Contacts of the helix formed by residues 231 - 239 (chain K) in PDB entry 1FQV
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 231 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207K VAL* 4.3 13.7 - - - +
211K HIS* 5.3 0.2 - - - +
230K LEU* 1.3 83.4 - - - +
232K ASP* 1.3 57.1 + - - +
233K PRO* 3.1 19.4 - - - +
234K ILE* 2.6 43.3 + - - +
235K VAL* 2.7 12.6 + - - +
254K GLY 3.1 13.2 - - - -
255K PHE* 4.2 4.3 - - - -
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Residues in contact with ASP 232 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231K SER* 1.3 70.2 - - - +
233K PRO* 1.4 73.8 - - + +
235K VAL* 4.4 0.4 - - - +
236K ASN* 2.7 41.0 + - - +
254K GLY 3.7 2.8 + - - +
255K PHE* 3.2 4.9 - - - +
256K SER* 3.0 44.1 + - - -
259K ALA* 3.6 11.9 - - + +
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Residues in contact with PRO 233 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211K HIS* 3.2 25.0 + - + +
231K SER* 3.1 17.7 - - - +
232K ASP* 1.4 94.0 - - + +
234K ILE* 1.3 53.4 + - - +
236K ASN* 4.1 5.5 - - + +
237K THR* 2.6 32.7 + - - -
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Residues in contact with ILE 234 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207K VAL* 3.2 25.6 - - + +
210K LEU* 3.5 26.0 - - + -
211K HIS* 3.6 25.1 - - + +
214K LEU* 3.8 27.3 - - + +
225K LEU* 4.6 1.3 - - + -
230K LEU* 4.0 31.4 - - + -
231K SER* 2.6 29.6 + - - +
233K PRO* 1.3 72.9 - - - +
235K VAL* 1.3 65.1 + - - +
237K THR* 3.2 6.2 + - - -
238K LEU* 3.2 21.0 + - + +
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Residues in contact with VAL 235 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230K LEU* 4.1 14.8 - - + -
231K SER 2.7 15.8 + - - +
234K ILE* 1.3 72.3 - - - +
236K ASN* 1.3 63.1 + - - +
238K LEU* 3.2 21.1 + - + +
239K ALA 3.6 2.4 + - - -
249K LEU* 5.4 2.2 - - + -
255K PHE* 3.3 44.2 - - + -
259K ALA* 3.3 39.3 - - + +
260K LEU* 3.9 5.6 - - - +
263K LEU* 3.8 24.2 - - + +
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Residues in contact with ASN 236 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232K ASP* 2.7 41.3 + - - +
233K PRO* 4.1 5.4 - - + +
235K VAL* 1.3 71.0 - - - +
237K THR* 1.3 56.0 + - - +
239K ALA* 2.7 35.9 + - - +
240K LYS* 4.1 1.2 + - - +
259K ALA* 3.9 10.3 - - - +
262K THR* 3.5 31.2 + - - +
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Residues in contact with THR 237 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211K HIS* 2.8 20.1 + - + -
214K LEU* 3.5 10.2 - - - +
215K SER* 3.0 40.8 - - - -
217K CYS 4.4 0.2 - - - +
233K PRO 2.6 20.9 + - - -
234K ILE* 3.2 6.7 + - - -
236K ASN* 1.3 77.8 - - - +
238K LEU* 1.3 62.6 + - - +
240K LYS* 3.2 44.1 + - - +
241K ASN* 3.9 2.9 - - - +
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Residues in contact with LEU 238 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214K LEU* 4.3 20.6 - - + -
220K LEU* 4.6 1.6 - - + -
223K LEU* 3.3 29.8 - - + -
225K LEU* 4.5 7.2 - - + -
230K LEU* 5.4 1.8 - - + -
234K ILE* 3.2 14.6 + - + +
235K VAL* 3.3 17.7 - - - +
236K ASN 3.0 0.6 - - - -
237K THR* 1.3 76.5 - - - +
239K ALA* 1.3 65.7 + - - +
241K ASN* 2.8 33.1 + - - +
244K LEU* 4.4 7.1 - - + +
247K LEU* 4.4 7.4 - - + -
249K LEU* 4.3 22.2 - - + -
263K LEU* 3.5 31.4 - - + +
267K CYS* 4.6 0.2 - - - -
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Residues in contact with ALA 239 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235K VAL 3.6 1.6 + - - -
236K ASN 2.7 17.7 + - - +
238K LEU* 1.3 78.2 - - - +
240K LYS* 1.3 61.0 + - - +
241K ASN 3.1 1.6 + - - -
242K SER* 3.4 6.9 + - - -
262K THR* 3.9 20.0 - - - +
263K LEU* 3.8 11.9 - - - +
266K SER* 2.6 38.8 + - - +
267K CYS* 4.8 0.3 - - - -
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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