Contacts of the helix formed by residues 202 - 212 (chain A) in PDB entry 2P80
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A HIS* 5.4 5.6 - - + -
144A TRP* 4.9 1.6 + - + +
186A PRO* 5.0 1.8 - - + -
196A TYR* 3.5 42.0 - - + -
198A ALA 4.1 1.5 + - - +
199A PRO 3.5 10.9 + - - +
200A GLY 3.0 1.4 - - - -
201A ASP* 1.3 79.0 - - - +
203A TYR* 1.3 57.5 + - - +
204A GLU 3.6 0.7 - - - -
205A ASP* 4.3 3.1 - - - -
206A THR* 2.3 43.6 + - - +
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Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLY 4.0 15.9 + - - -
141A MET* 4.2 16.9 - - + +
144A TRP* 3.4 53.7 - + + +
199A PRO 4.0 1.5 + - - -
200A GLY* 2.9 23.5 + - - +
201A ASP 3.4 0.6 - - - -
202A ALA* 1.3 77.8 - - - +
204A GLU* 1.3 72.9 + - + +
206A THR* 3.8 2.7 - - - -
207A VAL* 3.1 51.5 + - + +
313B GLU* 4.3 8.8 + - - -
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Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A GLY 4.8 0.6 + - - -
201A ASP 5.0 2.5 + - - +
202A ALA* 4.7 0.2 - - - +
203A TYR* 1.3 86.0 - - + +
205A ASP* 1.3 72.0 + - - +
207A VAL* 3.4 6.4 + - + +
208A LYS* 3.2 21.0 + - - +
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Residues in contact with ASP 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A PRO* 3.6 12.9 - - + +
194A LYS* 3.1 27.4 + - - -
196A TYR* 3.2 27.5 + - + +
201A ASP 5.0 3.6 + - - +
202A ALA 4.1 3.4 + - - +
203A TYR 3.4 0.2 - - - -
204A GLU* 1.3 86.1 - - - +
206A THR* 1.3 61.2 + - - +
208A LYS* 3.5 9.9 + - - +
209A VAL* 3.3 24.6 + - - +
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Residues in contact with THR 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TRP* 4.4 17.9 + - + +
147A VAL* 5.2 3.1 - - + -
184A TYR* 3.6 20.9 - - + +
186A PRO* 3.8 17.0 - - - +
202A ALA* 2.3 31.0 + - - +
203A TYR* 3.8 3.8 - - - -
204A GLU 3.2 0.4 - - - -
205A ASP* 1.3 76.7 - - - +
207A VAL* 1.3 66.7 + - - +
209A VAL* 2.9 5.4 + - - +
210A MET* 2.8 39.9 + - + +
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Residues in contact with VAL 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TRP* 5.9 1.6 - - + -
203A TYR* 3.1 49.1 + - + +
204A GLU* 3.7 7.2 - - + +
206A THR* 1.3 76.1 - - - +
208A LYS* 1.3 65.4 + - - +
210A MET* 3.0 19.0 + - + +
211A ARG* 2.9 32.6 + - - +
313B GLU* 3.7 34.5 - - + +
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Residues in contact with LYS 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A GLU 3.2 9.7 + - - +
205A ASP* 3.5 13.5 - - - +
206A THR 3.1 0.6 - - - -
207A VAL* 1.3 82.1 - - - +
209A VAL* 1.3 63.9 + - + +
211A ARG* 3.4 19.6 + - + +
212A THR* 3.4 15.5 - - + +
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A TYR* 3.5 36.8 - - + +
185A VAL 4.2 0.7 - - - +
186A PRO* 3.8 25.1 - - + -
187A ARG 5.2 0.9 - - - +
205A ASP 3.3 16.8 - - - +
206A THR* 2.9 7.0 + - - +
208A LYS* 1.3 78.3 - - + +
210A MET* 1.3 59.1 + - - +
212A THR* 2.4 33.7 + - + +
214A THR 4.4 4.5 - - - +
216A THR* 4.2 15.3 - - + -
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Residues in contact with MET 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A PRO* 3.6 44.9 - - + +
144A TRP* 4.0 7.2 - - + +
147A VAL* 4.2 9.4 - - + -
184A TYR* 3.7 33.0 - - + -
206A THR* 2.8 36.5 + - - +
207A VAL* 3.5 19.1 - - + +
209A VAL* 1.3 77.1 - - - +
211A ARG* 1.3 63.4 + - - +
213A LEU* 2.9 11.6 + - - -
309B ILE* 3.3 36.5 - - + +
313B GLU* 5.0 8.1 - - + +
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Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A VAL* 2.9 27.7 + - + +
208A LYS* 3.6 14.6 - - - +
209A VAL 3.2 0.4 - - - -
210A MET* 1.3 76.2 - - - +
212A THR* 1.3 59.7 + - + +
213A LEU* 2.8 18.2 + - - +
187B ARG* 4.5 18.2 - - - +
193B TYR* 3.8 20.2 + - - -
214B THR* 3.9 7.1 - - - +
215B PRO 5.5 0.9 - - - +
216B THR* 4.2 11.9 + - - +
217B HIS* 5.0 1.6 + - - -
309B ILE* 4.3 5.8 - - - +
313B GLU* 3.1 49.0 + - + +
314B LEU* 4.6 12.8 - - + +
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Residues in contact with THR 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LYS* 3.4 18.2 - - + +
209A VAL* 2.4 24.3 + - + +
211A ARG* 1.3 76.8 - - + +
213A LEU* 1.3 69.3 + - - +
214A THR* 3.0 29.0 + - - -
214B THR* 3.7 18.6 + - - +
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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