.1 8.1 + - + +
213C MET* 3.0 33.7 + - - +
218C LEU* 4.0 12.3 - - + -
228C VAL* 3.8 11.4 - - + +
231C THR* 3.5 25.1 - - + -
232C ALA 3.5 27.4 - - - +
235C LEU* 4.3 5.2 - - + -
237C MET* 3.7 30.1 - - + -
240C VAL* 3.7 31.9 - - + -
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Residues in contact with LEU 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C ARG* 3.5 24.5 - - - +
159C ILE* 6.1 0.4 - - + -
166C PHE* 3.7 35.4 - - + -
167C ARG 4.4 8.3 - - - +
168C ALA* 4.3 5.4 - - + -
173C LEU* 3.6 31.4 - - + -
206C PHE* 2.8 35.8 + - + +
207C CYS* 3.7 5.6 - - - +
209C LEU* 1.3 70.7 - - - +
211C ASP* 1.3 64.5 + - - +
213C MET* 3.1 22.0 + - - +
214C TYR* 3.3 28.2 + - + -
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Residues in contact with ASP 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C ARG* 3.0 31.2 + - - +
207C CYS* 2.9 34.8 + - - +
208C ILE* 3.7 8.5 - - - +
210C LEU* 1.3 75.3 - - - +
212C PHE* 1.3 58.7 + - - +
214C TYR 3.3 1.0 + - - -
215C THR* 2.6 41.2 + - + +
217C ARG 4.2 3.6 - - - +
219C ASN* 5.2 10.2 - - - +
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Residues in contact with PHE 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PHE* 3.6 44.0 - + + -
6C HIS* 3.6 31.6 + + - -
176C CYS* 5.8 1.8 - - + -
208C ILE 3.0 15.5 + - - +
209C LEU* 3.1 13.2 + - + +
211C ASP* 1.3 77.6 - - - +
213C MET* 1.3 70.5 + - + +
215C THR* 3.9 0.2 - - - -
216C SER* 2.8 39.7 + - - -
217C ARG 3.3 21.0 + - - +
218C LEU* 3.9 19.5 - - + -
237C MET* 5.1 8.3 - - + -
240C VAL* 3.8 24.5 - - + -
200D GLU* 4.4 9.6 - - - -
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Residues in contact with MET 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C HIS* 2.8 25.4 + - - -
142C LEU* 3.6 10.9 - - - +
172C VAL* 4.4 4.6 - - + +
173C LEU* 3.6 35.0 - - + -
176C CYS* 3.6 31.1 - - + -
177C SER* 4.1 17.7 - - - -
180C PHE* 4.5 4.5 - - + -
206C PHE* 5.4 1.3 - - + -
209C LEU 3.0 19.8 + - - +
210C LEU* 3.1 16.4 + - + +
212C PHE* 1.3 83.3 - - + +
214C TYR* 1.3 66.6 + - + +
235C LEU* 4.4 7.4 - - + -
237C MET* 3.8 31.6 - - + -
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Residues in contact with TYR 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LEU* 3.3 31.4 - - + +
143C LEU* 5.0 0.9 - - - -
145C LEU* 3.7 14.8 - - + -
146C ASN* 3.3 43.3 - - - +
149C ARG* 3.6 29.6 - - + +
168C ALA* 3.8 3.5 - - + -
169C HIS* 2.7 53.0 + - - +
172C VAL* 3.7 31.6 - - + +
173C LEU* 4.9 1.1 - - + -
210C LEU* 3.3 32.9 + - + +
211C ASP 3.3 4.1 + - - +
212C PHE 3.1 0.4 - - - -
213C MET* 1.3 79.8 - - + +
215C THR* 1.3 58.7 + - - +
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Residues in contact with THR 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LEU* 4.3 3.8 - - - -
146C ASN* 3.6 23.8 - - - +
149C ARG* 5.2 1.1 - - - +
211C ASP* 2.6 28.6 + - + +
214C TYR* 1.3 82.6 - - + +
216C SER* 1.3 72.3 + - - +
217C ARG* 3.0 28.4 + - - +
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Residues in contact with SER 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C ASP* 3.9 3.0 - - - +
3C PHE* 3.3 44.1 + - - +
6C HIS* 3.2 29.1 - - - +
7C SER* 4.0 6.1 + - - -
142C LEU* 3.7 8.1 - - - +
212C PHE* 2.8 22.3 + - - -
215C THR* 1.3 80.5 + - - +
217C ARG* 1.3 59.0 + - - +
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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