Contacts of the helix formed by residues 203 - 214 (chain C) in PDB entry 4GJ0
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 SER 203 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171C GLN* 4.8 5.5 + - - -
201C ILE* 4.2 0.5 - - - +
202C HIS* 1.3 81.0 - - - +
204C PRO* 1.3 67.6 - - - +
205C GLU* 3.3 17.1 + - - +
206C GLU* 2.9 27.6 + - - +
207C GLN* 2.9 26.9 + - - +
242C TYR* 3.7 11.7 - - - +
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Residues in contact with PRO 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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203C SER* 1.3 86.4 - - - +
205C GLU* 1.3 71.6 + - - +
207C GLN* 3.5 0.7 - - + +
208C ASP* 2.9 39.8 + - - +
242C TYR* 3.6 32.1 - - + +
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Residues in contact with GLU 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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170C PHE* 3.7 10.5 - - + -
171C GLN* 4.0 20.9 - - - +
203C SER* 3.3 20.2 + - - +
204C PRO* 1.3 80.9 - - - +
206C GLU* 1.3 65.8 + - - +
208C ASP* 3.3 8.4 + - - +
209C PHE* 3.1 23.0 + - - +
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Residues in contact with GLU 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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170C PHE* 3.7 14.9 - - + -
171C GLN* 5.2 2.9 - - - +
173C LYS* 2.8 24.8 + - - -
175C TYR* 2.6 38.6 + - + +
200C SER 3.2 11.4 - - - +
201C ILE* 3.6 3.8 - - + -
202C HIS* 2.8 31.0 + - - +
203C SER* 2.9 22.3 + - - +
205C GLU* 1.3 78.0 - - - +
207C GLN* 1.3 62.0 + - - +
209C PHE* 3.3 3.1 + - - +
210C LEU* 3.1 34.5 + - + +
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Residues in contact with GLN 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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201C ILE* 3.8 15.7 - - + +
203C SER 2.9 11.9 + - - +
204C PRO 3.5 7.6 - - - +
205C GLU 3.2 0.2 - - - -
206C GLU* 1.3 76.9 - - - +
208C ASP* 1.3 62.8 + - - +
210C LEU* 3.0 5.8 + - - +
211C THR* 2.8 53.6 + - - +
242C TYR* 3.1 27.1 - - + +
244C ASN* 3.5 12.2 + - - +
262C MET* 3.6 18.0 - - - -
266C GLY 3.3 18.3 + - - -
268C TRP* 2.9 29.1 + - - -
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Residues in contact with ASP 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 PRO* 2.9 26.2 + - - +
205C GLU* 3.3 7.6 + - - +
207C GLN* 1.3 81.3 - - - +
209C PHE* 1.3 62.6 + - - +
211C THR* 3.5 8.9 + - - -
212C LYS* 3.1 22.7 + - - +
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Residues in contact with PHE 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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168C ILE* 3.7 30.3 - - + -
169C ASN 4.0 2.5 - - - -
170C PHE* 3.6 47.8 - + + -
175C TYR* 3.5 33.0 - + - -
177C PHE* 4.0 13.0 - + - -
205C GLU 3.1 12.5 + - - +
206C GLU 3.6 7.9 - - - +
208C ASP* 1.3 74.5 - - - +
210C LEU* 1.3 73.8 + - + +
212C LYS* 3.1 10.6 + - - +
213C HIS* 2.9 54.2 + + - -
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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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175C TYR* 3.7 28.5 - - + -
177C PHE* 3.9 24.1 - - + -
199C VAL* 4.0 11.9 - - + -
201C ILE* 3.5 43.3 - - + -
206C GLU* 3.1 23.6 + - + +
207C GLN* 3.0 13.6 + - - +
209C PHE* 1.3 82.4 - - + +
211C THR* 1.3 52.9 + - - +
213C HIS 3.0 3.8 + - - -
214C ALA* 2.8 36.9 + - - +
262C MET* 4.3 10.8 - - + -
281C VAL* 4.2 9.6 - - + -
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Residues in contact with THR 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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207C GLN* 2.8 37.9 + - - +
208C ASP* 3.7 9.6 + - - -
209C PHE 3.3 0.2 - - - -
210C LEU* 1.3 75.9 - - - +
212C LYS* 1.3 59.4 + - - +
213C HIS 3.5 0.3 + - - -
214C ALA* 3.6 18.4 + - - +
216C HIS* 6.1 1.0 - - - -
264C GLY 3.8 9.8 - - - +
265C SER* 3.4 29.4 + - - +
266C GLY* 3.5 7.9 - - - -
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Residues in contact with LYS 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 ASP 3.1 13.7 + - - +
209C PHE* 3.1 14.6 + - + +
210C LEU 3.0 0.6 - - - -
211C THR* 1.3 78.3 - - - +
213C HIS* 1.3 72.5 + - + +
214C ALA 5.2 0.2 - - - +
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Residues in contact with HIS 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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168C ILE* 3.6 27.7 - - + +
177C PHE* 3.4 41.6 - + + +
179C LYS* 4.5 5.9 + - - -
209C PHE* 2.9 53.3 + + - -
210C LEU 3.0 2.6 + - - -
212C LYS* 1.3 93.1 - - + +
214C ALA* 1.3 67.3 + - - +
215C SER 3.8 0.5 + - - -
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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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177C PHE* 4.6 7.2 - - - -
179C LYS* 5.2 0.2 - - - -
210C LEU 2.8 15.6 + - - +
211C THR* 3.6 17.9 + - - +
212C LYS 3.6 1.9 - - - +
213C HIS* 1.3 82.6 - - - +
215C SER* 1.3 68.2 + - - +
216C HIS* 3.7 13.9 + - - -
219C SER* 5.0 1.3 - - - +
262C MET* 4.0 21.8 - - + +
263C ARG 4.6 10.1 - - - +
264C GLY* 4.7 4.4 - - - +
266C GLY 5.7 0.2 - - - +
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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