Contacts of the helix formed by residues 202 - 213 (chain Y) 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 ALA 202 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44X MET* 3.7 19.4 - - + +
49X LEU* 5.2 2.0 - - + -
52X ASN* 3.1 28.0 - - - +
195Y VAL* 5.1 2.5 - - + +
196Y LEU* 3.8 1.8 - - + +
199Y CYS* 4.3 9.0 - - - -
200Y PRO 2.3 27.8 + - - +
201Y LEU* 1.3 63.0 - - - +
203Y LEU* 1.3 65.8 + - - +
204Y ASP 3.3 0.4 - - - -
205Y ALA* 3.3 12.4 + - + +
206Y ILE* 3.1 25.1 + - - +
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Residues in contact with LEU 203 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44X MET* 4.9 0.2 - - - +
52X ASN* 4.7 5.0 + - - +
55X LEU* 3.9 20.2 - - + +
56X LEU* 3.6 43.0 - - + +
59X LEU* 4.2 10.1 - - + -
201Y LEU 2.8 13.8 + - - +
202Y ALA* 1.3 71.9 - - - +
204Y ASP* 1.3 50.8 - - - +
206Y ILE* 3.0 12.4 + - + +
207Y LEU* 2.6 36.7 + - - +
233Y LEU* 6.3 0.4 - - + -
235Y TRP* 3.7 30.1 - - + -
236Y LEU* 3.9 17.9 - - + -
239Y TRP* 4.2 26.0 - - + -
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Residues in contact with ASP 204 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X SER* 2.6 48.4 + - - +
52X ASN* 2.9 26.2 - - - +
55X LEU* 3.4 30.5 - - - +
180Y LYS* 5.6 0.2 + - - -
192Y TYR* 4.4 4.7 + - - -
202Y ALA 3.3 0.6 - - - -
203Y LEU* 1.3 71.7 - - - +
205Y ALA* 1.3 55.1 + - - +
207Y LEU* 3.5 15.5 - - + +
208Y GLY* 2.6 31.0 + - - -
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Residues in contact with ALA 205 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52X ASN* 3.9 5.9 - - - +
173Y MET* 5.9 0.4 - - + -
192Y TYR* 3.6 16.5 - - + -
195Y VAL* 3.6 30.7 - - + -
196Y LEU* 3.7 14.6 - - + -
202Y ALA* 3.3 20.0 + - + +
203Y LEU 3.3 0.2 - - - -
204Y ASP* 1.3 76.4 - - - +
206Y ILE* 1.3 63.9 + - - +
208Y GLY 3.4 0.3 + - - -
209Y LEU* 3.1 28.9 + - - +
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Residues in contact with ILE 206 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196Y LEU* 3.8 15.7 - - + -
201Y LEU 4.0 6.3 - - - +
202Y ALA 3.1 18.1 + - - +
203Y LEU* 3.0 23.9 + - + +
205Y ALA* 1.3 73.3 - - - +
207Y LEU* 1.3 58.4 + - - +
209Y LEU* 3.2 8.9 + - - +
210Y LEU* 2.9 50.9 + - + +
218Y GLU* 5.1 6.5 - - + -
222Y MET* 3.8 37.2 - - + -
236Y LEU* 4.4 7.6 - - + -
239Y TRP* 4.7 3.6 - - + -
240Y ILE* 4.1 22.9 - - + -
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Residues in contact with LEU 207 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X LEU* 3.8 25.4 - - + -
203Y LEU 2.6 20.3 + - - +
204Y ASP* 3.5 17.3 - - + +
206Y ILE* 1.3 71.0 - - - +
208Y GLY* 1.3 61.5 + - - +
210Y LEU* 3.4 9.7 + - - +
211Y SER* 3.0 22.2 + - - -
239Y TRP* 4.2 10.7 - - + -
243Y TYR* 4.0 31.6 - - + -
247Y HIS* 4.0 15.0 - - + +
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Residues in contact with GLY 208 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180Y LYS* 4.0 12.1 - - - -
192Y TYR* 4.0 14.1 - - - -
204Y ASP 2.6 20.3 + - - -
205Y ALA 3.8 1.8 - - - -
206Y ILE 3.2 0.2 - - - -
207Y LEU* 1.3 73.5 - - - +
209Y LEU* 1.3 56.3 + - - +
211Y SER* 2.4 26.8 + - - -
212Y LEU* 2.9 22.5 + - - +
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Residues in contact with LEU 209 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Y VAL* 3.6 32.5 - - + +
192Y TYR* 3.4 27.9 - - + -
193Y LYS* 4.8 4.3 - - + +
196Y LEU* 3.8 28.9 - - + -
205Y ALA 3.1 15.4 + - - +
206Y ILE* 3.2 9.4 + - - +
208Y GLY* 1.3 73.5 - - - +
210Y LEU* 1.3 53.4 + - - +
212Y LEU* 3.2 13.1 + - + +
213Y SER 2.8 41.4 + - - +
218Y GLU* 4.5 22.9 - - + -
221Y SER* 6.0 0.2 - - - +
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Residues in contact with LEU 210 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206Y ILE* 2.9 36.5 + - + +
207Y LEU* 3.8 6.1 - - - +
209Y LEU* 1.3 72.7 - - - +
211Y SER* 1.3 64.4 - - - +
213Y SER* 3.2 13.4 + - - +
215Y LYS* 4.0 31.9 - - + +
218Y GLU* 4.3 9.6 - - + -
239Y TRP* 4.2 5.6 - - + -
240Y ILE* 3.6 39.7 - - + +
243Y TYR* 3.6 18.4 - - + -
244Y ALA* 3.9 11.3 - - + +
247Y HIS* 3.2 30.8 - - + +
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Residues in contact with SER 211 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180Y LYS* 4.3 14.6 + - - +
185Y GLU* 4.8 3.3 - - - +
207Y LEU* 3.0 10.2 + - - -
208Y GLY* 2.4 30.5 + - - -
210Y LEU* 1.3 75.7 - - - +
212Y LEU* 1.3 59.6 + - - +
213Y SER* 3.5 1.6 + - - -
247Y HIS* 3.4 35.3 + - - +
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Residues in contact with LEU 212 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180Y LYS* 4.0 17.0 - - + -
185Y GLU* 3.9 48.3 - - + +
188Y SER* 3.8 16.8 - - - +
189Y VAL* 3.8 24.0 - - + +
192Y TYR* 3.7 30.5 - - + -
208Y GLY 2.9 15.0 + - - +
209Y LEU* 3.3 19.1 - - + +
211Y SER* 1.3 77.4 + - - +
213Y SER* 1.3 73.4 + - - +
214Y VAL* 5.2 1.2 - - - +
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Residues in contact with SER 213 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Y VAL* 5.7 2.6 - - - +
209Y LEU* 2.8 22.2 + - - +
210Y LEU* 3.2 14.1 + - - +
211Y SER 4.8 1.3 - - - -
212Y LEU* 1.3 87.4 + - - +
214Y VAL* 1.3 80.9 + - - +
215Y LYS* 3.3 5.2 - - - +
218Y GLU* 5.7 0.5 - - - +
247Y HIS* 5.6 5.8 - - - -
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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