Contacts of the helix formed by residues 231 - 240 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A VAL* 4.7 11.4 - - - +
230A LEU* 1.3 80.8 - - - +
232A ASP* 1.3 51.9 + - - +
233A PRO* 3.1 20.6 - - - +
234A ILE* 2.6 41.6 + - - +
235A VAL* 2.7 16.7 + - - +
254A GLY 2.9 14.5 + - - -
255A PHE* 4.1 4.7 - - - -
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Residues in contact with ASP 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A SER* 1.3 69.6 - - - +
233A PRO* 1.3 74.3 - - + +
235A VAL* 4.3 0.7 - - - +
236A ASN* 2.6 41.9 + - - +
254A GLY 3.8 1.3 + - - +
255A PHE* 3.2 5.4 - - - +
256A SER* 2.9 45.7 + - - -
258A PHE* 5.6 0.5 - - - +
259A ALA* 3.5 15.0 + - - +
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Residues in contact with PRO 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A HIS* 3.1 25.5 + - + +
231A SER* 3.1 18.4 - - - +
232A ASP* 1.3 93.5 - - + +
234A ILE* 1.3 53.4 + - - +
236A ASN* 4.2 5.6 - - + +
237A THR* 2.7 32.2 + - - -
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Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A VAL* 3.2 38.6 - - + +
210A LEU* 3.4 25.6 - - + -
211A HIS* 3.6 24.7 - - + +
214A LEU* 3.9 26.1 - - + +
225A LEU* 4.6 3.1 - - + -
230A LEU* 3.9 23.6 - - + -
231A SER* 2.6 24.1 + - - +
233A PRO* 1.3 70.2 - - - +
235A VAL* 1.3 67.8 + - - +
237A THR* 3.1 14.3 + - - -
238A LEU* 3.2 13.1 + - + +
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A LEU* 4.2 12.3 - - + -
231A SER 2.7 16.3 + - - +
234A ILE* 1.3 72.0 - - - +
236A ASN* 1.3 61.5 + - - +
238A LEU* 3.1 23.9 + - + +
239A ALA 3.5 3.8 + - - -
249A LEU* 5.3 3.1 - - + -
255A PHE* 3.3 44.2 - - + -
259A ALA* 3.2 41.5 - - + +
260A LEU* 3.9 4.3 - - - +
263A LEU* 3.8 23.0 - - + +
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Residues in contact with ASN 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A ASP* 2.6 43.9 + - - +
233A PRO* 4.2 4.8 - - + +
235A VAL* 1.3 68.9 - - - +
237A THR* 1.3 66.7 + - - +
238A LEU 3.0 1.3 - - - -
239A ALA* 3.0 24.4 + - - +
240A LYS* 4.1 1.9 + - - +
259A ALA* 3.9 11.0 - - - +
262A THR* 3.5 30.5 + - - +
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Residues in contact with THR 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A HIS* 2.9 17.1 + - - -
214A LEU* 3.1 12.8 - - - +
215A SER* 3.1 37.9 - - - -
233A PRO 2.7 22.5 + - - -
234A ILE* 3.1 6.1 + - - -
236A ASN* 1.3 78.1 - - - +
238A LEU* 1.3 62.4 + - - +
240A LYS* 3.1 50.5 + - - +
241A ASN* 3.8 3.1 - - - +
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Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 4.2 19.1 - - + -
220A LEU* 4.5 5.4 - - + -
223A LEU* 3.3 35.9 - - + -
225A LEU* 4.3 13.0 - - + -
230A LEU* 5.7 0.7 - - + -
234A ILE* 3.2 13.1 + - + +
235A VAL* 3.1 16.5 + - + +
236A ASN 3.0 0.6 - - - -
237A THR* 1.3 79.7 - - - +
239A ALA* 1.3 62.8 + - - +
241A ASN* 2.8 34.7 + - - +
244A LEU* 4.5 5.6 - - + +
247A LEU* 4.4 10.8 - - + -
249A LEU* 4.4 6.5 - - + -
263A LEU* 3.4 32.0 - - + +
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Residues in contact with ALA 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A VAL 3.5 2.8 + - - +
236A ASN 3.0 15.8 + - - +
238A LEU* 1.3 78.7 - - - +
240A LYS* 1.3 62.1 + - - +
241A ASN 3.1 1.4 + - - -
242A SER* 3.4 6.9 + - - -
262A THR* 3.8 20.6 - - - +
263A LEU* 3.7 9.8 - - - +
266A SER* 2.4 43.7 + - - +
267A CYS* 5.0 0.4 - - - -
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Residues in contact with LYS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A SER* 2.5 43.2 + - - +
216A GLN* 3.7 1.6 - - - +
217A CYS 3.2 17.9 + - - +
218A SER* 3.4 27.9 + - - +
236A ASN 4.9 0.9 - - - +
237A THR* 3.1 31.3 + - - +
239A ALA* 1.3 77.9 - - - +
241A ASN* 1.3 57.5 + - - +
242A SER* 2.7 14.9 + - - -
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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