Contacts of the helix formed by residues 208 - 220 (chain B) in PDB entry 5FHH
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 SER 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B GLN 3.9 3.2 + - - -
207B LEU* 1.3 73.1 - - - +
209B GLU* 1.3 56.2 + - - +
210B GLU* 3.3 14.9 + - - +
211B GLN* 3.0 24.2 + - - +
212B ALA* 2.4 34.7 + - - +
377B THR* 5.1 2.6 + - - -
378B LYS* 4.7 5.5 + - - +
380B TRP* 3.5 33.7 - - - -
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Residues in contact with GLU 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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207B LEU 3.6 1.4 + - - -
208B SER* 1.3 73.6 + - - +
210B GLU* 1.3 53.5 + - - +
212B ALA* 3.4 6.8 - - - +
213B ALA* 2.5 39.4 + - - +
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Residues in contact with GLU 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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208B SER* 3.2 8.5 + - - +
209B GLU* 1.3 74.4 - - - +
211B GLN* 1.3 68.3 + - + +
213B ALA* 3.3 7.6 + - - +
214B VAL* 3.3 26.9 + - - +
375B GLU 4.1 18.8 - - - +
376B LEU* 4.5 14.0 - - + +
377B THR* 5.0 12.3 - - + +
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Residues in contact with GLN 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLN 4.9 3.5 + - - +
207B LEU* 4.1 17.9 - - + +
208B SER* 3.0 29.7 + - - +
210B GLU* 1.3 80.1 - - + +
212B ALA* 1.3 63.0 + - - +
214B VAL* 3.4 11.5 + - - +
215B LEU* 3.4 7.8 + - - +
232B THR 4.7 4.5 + - - -
233B GLY* 4.9 4.1 - - - -
234B LYS 5.1 5.4 + - - -
236B TYR* 4.8 13.5 - - - -
237B LEU* 3.8 34.4 + - + +
376B LEU* 4.6 17.9 - - + +
380B TRP* 3.7 40.2 - - - +
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Residues in contact with ALA 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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207B LEU* 4.2 20.8 - - + +
208B SER 2.4 29.9 + - - +
209B GLU* 3.6 7.6 - - - +
211B GLN* 1.3 68.7 - - - +
213B ALA* 1.3 58.1 + - - +
215B LEU* 3.0 9.8 + - + +
216B ARG* 2.8 32.6 + - + +
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Residues in contact with ALA 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 GLU 2.5 21.7 + - - +
210B GLU* 3.6 10.8 - - - +
211B GLN 3.2 0.4 - - - -
212B ALA* 1.3 72.0 - - - +
214B VAL* 1.3 53.5 + - + +
216B ARG* 3.6 4.9 - - - +
217B ALA* 2.6 39.7 + - + +
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B GLU 3.3 15.2 + - - +
211B GLN 3.7 0.7 - - - +
212B ALA 3.3 0.2 - - - -
213B ALA* 1.3 74.3 - - + +
215B LEU* 1.3 52.8 + - - +
217B ALA* 3.1 6.3 + - - +
218B VAL* 2.7 39.7 + - + +
224B ILE* 4.3 15.0 - - + +
226B PHE* 3.6 49.1 - - + -
237B LEU* 3.6 22.0 - - + -
241B ILE* 4.2 8.3 - - + -
374B LEU* 4.1 16.2 - - + -
375B GLU 5.6 0.2 - - - +
376B LEU* 4.3 5.4 - - + -
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Residues in contact with LEU 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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207B LEU* 3.6 29.2 - - + -
211B GLN 3.4 8.9 + - - +
212B ALA* 3.0 10.6 + - - +
214B VAL* 1.3 76.0 - - - +
216B ARG* 1.3 59.4 + - - +
218B VAL* 2.8 24.1 + - + +
219B LEU* 3.0 40.1 + - + +
237B LEU* 4.4 6.8 - - + +
240B ARG* 5.1 6.3 - - + -
241B ILE* 3.8 29.8 - - + +
244B SER* 3.8 19.7 - - - +
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Residues in contact with ARG 216 (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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212B ALA* 2.8 18.9 + - + +
213B ALA* 3.9 4.0 - - - +
215B LEU* 1.3 75.1 - - - +
217B ALA* 1.3 60.5 + - - +
219B LEU* 4.3 7.3 - - - +
220B LYS* 3.7 17.8 + - - +
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Residues in contact with ALA 217 (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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213B ALA 2.6 25.2 + - - +
214B VAL* 3.5 7.0 - - - +
216B ARG* 1.3 76.3 - - - +
218B VAL* 1.3 61.5 + - - +
220B LYS* 3.7 10.8 + - - +
222B GLN* 3.5 32.8 - - - +
224B ILE* 5.0 11.0 - - + -
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Residues in contact with VAL 218 (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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214B VAL* 2.7 18.9 + - + +
215B LEU* 2.8 22.1 + - - +
217B ALA* 1.3 69.7 - - - +
219B LEU* 1.3 63.7 + - + +
220B LYS 3.1 2.0 - - - -
221B GLY* 2.7 23.4 + - - -
222B GLN 3.7 17.5 - - - +
223B SER* 5.8 0.2 - - - -
224B ILE* 4.5 14.1 - - + +
241B ILE* 3.8 36.6 - - + -
245B LEU* 4.4 18.3 - - + +
337B GLN* 6.6 0.9 - - + -
338B LEU 5.8 2.0 - - - +
339B ILE* 5.5 11.4 - - + -
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Residues in contact with LEU 219 (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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215B LEU* 3.0 58.8 + - + +
216B ARG* 4.0 6.3 + - - +
218B VAL* 1.3 76.3 - - + +
220B LYS* 1.3 57.9 + - - +
221B GLY* 2.9 10.6 + - - -
244B SER* 3.6 34.5 - - - +
245B LEU* 4.4 20.7 - - + +
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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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216B ARG 3.7 11.2 + - - +
217B ALA* 3.7 14.7 + - - +
218B VAL 3.1 0.8 - - - -
219B LEU* 1.3 75.4 - - - +
221B GLY* 1.3 56.3 + - - +
222B GLN* 3.3 7.2 + - + +
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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