Contacts of the helix formed by residues 202 - 215 (chain B) in PDB entry 1TAR
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 GLN 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B ARG* 1.3 72.9 - - - +
203B GLU* 1.3 60.9 + - + +
205B TRP* 2.9 28.3 + - - +
206B LYS* 3.2 21.7 + - - +
238B TRP* 3.4 57.2 + - + +
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Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B ARG* 2.3 61.2 + - - +
202B GLN* 1.3 81.9 + - + +
204B GLN* 1.3 64.8 + - + +
206B LYS* 3.4 14.4 + - + +
207B GLU* 3.4 27.0 + - - +
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Residues in contact with GLN 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LEU* 3.6 14.7 - - - +
170B PHE* 3.4 49.0 - - + +
199B ASP 4.5 0.8 + - - -
200B PRO* 3.3 17.6 - - + +
201B ARG* 2.8 72.6 + - - +
203B GLU* 1.3 79.1 - - + +
205B TRP* 1.3 60.2 + - - +
207B GLU* 3.7 0.8 + - - +
208B LEU* 3.1 32.7 + - - +
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Residues in contact with TRP 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B TYR* 6.5 0.7 - + - -
188B LEU* 4.6 15.9 - - + -
189B HIS 3.7 24.5 - - - -
190B ALA 4.0 8.7 + - - -
191B CYS* 5.8 0.4 - - - -
199B ASP* 5.5 2.3 - - + +
200B PRO* 3.6 40.9 + - + +
201B ARG 3.0 22.6 + - - -
202B GLN* 2.9 13.2 + - - +
204B GLN* 1.3 74.1 - - - +
206B LYS* 1.4 52.9 + - - +
208B LEU* 3.0 17.2 + - + +
209B ALA* 2.8 37.1 + - - +
221B PHE* 4.1 17.9 - + - -
238B TRP* 3.8 16.2 - + + -
239B ALA* 3.4 24.5 - - + +
242B HIS* 5.0 2.0 - - + -
243B PHE* 3.5 38.4 - + + -
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Residues in contact with LYS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B GLN* 3.2 22.4 + - - +
203B GLU* 3.4 13.7 + - + +
205B TRP* 1.4 73.8 - - - +
207B GLU* 1.3 59.8 + - + +
209B ALA* 3.0 4.5 + - - +
210B SER* 2.8 30.2 + - - -
238B TRP* 3.8 25.0 - - + -
242B HIS* 3.5 38.7 + - + +
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Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B PHE* 3.4 36.8 - - + -
174B MET* 4.1 16.9 - - + +
203B GLU* 3.4 12.4 + - - +
204B GLN* 3.8 2.7 - - - +
205B TRP 3.2 0.4 - - - -
206B LYS* 1.3 81.0 - - + +
208B LEU* 1.3 59.7 + - - +
210B SER* 3.2 21.2 + - - +
211B VAL* 3.2 15.1 + - - +
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B TYR* 6.1 2.5 - - + -
168B LEU* 5.6 1.3 - - + -
170B PHE* 4.3 10.5 - - + -
173B ALA* 5.1 6.5 - - + -
174B MET* 4.1 19.5 - - + -
177B ILE* 4.0 29.1 - - + +
188B LEU* 5.8 7.6 - - + -
200B PRO* 3.9 28.0 - - + -
204B GLN 3.1 20.8 + - - +
205B TRP* 3.0 21.1 + - + +
207B GLU* 1.3 72.8 - - - +
209B ALA* 1.3 62.6 + - - +
211B VAL* 3.4 3.3 + - + +
212B VAL* 2.9 34.8 + - + +
243B PHE* 4.3 9.6 - - + -
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B TRP 2.8 13.2 + - - +
206B LYS 3.5 4.0 - - - +
208B LEU* 1.3 79.2 - - - +
210B SER* 1.4 51.9 + - - +
212B VAL* 3.2 1.7 + - - +
213B LYS* 2.8 36.6 + - - +
242B HIS* 3.8 17.5 - - + +
243B PHE* 3.4 39.9 - - + -
246B GLN* 4.8 8.7 - - + -
248B ILE* 3.7 6.4 - - + +
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Residues in contact with SER 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206B LYS 2.8 13.9 + - - -
207B GLU* 3.2 13.6 + - - +
208B LEU 3.3 0.2 - - - -
209B ALA* 1.4 76.2 - - - +
211B VAL* 1.3 67.3 + - - +
213B LYS* 3.7 6.2 + - - +
214B LYS* 3.3 36.5 + - - +
246B GLN* 6.1 0.2 - - - +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B MET* 3.5 33.9 - - + +
177B ILE* 4.1 19.3 - - + -
178B SER* 4.2 20.2 - - - +
207B GLU 3.2 6.6 + - - +
208B LEU* 4.0 6.1 - - - +
209B ALA 3.2 0.4 - - - -
210B SER* 1.3 80.3 + - - +
212B VAL* 1.3 69.6 + - - +
214B LYS* 3.2 22.0 + - + +
215B ARG* 2.9 39.6 + - + +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ILE* 4.4 18.2 - - + -
186B ILE* 4.6 10.5 - - + -
188B LEU* 5.0 4.0 - - + -
208B LEU* 2.9 24.5 + - + +
209B ALA 3.2 3.3 + - - +
211B VAL* 1.3 80.3 - - - +
213B LYS* 1.4 61.5 + - - +
215B ARG 3.7 0.7 + - - -
216B ASN* 3.4 2.1 + - - -
217B LEU* 3.3 53.3 + - + +
219B ALA* 4.5 8.3 - - + -
243B PHE* 4.0 22.2 - - + -
248B ILE* 3.6 19.3 - - + -
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Residues in contact with LYS 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ALA 2.8 20.3 + - - +
210B SER* 4.0 6.7 - - - +
211B VAL 3.2 0.2 - - - -
212B VAL* 1.4 68.6 - - - +
214B LYS* 1.3 67.7 + - - +
216B ASN* 2.9 20.1 + - - +
246B GLN* 2.9 42.7 + - + +
247B GLY* 5.1 5.5 - - - +
248B ILE* 4.0 16.8 - - + -
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Residues in contact with LYS 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B GLU* 4.5 5.9 - - - +
210B SER* 3.3 27.6 + - - +
211B VAL* 3.2 27.7 + - + +
213B LYS* 1.3 79.0 - - - +
215B ARG* 1.3 64.1 + - + +
216B ASN* 3.0 9.2 + - - +
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Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ILE 3.9 4.9 - - - +
178B SER* 2.5 44.3 + - - +
179B LYS* 4.2 4.2 + - - +
180B ILE 2.6 30.7 + - - -
181B PRO* 3.7 2.6 - - - +
182B GLU* 3.1 52.5 - - - +
183B LYS 3.5 0.2 + - - -
211B VAL* 2.9 26.9 + - + +
214B LYS* 1.3 79.6 - - + +
216B ASN* 1.3 66.5 + - - +
217B LEU* 3.2 19.2 + - + +
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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