Contacts of the helix formed by residues 256 - 267 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232M ASP* 2.8 30.4 + - - -
255M PHE* 1.3 83.8 - - - +
257M GLU* 1.3 70.0 + - - +
258M PHE* 3.0 23.9 + - - +
259M ALA 3.3 14.2 + - - -
260M LEU* 3.3 16.5 + - - +
285M HIS* 3.5 4.5 - - - -
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Residues in contact with GLU 257 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256M SER* 1.3 77.4 - - - +
258M PHE* 1.3 95.4 + - + +
260M LEU* 3.9 5.4 - - - -
261M GLN* 3.1 19.2 + - - +
284M LYS* 3.6 40.5 + - + +
285M HIS* 3.5 31.2 + - + +
288M VAL* 3.2 36.1 - - + +
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Residues in contact with PHE 258 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232M ASP* 5.5 0.2 - - - +
256M SER* 3.0 18.4 - - - +
257M GLU* 1.3 104.6 - - + +
259M ALA* 1.3 67.9 + - - +
260M LEU 3.1 0.9 - - - -
261M GLN* 2.9 30.0 + - - +
262M THR* 3.0 18.3 + - + +
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Residues in contact with ALA 259 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232M ASP* 3.6 40.4 + - + +
235M VAL* 3.4 24.7 - - + +
236M ASN* 4.0 11.2 - - - +
255M PHE* 4.4 1.1 - - + -
256M SER* 3.3 6.8 + - - +
258M PHE* 1.3 78.4 - - - +
260M LEU* 1.3 63.5 + - - +
262M THR* 3.2 12.8 + - - +
263M LEU 2.9 18.4 + - - -
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Residues in contact with LEU 260 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235M VAL* 3.9 8.6 - - - +
249M LEU* 5.4 0.7 - - + -
255M PHE* 4.0 21.7 - - + -
256M SER 3.3 14.5 + - - +
257M GLU 3.8 3.4 - - - +
258M PHE 3.1 0.2 - - - -
259M ALA* 1.3 78.9 - - - +
261M GLN* 1.3 57.0 + - - +
263M LEU* 3.2 9.9 + - + +
264M LEU* 2.8 61.1 + - + +
275M LEU* 3.9 30.3 - - + -
281M PHE* 4.6 1.6 - - + -
285M HIS* 3.6 39.5 - - + +
288M VAL* 4.0 8.1 - - + -
289M ALA 4.4 1.6 - - - +
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Residues in contact with GLN 261 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257M GLU 3.1 15.3 + - - +
258M PHE* 2.9 28.0 + - - +
260M LEU* 1.3 80.8 - - - +
262M THR* 1.3 53.8 + - + +
264M LEU* 4.1 2.5 - - - +
265M SER* 2.6 39.8 + - - +
288M VAL* 3.6 17.8 - - + +
292M HIS* 3.1 40.2 + - + +
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Residues in contact with THR 262 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236M ASN* 3.5 24.5 + - - +
239M ALA* 3.8 14.9 - - - +
258M PHE* 3.0 17.9 + - + +
259M ALA* 3.5 8.0 + - - +
261M GLN* 1.3 73.7 - - + +
263M LEU* 1.3 61.9 + - - +
265M SER* 3.7 5.5 - - - -
266M SER* 2.8 33.3 + - - -
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Residues in contact with LEU 263 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235M VAL* 3.8 24.0 - - + +
238M LEU* 3.5 32.1 - - + +
239M ALA* 3.7 13.0 - - - +
244M LEU* 4.6 0.9 - - + -
247M LEU* 3.8 25.6 - - + -
249M LEU* 3.9 17.7 - - + -
259M ALA 2.9 16.3 + - - +
260M LEU* 3.6 11.4 - - + +
262M THR* 1.3 80.7 + - - +
264M LEU* 1.3 62.1 + - + +
266M SER* 3.2 1.4 + - - -
267M CYS* 3.0 53.2 + - - -
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Residues in contact with LEU 264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247M LEU* 5.7 1.8 - - + -
260M LEU* 2.8 44.2 + - + +
263M LEU* 1.3 81.5 - - + +
265M SER* 1.3 65.9 + - - +
266M SER 3.3 0.3 + - - -
267M CYS* 3.3 20.5 + - + +
268M SER* 5.1 0.7 - - - -
270M LEU* 4.8 10.8 - - + -
273M LEU* 3.8 28.9 - - + -
275M LEU* 4.9 0.9 - - + -
288M VAL* 4.2 7.2 - - + +
289M ALA* 3.6 37.0 - - + +
292M HIS* 3.2 26.4 - - + +
293M VAL* 4.1 7.2 - - + -
294M SER* 4.6 3.6 + - - -
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Residues in contact with SER 265 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261M GLN* 2.6 28.0 + - - +
262M THR* 3.7 6.5 - - - -
264M LEU* 1.3 77.9 - - - +
266M SER* 1.3 60.4 + - - +
267M CYS 3.7 0.2 + - - -
268M SER* 4.4 9.7 + - - -
292M HIS* 3.3 28.0 + - - -
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Residues in contact with SER 266 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239M ALA* 2.5 41.3 + - - +
242M SER* 3.3 20.4 - - - -
262M THR 2.8 19.2 + - - -
263M LEU 3.5 4.0 - - - -
265M SER* 1.3 80.0 - - - +
267M CYS* 1.3 57.9 + - - +
268M SER* 3.2 9.9 + - - -
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Residues in contact with CYS 267 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238M LEU 4.7 1.1 - - - -
241M ASN 3.6 13.2 - - - -
242M SER* 4.1 7.2 - - - +
244M LEU* 3.6 36.6 - - + +
247M LEU* 5.2 2.0 - - - -
263M LEU* 3.0 33.4 + - - +
264M LEU* 3.3 10.8 + - - +
266M SER* 1.3 75.8 - - - +
268M SER* 1.3 56.2 + - - +
269M ARG 3.3 9.8 + - - -
270M LEU* 3.4 32.9 - - + +
294M SER* 3.4 8.1 - - - -
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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