Contacts of the helix formed by residues 219 - 231 (chain B) in PDB entry 4F4W
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 GLY 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B GLU* 2.8 25.5 + - - -
217B ILE 3.8 0.6 - - - -
218B THR* 1.3 95.5 + - - +
220B LYS* 1.3 65.5 + - - -
221B ALA 3.6 1.6 - - - -
222B LYS 3.6 1.0 + - - -
223B ALA* 3.1 7.4 + - - +
12F C 3.3 14.4 - - - -
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Residues in contact with LYS 220 (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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211B TYR* 3.4 29.6 - - - +
215B GLU* 3.9 11.0 + - + +
219B GLY* 1.3 67.7 - - - -
221B ALA* 1.3 68.6 + - - +
223B ALA* 3.1 3.5 + - - +
224B LEU* 3.0 48.6 + - + +
12F C 3.5 13.3 + - - +
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Residues in contact with ALA 221 (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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219B GLY 3.6 0.4 - - - -
220B LYS* 1.3 82.8 - - + +
222B LYS* 1.3 62.8 + - + +
224B LEU* 3.4 8.4 + - - +
225B TYR* 3.1 24.8 + - - +
11F T 3.4 46.4 + - - +
12F C 3.1 14.0 + - - +
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Residues in contact with LYS 222 (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 GLY* 2.7 32.2 + - - +
187B ILE* 4.0 12.3 - - + +
188B GLY 5.1 2.4 - - - +
191B LEU* 4.4 15.1 - - + +
218B THR* 3.5 32.5 - - + +
219B GLY 3.6 1.4 + - - -
220B LYS 3.3 0.6 - - - -
221B ALA* 1.3 81.9 - - + +
223B ALA* 1.3 58.2 + - - +
225B TYR* 3.7 12.7 - - + +
226B LEU* 3.0 37.4 + - + +
11E G 5.8 6.1 - - - -
12E G 5.4 3.4 + - - -
11F T 4.8 20.4 - - - +
12F C 5.2 2.0 + - - +
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Residues in contact with ALA 223 (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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211B TYR* 3.7 24.0 - - + -
214B LEU* 3.7 17.1 - - + +
215B GLU 4.0 10.3 - - - +
218B THR* 3.2 17.6 + - - +
219B GLY 3.1 14.0 + - - +
220B LYS 3.1 5.1 + - - +
222B LYS* 1.3 74.1 - - - +
224B LEU* 1.3 65.8 + - - +
227B LEU* 3.0 31.5 + - - +
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Residues in contact with LEU 224 (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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211B TYR* 3.9 24.5 - - + -
220B LYS* 3.0 43.1 + - + +
221B ALA* 3.8 8.1 - - - +
223B ALA* 1.3 75.8 - - - +
225B TYR* 1.3 62.7 + - - +
227B LEU* 4.0 5.2 - - + +
228B LYS* 3.1 32.1 + - - +
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Residues in contact with TYR 225 (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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150B ILE* 3.4 34.5 - - + +
184B ILE* 3.4 23.2 - - + +
185B PRO* 2.7 30.0 + - - +
186B GLY* 4.9 3.1 - - - -
187B ILE* 4.3 6.7 - - + -
221B ALA 3.1 15.7 + - - +
222B LYS* 3.7 19.7 - - + +
224B LEU* 1.3 80.0 - - - +
226B LEU* 1.3 65.9 + - + +
228B LYS* 3.3 8.8 + - - +
229B LEU* 2.9 38.5 + - + +
234B TYR* 4.3 23.1 - + - -
11F T 6.1 1.1 - - - +
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Residues in contact with LEU 226 (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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181B ILE* 4.8 2.5 - - + -
184B ILE* 3.8 34.5 - - + -
187B ILE* 3.9 30.1 - - + -
195B LEU* 4.4 9.0 - - + -
203B LEU* 3.9 9.6 - - + +
206B ILE* 3.9 23.6 - - + +
214B LEU* 4.3 9.6 - - + -
218B THR* 4.2 22.7 - - + -
222B LYS* 3.0 20.8 + - + +
223B ALA 4.0 2.5 - - - +
225B TYR* 1.3 79.8 - - + +
227B LEU* 1.3 58.8 + - - +
229B LEU* 3.8 3.4 - - + +
230B ALA* 2.9 31.5 + - - +
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Residues in contact with LEU 227 (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 ILE* 3.5 31.0 - - + +
207B LEU* 5.0 8.5 - - + -
209B LYS 4.0 12.3 - - - +
211B TYR* 3.7 39.7 - - + +
214B LEU* 3.9 12.8 - - + -
223B ALA 3.0 23.3 + - - +
224B LEU* 4.0 4.5 - - + +
226B LEU* 1.3 77.2 - - - +
228B LYS* 1.3 62.1 + - - +
230B ALA* 3.6 2.0 + - - +
231B GLN* 2.9 37.4 + - - +
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Residues in contact with LYS 228 (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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224B LEU* 3.1 23.9 + - - +
225B TYR* 3.6 7.1 - - - +
227B LEU* 1.3 76.2 - - - +
229B LEU* 1.3 63.3 + - - +
231B GLN* 3.1 10.2 + - - -
233B GLU* 2.8 67.5 + - + +
234B TYR* 3.3 17.7 - - + +
236B GLU* 3.2 25.4 + - - +
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Residues in contact with LEU 229 (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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148B ASN* 5.9 0.9 - - - +
150B ILE* 3.3 33.7 - - + -
151B LEU* 5.2 2.7 - - + -
154B ILE* 5.0 0.4 - - + -
176B LEU* 3.6 22.4 - - + +
179B LEU* 4.9 4.3 - - + -
184B ILE* 3.9 32.1 - - + -
203B LEU* 3.8 24.7 - - + -
225B TYR* 2.9 30.0 + - + +
226B LEU* 3.8 6.1 - - + +
228B LYS* 1.3 76.4 - - - +
230B ALA* 1.3 62.9 + - - +
232B ASP* 2.9 15.4 + - - +
233B GLU 4.8 0.2 - - - +
234B TYR* 4.2 21.1 - - + +
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Residues in contact with ALA 230 (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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176B LEU* 4.6 9.2 - - - +
203B LEU* 3.8 34.7 - - + +
204B ARG* 5.2 1.5 - - - +
206B ILE* 4.2 6.3 - - + -
207B LEU* 3.9 31.8 - - + +
226B LEU 2.9 18.6 + - - +
227B LEU 3.8 5.4 - - - +
228B LYS 3.2 0.2 - - - -
229B LEU* 1.3 78.9 - - - +
231B GLN* 1.3 58.3 + - - +
232B ASP 3.3 1.0 + - - -
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Residues in contact with GLN 231 (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* 3.7 23.9 - - + +
227B LEU* 2.9 27.8 - - - +
228B LYS* 3.1 8.2 + - - +
229B LEU 3.0 0.4 - - - -
230B ALA* 1.3 76.0 - - - +
232B ASP* 1.3 70.9 + - - +
233B GLU* 3.1 38.5 + - - +
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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