Contacts of the helix formed by residues 202 - 213 (chain P) in PDB entry 5G04
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 HIS 202 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1M MET 6.3 0.2 - - - -
39P ILE* 3.6 8.9 - - + +
43P THR* 4.0 4.8 - - - +
48P LEU* 3.9 15.5 - - + +
51P SER* 3.5 24.8 + - - -
170P PHE* 4.0 20.6 - + + -
173P TYR* 3.6 28.4 - + + -
199P LEU* 4.0 24.4 - - + +
200P PRO* 3.2 4.2 + - - +
201P LEU* 1.3 75.5 - - - +
203P TRP* 1.3 64.2 + - - +
204P GLY* 3.3 22.7 + - - -
205P ALA* 3.3 37.1 + - + +
206P TRP* 3.5 13.3 + - - -
229P MET* 4.0 1.3 - - - -
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Residues in contact with TRP 203 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50P HIS 5.7 0.2 - - - -
51P SER* 4.6 9.5 + - - +
54P TRP* 3.4 72.6 - + + -
55P SER* 6.1 0.8 - - - -
201P LEU 3.4 5.3 + - - -
202P HIS* 1.3 74.6 + - - +
204P GLY* 1.3 54.9 + - - +
206P TRP* 3.1 19.4 + + + +
207P LEU* 2.7 76.6 + - + +
210P CYS* 4.9 3.4 - - - -
229P MET* 3.5 25.1 - - + -
232P PHE* 4.3 28.5 - - + -
233P PHE* 4.4 11.0 - - + -
236P HIS* 4.4 9.6 - + + -
264P TYR* 3.9 19.1 - + - -
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Residues in contact with GLY 204 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1M MET* 5.6 4.3 - - - -
51P SER* 3.8 9.0 - - - -
173P TYR* 3.4 15.0 - - - -
202P HIS* 3.3 19.5 + - - -
203P TRP* 1.3 80.4 - - - +
205P ALA* 1.3 55.4 + - - +
207P LEU* 3.5 7.7 + - - +
208P GLU* 3.0 37.4 + - - +
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Residues in contact with ALA 205 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173P TYR* 3.6 15.9 - - + -
192P PHE* 4.0 12.5 - - + +
195P ALA* 4.5 17.0 - - + -
196P THR* 4.3 19.6 - - + +
199P LEU 5.4 2.9 - - - +
202P HIS* 3.3 29.1 + - + +
203P TRP 3.2 0.8 - - - -
204P GLY* 1.3 73.8 - - - +
206P TRP* 1.3 64.7 + - + +
208P GLU* 3.4 4.9 + - - +
209P LEU* 3.4 17.3 + - - +
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Residues in contact with TRP 206 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196P THR* 3.8 25.1 - - + +
199P LEU 5.7 0.4 - - - -
200P PRO* 4.3 3.6 - - + +
201P LEU 4.1 10.3 - - - +
202P HIS 3.5 20.6 - - - -
203P TRP* 3.1 21.9 + + + +
205P ALA* 1.3 79.5 - - + +
207P LEU* 1.3 62.9 + - - +
209P LEU* 3.1 22.2 + - + +
210P CYS* 3.2 7.3 + - - -
224P LEU* 3.9 21.1 - - + -
225P PRO* 3.7 37.7 - - + -
227P THR* 4.8 3.4 - - - -
229P MET* 3.5 32.7 - - + +
230P LYS* 4.1 20.9 - - + -
233P PHE* 3.2 56.9 - + + -
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Residues in contact with LEU 207 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M MET* 4.8 21.5 - - + -
203P TRP* 2.7 62.9 + - + +
204P GLY* 3.7 8.1 - - - +
206P TRP* 1.3 71.3 - - - +
208P GLU* 1.3 68.1 + - - +
210P CYS* 3.0 23.9 + - + +
211P ASN* 3.5 13.2 + - - +
236P HIS* 3.8 24.7 - - + +
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Residues in contact with GLU 208 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M MET* 3.1 29.5 - - - +
2M ASP* 4.0 2.4 - - - +
173P TYR* 2.9 35.3 + - + -
177P VAL* 4.5 2.5 - - + -
180P ARG* 2.7 31.3 + - - +
192P PHE* 3.4 33.9 - - + -
204P GLY* 3.0 22.5 + - - +
205P ALA 3.9 0.9 - - - +
206P TRP 3.3 0.4 - - - -
207P LEU* 1.3 77.8 - - - +
209P LEU* 1.3 62.5 + - - +
211P ASN* 3.1 21.6 + - - +
212P LEU* 3.3 17.0 + - - +
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Residues in contact with LEU 209 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189P ILE* 4.1 34.8 - - + +
192P PHE* 3.6 25.7 - - + -
193P VAL* 4.3 15.3 - - + +
196P THR* 4.7 13.2 - - + -
205P ALA 3.4 7.1 + - - +
206P TRP* 3.1 14.7 + - + +
207P LEU 3.1 0.6 - - - -
208P GLU* 1.3 77.9 - - - +
210P CYS* 1.3 59.4 + - - +
212P LEU* 3.2 3.1 + - - -
213P ILE* 3.1 36.9 + - + +
222P LEU* 4.7 1.6 - - + -
224P LEU* 4.2 21.8 - - + -
233P PHE* 3.8 23.3 - - + -
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Residues in contact with CYS 210 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203P TRP* 4.9 2.2 - - - -
206P TRP 3.4 14.8 - - - -
207P LEU* 3.0 20.4 + - + +
209P LEU* 1.3 76.7 - - - +
211P ASN* 1.3 63.9 + - - +
212P LEU 3.5 0.2 + - - -
213P ILE* 3.8 14.1 + - - +
233P PHE* 3.7 22.9 - - - -
236P HIS* 3.3 38.6 - - + +
237P ILE* 4.5 13.5 - - + +
240P GLU* 3.0 21.2 - - + +
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Residues in contact with ASN 211 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1M MET* 5.0 7.1 - - - +
180P ARG* 4.6 11.3 - - - +
207P LEU* 3.5 13.2 + - - +
208P GLU* 3.1 24.8 + - - +
210P CYS* 1.3 79.6 - - - +
212P LEU* 1.3 68.8 + - + +
213P ILE 4.2 3.1 - - - +
214P THR* 4.9 5.0 - - - +
236P HIS* 5.7 0.3 + - - -
240P GLU* 3.6 21.9 - - - +
363P ARG* 6.1 3.7 - - - +
397P ARG* 5.4 3.8 - - - +
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Residues in contact with LEU 212 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180P ARG* 3.6 28.5 - - + -
185P VAL* 3.8 32.8 - - + +
188P ALA* 3.6 31.6 - - + -
189P ILE* 3.7 32.5 - - + +
192P PHE* 3.8 22.9 - - + -
208P GLU 3.3 7.8 + - - +
209P LEU* 3.2 8.2 + - + +
211P ASN* 1.3 78.8 - - + +
213P ILE* 1.3 63.3 + - - +
214P THR* 3.4 12.8 + - - +
218P MET* 4.3 1.4 - - - +
363P ARG* 6.3 0.2 - - - +
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Residues in contact with ILE 213 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189P ILE* 4.0 18.4 - - + -
209P LEU* 3.1 30.9 + - + +
210P CYS* 3.8 13.9 + - - +
211P ASN 3.6 2.1 - - - +
212P LEU* 1.3 74.1 - - - +
214P THR* 1.3 63.2 + - - +
215P ASP 3.4 26.9 - - - +
218P MET* 3.7 15.0 - - + -
219P LEU* 4.2 14.6 - - + +
222P LEU* 3.7 29.4 - - + -
233P PHE* 4.9 8.7 - - + -
237P ILE* 4.7 16.1 - - + +
240P GLU* 5.1 0.5 - - - +
241P LEU* 4.4 7.1 - - + +
397P ARG* 4.4 6.8 - - - +
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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