Contacts of the helix formed by residues 200 - 215 (chain B) in PDB entry 4F5G
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 THR 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198B ASP 3.5 3.3 + - - +
199B PRO* 1.3 75.3 - - - +
201B LEU* 1.3 58.7 + - - +
202B GLU* 3.5 9.2 + - - +
203B GLN* 2.8 43.0 + - - +
204B TRP* 2.8 27.6 + - - -
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Residues in contact with LEU 201 (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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200B THR* 1.3 74.2 - - - +
202B GLU* 1.3 57.6 + - - +
204B TRP* 3.1 9.9 + - + +
205B GLN* 2.8 58.9 + - + +
229B ARG* 5.9 1.6 - - - +
236B GLU* 3.6 42.2 - - + +
240B ALA* 4.4 13.7 - - + -
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Residues in contact with GLU 202 (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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200B THR* 3.2 8.8 + - - +
201B LEU* 1.3 77.7 - - - +
203B GLN* 1.3 59.7 + - + +
205B GLN* 3.2 16.2 + - - +
206B THR* 2.9 36.1 + - - +
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Residues in contact with GLN 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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167B LEU* 4.5 8.4 + - - +
169B PHE* 3.3 58.9 - - + +
198B ASP 4.3 1.7 - - - +
199B PRO* 3.2 12.3 - - + +
200B THR* 2.8 43.3 + - - +
202B GLU* 1.3 76.7 - - + +
204B TRP* 1.3 59.5 + - - +
206B THR* 3.1 4.2 + - - -
207B LEU* 2.8 34.3 + - - +
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Residues in contact with TRP 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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187B PHE* 3.7 28.0 - + + -
188B HIS 3.3 27.8 - - - -
189B GLY* 3.5 17.9 + - - -
190B CYS* 5.5 0.7 - - - -
198B ASP* 5.2 2.0 - - + +
199B PRO* 3.4 38.9 + - + +
200B THR 2.8 28.5 + - - -
201B LEU* 3.4 12.8 - - + +
203B GLN* 1.3 72.3 - - - +
205B GLN* 1.3 57.8 + - - +
207B LEU* 3.3 10.0 + - + +
208B ALA* 2.8 29.8 + - - +
220B ILE* 4.7 4.7 - - + -
236B GLU* 5.5 1.3 - - + -
237B GLY* 3.3 35.2 - - - +
240B ALA* 4.3 8.4 - - + +
241B PHE* 3.5 39.9 - + - -
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Residues in contact with GLN 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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201B LEU* 2.8 47.7 + - + +
202B GLU* 3.6 17.2 - - - +
204B TRP* 1.3 75.6 - - - +
206B THR* 1.3 57.5 + - - +
208B ALA* 3.3 7.1 + - - +
209B GLN* 3.0 29.6 + - - +
240B ALA* 4.1 10.4 - - + +
244B MET* 5.5 1.7 - - - +
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Residues in contact with THR 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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169B PHE* 3.9 25.5 - - + -
173B ILE* 4.3 10.3 - - + -
202B GLU* 2.9 20.3 + - - +
203B GLN* 3.1 8.6 + - - -
205B GLN* 1.3 76.8 - - - +
207B LEU* 1.3 56.1 + - - +
209B GLN* 3.4 6.9 + - - +
210B LEU* 2.9 29.5 + - + +
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Residues in contact with LEU 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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169B PHE* 3.8 11.7 - - + -
172B LEU* 3.9 20.2 - - + -
173B ILE* 3.7 24.9 - - + -
176B LEU* 4.4 7.4 - - + -
187B PHE* 3.9 29.8 - - + -
199B PRO* 4.2 13.0 - - + -
203B GLN 2.8 23.2 + - - +
204B TRP* 3.5 22.0 - - + +
206B THR* 1.3 70.5 - - - +
208B ALA* 1.3 59.7 + - - +
210B LEU* 3.3 7.4 + - + +
211B SER* 2.9 30.3 + - - -
216B TRP* 4.2 2.8 - - + -
241B PHE* 3.9 15.5 - - + -
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Residues in contact with ALA 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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204B TRP 2.8 19.9 + - - +
205B GLN* 3.6 6.5 - - - +
206B THR 3.3 0.2 - - - -
207B LEU* 1.3 73.8 - - - +
209B GLN* 1.3 62.3 + - - +
211B SER* 3.2 5.0 + - - -
212B VAL* 3.1 26.8 + - - +
240B ALA 3.6 25.4 - - - +
241B PHE* 3.9 26.6 - - + -
244B MET* 4.0 12.3 - - + +
245B HIS* 5.0 0.3 - - - -
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Residues in contact with GLN 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 GLN 3.0 16.6 + - - +
206B THR* 3.7 6.7 - - - +
208B ALA* 1.3 76.4 - - - +
210B LEU* 1.3 61.9 + - - +
212B VAL* 3.1 8.4 + - - +
213B GLU* 3.0 56.0 + - - +
244B MET* 3.3 33.7 - - + +
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Residues in contact with LEU 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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173B ILE* 3.8 47.8 - - + +
176B LEU* 4.7 0.4 - - + -
177B ASN* 5.1 1.8 - - - +
206B THR* 2.9 18.8 + - + +
207B LEU* 3.6 7.4 - - + +
209B GLN* 1.3 75.9 - - - +
211B SER* 1.3 56.9 + - - +
213B GLU* 3.1 16.3 + - - +
214B LYS* 2.8 69.2 + - + +
216B TRP* 3.3 28.3 - - + -
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Residues in contact with SER 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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207B LEU 2.9 16.7 + - - -
208B ALA 3.2 5.8 + - - -
210B LEU* 1.3 77.7 - - - +
212B VAL* 1.3 56.4 + - - +
215B GLY* 2.8 24.8 + - - -
216B TRP* 3.3 41.0 + - - +
218B PRO* 3.5 22.2 - - - +
241B PHE* 3.7 14.1 - - - -
245B HIS* 3.6 8.0 + - - -
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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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8A HIS* 3.6 16.3 - - - +
208B ALA 3.1 14.6 + - - +
209B GLN* 3.1 15.0 + - - +
211B SER* 1.3 76.4 - - - +
213B GLU* 1.3 66.7 + - + +
214B LYS 3.5 0.3 + - - -
215B GLY* 3.6 1.0 + - - -
244B MET* 3.2 44.0 - - + +
245B HIS* 3.7 17.7 - - + -
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Residues in contact with GLU 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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8A HIS* 2.5 25.2 + - - -
209B GLN* 3.0 45.2 + - - +
210B LEU* 3.6 21.8 - - - +
212B VAL* 1.3 78.7 - - + +
214B LYS* 1.3 61.1 + - + +
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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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8A HIS* 3.2 12.0 + - - -
176B LEU 5.5 0.7 - - - +
177B ASN* 3.0 35.6 + - - +
179B ALA 4.9 4.7 - - - +
181B ALA* 3.2 28.1 + - - +
210B LEU* 2.8 45.4 + - + +
213B GLU* 1.3 77.8 - - + +
215B GLY* 1.3 59.5 + - - +
216B TRP* 3.2 32.5 - - + +
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Residues in contact with GLY 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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8A HIS* 3.4 26.7 - - - +
9A VAL* 6.1 1.3 - - - -
11A THR* 5.3 1.6 + - - -
181B ALA* 3.4 3.9 - - - +
182B GLY* 2.9 22.5 + - - -
211B SER 2.8 10.5 + - - -
212B VAL 3.6 1.5 + - - -
213B GLU 3.5 0.2 - - - -
214B LYS* 1.3 78.6 - - - +
216B TRP* 1.3 64.9 + - - +
245B HIS* 4.8 3.8 - - - -
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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