Contacts of the helix formed by residues 198 - 219 (chain C) in PDB entry 2GER
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 PRO 198 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A PRO* 3.9 11.7 - - + -
193C VAL* 4.9 0.2 - - - -
197C LEU* 1.4 87.4 - - + +
199C ARG* 1.3 67.5 + - - +
200C ARG* 3.3 3.8 - - + +
201C LEU* 2.8 45.0 + - + +
202C ALA 3.0 10.2 + - - -
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Residues in contact with ARG 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LYS* 2.8 32.1 - - - +
229A ASP* 3.0 41.7 + - + +
232A SER 6.1 1.3 - - - +
234A PRO* 4.6 5.0 - - + +
185C LEU 5.1 0.2 - - - -
186C ASP* 2.6 27.5 + - - +
189C ALA* 3.1 18.4 + - - +
190C ASP* 2.9 12.7 + - - -
193C VAL* 3.7 26.8 - - + +
197C LEU 3.7 2.6 + - - -
198C PRO* 1.3 70.0 - - - +
200C ARG* 1.3 66.5 + - - +
202C ALA* 2.8 14.2 + - - +
203C VAL* 3.0 40.1 + - + +
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Residues in contact with ARG 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C PRO* 3.2 3.9 + - + +
199C ARG* 1.3 79.6 - - - +
201C LEU* 1.3 62.3 + - - +
203C VAL* 3.5 8.1 - - - +
204C ARG* 3.1 70.7 + - - +
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Residues in contact with LEU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C LEU* 4.7 10.1 - - + -
198C PRO* 2.8 40.2 + - + +
200C ARG* 1.3 78.1 - - - +
202C ALA* 1.3 63.5 + - - +
203C VAL 3.2 1.3 - - - -
204C ARG* 4.7 4.9 - - + +
205C LEU* 3.0 55.0 + - + +
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Residues in contact with ALA 202 (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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189C ALA* 3.4 35.6 - - + +
192C GLY* 4.6 6.1 - - - -
193C VAL* 3.9 21.8 - - + +
197C LEU* 4.2 14.1 - - + +
198C PRO 3.0 7.2 + - - +
199C ARG 2.8 12.1 + - - +
201C LEU* 1.3 72.0 - - - +
203C VAL* 1.3 58.5 + - - +
205C LEU* 3.4 1.8 - - - +
206C GLY* 2.9 27.2 + - - -
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Residues in contact with VAL 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 5.0 12.9 - - + +
189C ALA* 3.4 10.4 - - + +
199C ARG* 3.0 52.7 - - + +
200C ARG* 3.5 9.2 - - - +
202C ALA* 1.3 75.2 - - - +
204C ARG* 1.3 66.7 + - - +
206C GLY* 3.4 0.7 + - - -
207C ALA* 2.8 32.3 + - + +
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Residues in contact with ARG 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C ARG* 3.1 60.1 + - - +
201C LEU* 4.7 5.6 - - + +
203C VAL* 1.3 87.6 - - - +
205C LEU* 1.3 58.5 + - - +
207C ALA* 3.2 8.4 - - - +
208C GLN* 2.8 31.5 + - - +
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Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C LEU* 4.0 19.3 - - + -
201C LEU* 3.0 49.6 + - + +
202C ALA* 3.4 3.1 - - - +
204C ARG* 1.3 76.5 - - - +
206C GLY* 1.3 55.6 + - - +
208C GLN* 3.1 8.7 + - + +
209C ALA* 2.7 35.1 + - - +
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Residues in contact with GLY 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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185C LEU* 3.9 13.7 - - - -
188C LEU* 4.9 14.9 - - - +
189C ALA* 5.6 1.1 - - - -
202C ALA 2.9 18.8 + - - -
203C VAL 3.9 0.7 - - - -
205C LEU* 1.3 71.5 - - - +
207C ALA* 1.3 64.3 + - - +
209C ALA* 2.9 10.3 + - - +
210C LEU* 2.8 27.2 + - - +
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Residues in contact with ALA 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 3.9 23.8 - - + +
203C VAL* 2.8 21.5 + - + +
204C ARG* 3.2 13.9 - - - +
206C GLY* 1.3 76.6 - - - +
208C GLN* 1.3 54.0 + - - +
210C LEU* 3.0 3.3 + - - +
211C LEU* 2.7 36.5 + - - +
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Residues in contact with GLN 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 ARG 2.8 20.7 + - - +
205C LEU* 3.5 7.9 - - + +
207C ALA* 1.3 73.4 - - - +
209C ALA* 1.3 65.3 + - - +
211C LEU* 3.4 26.7 - - - +
212C GLY* 2.7 28.5 + - - +
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Residues in contact with ALA 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C LEU* 6.2 1.8 - - + -
205C LEU 2.7 17.9 + - - +
206C GLY* 2.9 14.8 + - - +
208C GLN* 1.3 73.3 - - - +
210C LEU* 1.3 66.5 + - + +
212C GLY* 3.8 0.5 - - - -
213C ALA* 2.9 24.3 + - - +
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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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181C ALA* 4.9 9.4 - - + +
184C ALA* 4.8 12.1 - - + -
185C LEU* 3.4 35.0 - - + -
188C LEU* 4.6 13.9 - - + -
206C GLY 2.8 13.6 + - - +
207C ALA* 3.3 7.4 - - - +
209C ALA* 1.3 71.3 - - + +
211C LEU* 1.3 70.9 + - - +
213C ALA* 2.8 21.6 + - + +
214C ALA* 3.0 14.0 + - - +
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Residues in contact with LEU 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C GLU* 6.5 1.1 - - + -
207C ALA 2.7 19.3 + - - +
208C GLN* 3.4 25.8 - - - +
210C LEU* 1.3 76.6 - - - +
212C GLY* 1.3 67.2 + - - +
214C ALA* 3.3 5.9 + - - +
215C LYS* 3.0 33.0 + - + -
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Residues in contact with GLY 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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208C GLN* 2.7 24.8 + - - +
209C ALA 3.8 0.9 - - - -
211C LEU* 1.3 79.7 - - - +
213C ALA* 1.3 51.4 + - - +
215C LYS* 3.4 5.4 + - - +
216C MET* 2.8 39.6 + - - +
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Residues in contact with ALA 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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209C ALA 2.9 14.6 + - - +
210C LEU* 2.8 23.7 + - + +
212C GLY* 1.3 69.4 - - - +
214C ALA* 1.3 51.4 + - - +
216C MET* 2.7 29.3 - - - +
217C LEU* 2.7 17.4 + - - +
227C LEU* 5.8 0.2 - - - +
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Residues in contact with ALA 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 LEU 3.0 7.5 + - - +
211C LEU* 3.5 10.3 - - - +
213C ALA* 1.3 74.1 - - - +
215C LYS* 1.3 69.1 + - - +
216C MET 2.9 1.1 - - - -
217C LEU* 2.8 9.2 + - - +
218C LEU* 2.8 32.8 + - + +
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Residues in contact with LYS 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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211C LEU* 3.0 21.4 + - + +
212C GLY* 3.7 9.6 - - - +
214C ALA* 1.3 78.0 - - - +
216C MET* 1.3 63.3 + - - +
218C LEU* 3.3 11.4 + - + +
219C HIS* 3.1 66.4 + - + +
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Residues in contact with MET 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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212C GLY 2.8 16.7 + - - +
213C ALA* 2.7 18.8 - - - +
215C LYS* 1.3 80.1 - - - +
217C LEU* 1.3 62.4 + - - +
219C HIS* 4.3 1.9 - - - +
220C SER* 3.1 22.1 + - - -
227C LEU* 4.4 30.1 - - + -
230C ASN* 6.2 0.4 - - - +
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Residues in contact with LEU 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 ALA 2.7 15.4 + - - +
214C ALA* 2.8 12.8 + - - +
216C MET* 1.3 68.8 - - - +
218C LEU* 1.3 67.7 - - + +
220C SER* 2.9 23.8 + - - +
222C GLN 4.1 12.0 - - - +
224C PRO* 4.0 40.6 - - + -
227C LEU* 3.9 23.3 - - + +
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Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C GLU* 6.1 1.1 - - - +
214C ALA* 2.8 24.8 + - + +
215C LYS* 3.5 15.0 - - - +
217C LEU* 1.3 76.1 - - + +
219C HIS* 1.3 67.1 + - + +
220C SER 3.1 10.9 + - - +
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Residues in contact with HIS 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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129C ARG* 5.9 4.3 - - - -
215C LYS* 3.1 58.3 + - + +
216C MET* 4.3 1.8 - - - +
218C LEU* 1.3 75.9 - - + +
220C SER* 1.3 58.3 + - - +
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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
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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