Contacts of the helix formed by residues 202 - 215 (chain B) in PDB entry 1AHF
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 LEU 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 THR* 1.3 72.7 - - - +
203B GLU* 1.3 68.0 + - - +
205B TRP* 3.5 11.1 + - + -
206B GLN* 2.9 48.7 + - - +
238B GLU* 3.5 58.3 - - + +
239B GLY 4.7 0.2 - - - +
242B ALA* 4.9 3.6 - - + -
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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 THR* 3.0 10.5 + - - +
202B LEU* 1.3 86.9 - - - +
204B GLN* 1.3 66.3 + - + +
206B GLN* 2.9 19.6 + - - +
207B THR* 2.8 27.3 + - - +
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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* 3.2 20.9 + - - +
170B PHE* 3.6 40.7 - - + +
199B ASP 4.5 0.3 - - - +
200B PRO* 3.0 17.5 - - + +
201B THR* 2.8 51.8 + - + +
203B GLU* 1.3 72.1 - - + +
205B TRP* 1.3 58.2 + - - +
207B THR* 3.1 6.2 - - - -
208B LEU* 2.8 35.7 + - - +
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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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188B PHE* 4.0 32.3 - + + -
189B HIS 3.7 24.0 - - - -
190B GLY 3.8 13.7 + - - -
199B ASP* 5.1 3.3 - - + +
200B PRO* 3.4 48.2 + - + +
201B THR 3.0 21.2 + - - -
202B LEU* 3.5 15.5 - - + +
204B GLN* 1.3 76.6 - - - +
206B GLN* 1.3 63.2 + - - +
208B LEU* 3.4 5.3 + - + -
209B ALA* 2.9 24.5 + - - +
221B PHE* 4.1 10.8 - + - -
238B GLU* 5.7 0.9 - - + -
239B GLY* 3.6 32.3 - - - +
242B ALA* 5.0 4.0 - - + -
243B PHE* 3.6 34.8 - + - -
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Residues in contact with GLN 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 LEU* 2.9 39.9 + - - +
203B GLU* 2.9 27.6 + - + +
205B TRP* 1.3 76.1 - - - +
207B THR* 1.3 63.1 + - - +
209B ALA* 2.9 23.5 + - + +
210B GLN* 3.0 9.8 + - - +
242B ALA* 4.7 13.9 - - + +
246B MET* 5.5 0.9 - - - +
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Residues in contact with THR 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 27.7 - - + -
174B ILE* 4.4 8.1 - - + -
203B GLU* 2.8 14.1 + - - +
204B GLN* 3.1 11.4 - - - -
206B GLN* 1.3 75.3 - - - +
208B LEU* 1.3 55.5 + - + +
209B ALA 3.1 0.5 + - - -
210B GLN* 3.1 6.8 + - - +
211B LEU* 2.8 39.8 + - + +
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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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170B PHE* 3.6 23.8 - - + -
173B LEU* 3.8 26.5 - - + -
174B ILE* 4.6 10.1 - - + -
177B LEU* 5.0 8.7 - - + -
188B PHE* 4.5 18.9 - - + -
200B PRO* 4.2 18.8 - - + -
204B GLN 2.8 26.1 + - - +
205B TRP* 3.7 12.1 - - + +
207B THR* 1.3 71.9 - - - +
209B ALA* 1.3 58.0 + - - +
211B LEU* 3.3 11.3 + - + +
212B SER* 2.9 33.1 + - - -
217B TRP* 5.0 3.0 - - + -
243B PHE* 3.9 14.8 - - + -
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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 2.9 15.2 + - - +
206B GLN* 2.9 18.5 + - + +
208B LEU* 1.3 75.3 - - - +
210B GLN* 1.3 60.3 + - - +
212B SER* 3.1 15.7 + - - -
213B VAL* 3.2 9.4 + - - +
242B ALA* 4.2 8.5 - - + +
243B PHE* 3.8 25.0 - - + -
246B MET* 4.2 24.0 - - + -
247B HIS* 3.5 7.0 + - - -
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Residues in contact with GLN 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 GLN 3.0 7.7 + - - +
207B THR* 3.7 7.6 - - - +
209B ALA* 1.3 77.1 - - - +
211B LEU* 1.3 65.3 + - - +
213B VAL* 3.1 26.7 - - - +
214B GLU* 2.6 43.0 + - - +
246B MET* 3.6 20.8 - - + +
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Residues in contact with LEU 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 ILE* 4.6 33.0 - - + +
177B LEU* 5.9 1.3 - - + -
178B ASN* 4.9 7.0 - - - +
207B THR* 2.8 20.1 + - + +
208B LEU* 3.5 13.0 - - + +
210B GLN* 1.3 77.6 - - - +
212B SER* 1.3 58.4 + - - +
214B GLU* 3.1 18.0 + - - +
215B LYS* 2.9 45.5 + - + +
217B TRP* 4.2 21.1 - - + -
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Residues in contact with SER 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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186B VAL* 4.9 2.5 - - - -
188B PHE* 5.3 0.9 - - - -
208B LEU 2.9 20.4 + - - -
209B ALA 3.1 7.8 + - - -
211B LEU* 1.3 70.2 - - - +
213B VAL* 1.3 63.5 + - - +
215B LYS 4.3 0.2 - - - +
216B GLY* 3.1 16.8 + - - -
217B TRP* 3.0 51.5 + - - +
219B PRO* 5.2 1.1 - - - -
243B PHE* 3.4 13.8 - - - -
247B HIS* 3.2 18.9 + - - -
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Residues in contact with VAL 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 3.2 9.3 + - - +
210B GLN* 3.1 28.2 + - - +
212B SER* 1.3 80.7 + - - +
214B GLU* 1.3 66.7 + - + +
216B GLY* 3.4 9.2 + - - -
246B MET* 3.6 47.8 - - + +
247B HIS* 3.9 12.3 - - + +
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Residues in contact with GLU 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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210B GLN* 2.6 51.9 + - - +
211B LEU* 3.1 16.2 + - - +
213B VAL* 1.3 81.0 - - + +
215B LYS* 1.3 65.4 + - + +
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Residues in contact with LYS 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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178B ASN* 3.6 38.7 + - - +
180B ALA 4.6 4.9 - - - +
182B ALA* 2.8 28.3 + - - +
211B LEU* 2.9 37.9 + - + +
212B SER 3.6 0.2 + - - -
213B VAL 3.4 0.2 - - - -
214B GLU* 1.3 81.5 - - + +
216B GLY* 1.3 59.3 + - - +
217B TRP* 3.3 40.1 + - + +
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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