Contacts of the helix formed by residues 200 - 219 (chain C) in PDB entry 1REP
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 ARG 200 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A T 3.8 14.7 + - + +
4A G 2.7 23.1 + - - -
5A T 2.6 30.7 + - - +
38B C 4.7 4.1 - - - -
39B A 3.2 12.3 + - - +
40B C 4.2 3.0 - - - +
197C SER* 3.5 11.3 + - - +
198C TYR 3.0 2.2 - - - -
199C GLN* 1.3 77.8 - - - +
201C MET* 1.3 53.8 + - - +
202C PRO* 3.5 31.7 - - + +
203C ASP* 2.7 63.9 + - - +
204C PHE* 3.3 3.1 + - - +
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Residues in contact with MET 201 (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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3A T 3.6 16.2 - - - +
185C ILE* 3.4 46.7 - - + -
189C ILE* 6.0 0.4 - - + -
198C TYR 5.2 1.6 - - - +
199C GLN 3.5 12.1 + - - +
200C ARG* 1.3 69.8 - - - +
202C PRO* 1.3 70.7 - - + +
203C ASP 3.0 1.2 + - - -
204C PHE* 3.0 28.9 + - + +
205C ARG* 3.0 49.8 + - - +
228C GLU* 5.0 1.1 - - - +
235C THR* 4.2 18.6 - - - +
238C ILE* 6.1 0.4 - - - -
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Residues in contact with PRO 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A T 3.5 37.5 - - + +
4A G 3.3 40.8 + - + +
5A T 4.1 7.0 - - + +
200C ARG* 3.2 36.3 - - + +
201C MET* 1.3 94.0 - - + +
203C ASP* 1.3 59.0 + - - +
205C ARG* 4.0 5.5 + - + +
206C ARG* 3.7 19.9 + - - +
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Residues in contact with ASP 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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5A T 4.1 3.3 - - - +
37B T 3.6 17.6 - - + +
38B C 3.3 33.3 + - - -
197C SER* 3.5 20.7 - - - +
198C TYR* 3.8 7.5 - - + -
200C ARG* 2.7 44.4 + - - +
202C PRO* 1.3 71.7 - - - +
204C PHE* 1.3 58.0 + - - +
205C ARG 3.2 1.8 - - - -
206C ARG* 4.1 10.9 + - - +
207C ARG* 3.0 34.7 + - - +
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Residues in contact with PHE 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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185C ILE* 4.0 37.5 - - + -
188C ILE* 4.0 22.7 - - + -
189C ILE* 4.4 5.6 - - + -
194C LEU* 4.2 5.4 - - + -
198C TYR* 3.5 38.9 - - + +
200C ARG 3.3 1.6 + - - -
201C MET* 3.0 26.4 + - + +
203C ASP* 1.3 75.2 - - - +
205C ARG* 1.3 65.2 + - + +
208C PHE* 3.2 45.1 + + - +
209C LEU* 2.8 48.3 + - + -
238C ILE* 4.6 3.4 - - + -
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Residues in contact with ARG 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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3A T 3.1 33.6 + - - -
4A G 3.0 34.0 + - - +
201C MET* 3.0 34.6 + - + +
202C PRO* 4.0 11.0 - - - +
204C PHE* 1.3 81.6 - - + +
206C ARG* 1.3 60.0 + - + +
209C LEU* 3.9 13.9 - - + -
210C GLN* 2.8 49.7 + - - +
226C TYR* 5.8 1.3 - - - -
228C GLU* 2.7 42.6 + - - -
230C LYS* 3.7 5.1 - - - +
235C THR* 3.1 13.9 + - - -
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Residues in contact with ARG 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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4A G 6.0 0.7 - - + -
5A T 3.6 42.0 - - + +
6A G 2.9 44.1 + - - -
7A A 3.7 5.7 - - - +
37B T 3.5 17.4 + - - +
38B C 4.1 2.8 - - - +
202C PRO 3.7 13.4 + - - +
203C ASP* 3.6 8.9 + - - +
204C PHE 3.5 0.2 - - - -
205C ARG* 1.3 83.6 - - + +
207C ARG* 1.3 89.0 + - + +
210C GLN* 3.4 24.1 + - - +
211C VAL* 3.7 14.6 - - - +
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Residues in contact with ARG 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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7A A 3.7 15.0 - - - +
8A C 4.1 2.0 - - - +
35B T 3.8 37.7 + - + +
36B G 2.3 52.8 + - - +
37B T 3.7 7.7 + - + -
159C ASN* 5.0 3.3 + - - -
161C TYR* 6.1 0.7 - - - -
198C TYR* 2.9 44.2 + - + +
203C ASP* 3.0 10.2 + - - +
206C ARG* 1.3 107.4 + - + +
208C PHE* 1.3 58.5 + - - +
211C VAL* 3.3 27.0 - - - +
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Residues in contact with PHE 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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161C TYR* 4.0 25.1 - + + -
165C LEU* 4.5 18.2 - - + -
188C ILE* 3.9 22.2 - - + -
192C TYR* 4.4 13.7 - + - -
194C LEU* 4.5 10.8 - - + -
198C TYR* 4.4 18.6 - - + -
204C PHE* 3.2 55.2 + + + +
206C ARG 3.6 0.2 - - - -
207C ARG* 1.3 78.7 - - - +
209C LEU* 1.3 88.2 + - + +
210C GLN 3.7 0.4 - - - -
211C VAL* 3.8 1.0 - - - +
212C CYS* 3.0 50.8 + - + -
240C PHE* 5.6 0.4 - + - -
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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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165C LEU* 5.3 2.2 - - + -
204C PHE* 2.8 33.8 + - + +
205C ARG* 3.5 14.8 - - + +
208C PHE* 1.3 83.8 - - + +
210C GLN* 1.3 68.2 + - - +
212C CYS* 4.0 1.2 - - - +
213C VAL* 2.9 35.4 + - + +
226C TYR* 3.4 36.1 - - + +
228C GLU* 4.8 6.3 - - - +
238C ILE* 3.5 22.4 - - + -
240C PHE* 3.9 33.2 - - + -
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Residues in contact with GLN 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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205C ARG* 2.8 40.0 + - - +
206C ARG* 3.4 29.1 - - - +
209C LEU* 1.3 72.8 - - - +
211C VAL* 1.3 62.8 + - + +
213C VAL* 3.4 4.4 + - - +
214C ASN* 2.9 38.5 + - - +
226C TYR* 3.4 22.5 + - + +
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Residues in contact with VAL 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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35B T 3.7 36.8 - - - +
159C ASN* 3.9 15.9 - - + +
206C ARG 3.7 13.6 + - - +
207C ARG* 3.3 31.0 - - - +
208C PHE 3.6 1.1 + - - +
209C LEU 3.2 0.6 - - - -
210C GLN* 1.3 81.0 - - + +
212C CYS* 1.3 67.6 + - - +
214C ASN* 3.9 5.2 - - - +
215C GLU* 3.1 24.8 + - - +
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Residues in contact with CYS 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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159C ASN* 4.3 2.9 - - - -
161C TYR* 3.9 4.5 - - - -
162C ALA* 3.5 42.6 - - + -
165C LEU* 4.1 18.2 - - + -
208C PHE* 3.0 42.5 + - + +
209C LEU* 4.0 1.8 - - - +
211C VAL* 1.3 81.1 - - - +
213C VAL* 1.3 66.4 + - - +
215C GLU* 3.5 1.0 + - - +
216C ILE* 2.9 30.6 + - - +
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Residues in contact with VAL 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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165C LEU* 5.1 4.0 - - + -
209C LEU* 2.9 28.5 + - + +
210C GLN* 3.7 4.3 - - - +
212C CYS* 1.3 78.4 - - - +
214C ASN* 1.3 71.2 + - - +
216C ILE* 3.3 3.0 + - - +
217C ASN* 3.0 39.7 + - - +
224C LEU* 3.9 25.7 - - + +
225C SER* 5.5 0.4 - - - -
226C TYR* 3.8 34.1 - - + -
240C PHE* 4.8 6.3 - - + -
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Residues in contact with ASN 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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210C GLN* 2.9 25.6 + - - +
211C VAL* 3.9 4.6 - - - +
213C VAL* 1.3 83.8 - - - +
215C GLU* 1.3 65.9 + - - +
217C ASN* 2.9 17.2 + - - +
218C SER* 3.1 20.1 + - - +
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Residues in contact with GLU 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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35B T 5.3 3.4 + - - -
157C ILE* 4.3 10.8 - - + -
158C THR* 3.6 15.4 + - - +
159C ASN* 2.7 45.4 + - - +
162C ALA* 3.9 7.6 - - + +
211C VAL* 3.1 18.5 + - - +
212C CYS 3.7 5.4 - - - +
213C VAL 3.4 0.2 - - - -
214C ASN* 1.3 78.5 - - - +
216C ILE* 1.3 57.1 + - - +
218C SER* 4.8 0.7 - - - -
219C ARG* 2.9 67.6 + - - +
220C THR* 4.6 0.2 - - - +
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Residues in contact with ILE 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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157C ILE* 5.0 3.1 - - + -
162C ALA* 3.8 16.4 - - + +
165C LEU* 4.3 11.4 - - + -
166C TYR* 3.7 44.6 - - + +
169C LEU* 4.5 9.6 - - + -
212C CYS 2.9 18.4 + - - +
213C VAL* 3.6 3.8 - - - +
214C ASN 3.1 0.8 - - - -
215C GLU* 1.3 72.6 - - - +
217C ASN* 1.3 54.2 + - - +
218C SER 2.8 15.1 + - - -
220C THR* 2.8 49.3 + - - +
222C MET* 3.5 21.6 - - + +
224C LEU* 4.3 13.0 - - + -
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Residues in contact with ASN 217 (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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213C VAL* 3.0 29.2 + - - +
214C ASN* 2.9 7.6 + - - +
216C ILE* 1.3 72.8 - - - +
218C SER* 1.3 64.9 + - - +
222C MET 3.4 0.9 - - - +
223C ARG* 2.9 37.0 + - - +
224C LEU* 2.7 49.1 + - - +
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Residues in contact with SER 218 (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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156C GLU* 4.2 5.5 - - - +
214C ASN* 3.1 17.3 + - - +
215C GLU* 4.0 2.0 - - - -
216C ILE 2.8 2.2 + - - -
217C ASN* 1.3 84.9 + - - +
219C ARG* 1.3 71.6 + - - +
220C THR 3.6 1.3 - - - -
223C ARG* 4.1 5.6 - - - +
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Residues in contact with ARG 219 (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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152C SER 4.5 4.3 - - - +
153C GLU 3.7 5.2 - - - +
156C GLU* 3.2 70.1 + - + +
157C ILE* 4.2 6.3 - - + +
158C THR* 3.0 25.3 + - - -
215C GLU* 2.9 49.9 + - - +
218C SER* 1.3 84.5 - - - +
220C THR* 1.3 63.2 - - - +
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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