Contacts of the helix formed by residues 256 - 267 (chain I) 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 256 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I ASP* 2.7 32.1 + - - -
255I PHE* 1.3 83.4 - - - +
257I GLU* 1.3 67.2 + - - +
258I PHE* 2.9 23.9 + - - +
259I ALA 3.2 13.5 + - - -
260I LEU* 3.3 15.9 + - - +
285I HIS* 3.4 6.5 - - - -
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Residues in contact with GLU 257 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256I SER* 1.3 76.8 - - - +
258I PHE* 1.3 93.7 + - + +
260I LEU* 3.9 6.5 - - - -
261I GLN* 3.2 15.4 + - - +
282I THR* 5.8 0.2 - - - +
284I LYS* 3.6 45.3 + - + +
285I HIS* 3.4 31.9 + - + -
288I VAL* 3.2 36.3 - - + +
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Residues in contact with PHE 258 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I ASP* 5.4 0.4 - - - +
256I SER* 2.9 19.4 - - - +
257I GLU* 1.3 109.3 - - + +
259I ALA* 1.3 67.3 + - - +
260I LEU 3.1 1.3 - - - -
261I GLN* 3.0 27.3 + - - +
262I THR* 2.9 22.6 + - + +
284I LYS* 6.0 0.2 - - + -
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Residues in contact with ALA 259 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I ASP* 3.6 37.0 + - + +
235I VAL* 3.3 31.9 - - + +
236I ASN* 3.9 17.5 - - - +
255I PHE* 4.3 1.8 - - + -
256I SER* 3.2 7.4 + - - +
258I PHE* 1.3 78.1 - - - +
260I LEU* 1.3 61.8 + - - +
262I THR* 3.3 4.6 + - - +
263I LEU 3.1 17.2 + - - -
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Residues in contact with LEU 260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235I VAL* 3.9 7.8 - - - +
249I LEU* 5.3 0.2 - - + -
255I PHE* 4.1 22.0 - - + -
256I SER 3.3 15.0 + - - +
257I GLU* 3.8 4.0 - - - +
259I ALA* 1.3 79.9 - - - +
261I GLN* 1.3 57.3 + - - +
263I LEU* 3.1 12.5 + - + +
264I LEU* 2.9 56.7 + - + +
275I LEU* 4.1 28.9 - - + -
281I PHE* 4.6 2.0 - - + -
285I HIS* 3.5 38.6 - - + +
288I VAL* 4.0 11.4 - - + -
289I ALA 4.4 1.6 - - - +
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Residues in contact with GLN 261 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257I GLU 3.2 14.8 + - - +
258I PHE* 3.0 26.3 + - - +
260I LEU* 1.3 78.4 - - - +
262I THR* 1.3 61.7 + - + +
264I LEU* 4.3 0.3 - - - +
265I SER* 2.8 36.4 + - - +
288I VAL* 3.4 19.2 - - + +
292I HIS* 3.0 42.3 + - + +
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Residues in contact with THR 262 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236I ASN* 3.5 23.1 + - - +
239I ALA* 3.8 14.6 - - - +
258I PHE 2.9 19.5 - - - +
259I ALA* 3.6 6.2 + - - +
261I GLN* 1.3 75.5 - - + +
263I LEU* 1.3 60.1 + - - +
265I SER* 3.9 5.1 - - - -
266I SER* 2.8 33.1 + - - -
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Residues in contact with LEU 263 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235I VAL* 3.9 18.2 - - + +
238I LEU* 3.5 45.3 - - + +
239I ALA* 3.7 5.8 - - - +
244I LEU* 4.8 0.9 - - + -
247I LEU* 3.7 27.6 - - + -
249I LEU* 3.9 20.2 - - + -
259I ALA 3.1 12.7 + - - +
260I LEU* 3.1 16.9 + - + +
262I THR* 1.3 80.5 + - - +
264I LEU* 1.3 63.2 + - + +
266I SER* 3.5 0.9 - - - -
267I CYS* 2.9 38.5 + - - -
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Residues in contact with LEU 264 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247I LEU* 5.5 0.9 - - + -
260I LEU* 2.9 40.4 + - + +
263I LEU* 1.3 81.7 - - + +
265I SER* 1.3 66.7 + - - +
266I SER 3.2 0.5 + - - -
267I CYS* 3.2 22.2 + - + +
268I SER* 4.9 0.3 - - - -
270I LEU* 4.8 9.6 - - + -
273I LEU* 3.7 29.2 - - + -
275I LEU* 4.8 3.4 - - + -
288I VAL* 4.1 6.3 - - + +
289I ALA* 3.5 40.4 - - + +
292I HIS* 3.2 24.4 - - + +
293I VAL* 3.9 9.4 - - + +
294I SER* 4.7 2.9 + - - -
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Residues in contact with SER 265 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261I GLN* 2.8 26.9 + - - +
262I THR* 3.9 5.6 - - - -
264I LEU* 1.3 77.6 - - - +
266I SER* 1.3 63.0 + - - +
268I SER* 4.2 10.0 + - - -
292I HIS* 3.2 29.1 + - - -
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Residues in contact with SER 266 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239I ALA* 2.4 41.7 + - - +
242I SER* 3.6 19.7 - - - -
262I THR 2.8 19.6 + - - -
263I LEU 3.5 4.0 - - - -
265I SER* 1.3 78.7 - - - +
267I CYS* 1.3 58.0 + - - +
268I SER* 2.9 13.2 + - - -
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Residues in contact with CYS 267 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238I LEU 4.5 1.1 - - - -
241I ASN 3.6 12.3 - - - -
242I SER* 4.0 7.2 - - - +
244I LEU* 3.5 39.0 - - + +
247I LEU* 5.2 2.7 - - - -
263I LEU* 2.9 32.9 + - - +
264I LEU* 3.2 9.9 + - - +
266I SER* 1.3 74.0 - - - +
268I SER* 1.3 59.7 + - - +
269I ARG 3.3 7.5 + - - -
270I LEU* 3.4 33.7 - - + +
294I SER* 3.5 7.8 + - - -
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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