Contacts of the helix formed by residues 256 - 267 (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 256 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232K ASP* 3.0 23.1 + - - -
255K PHE* 1.3 82.9 - - - +
257K GLU* 1.3 67.3 + - - +
258K PHE* 3.0 23.0 + - - +
259K ALA* 3.3 17.0 + - - +
260K LEU* 3.3 16.5 + - - +
285K HIS* 3.5 7.0 - - - -
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Residues in contact with GLU 257 (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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256K SER* 1.3 77.9 - - - +
258K PHE* 1.3 92.7 + - + +
260K LEU* 3.8 6.0 - - - +
261K GLN* 3.1 24.9 + - - +
284K LYS* 3.7 34.5 + - + +
285K HIS* 3.4 41.3 + - + +
288K VAL* 3.3 28.6 - - + +
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Residues in contact with PHE 258 (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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256K SER* 3.0 19.5 - - - +
257K GLU* 1.3 105.9 - - + +
259K ALA* 1.3 66.5 + - - +
260K LEU 3.1 1.1 - - - -
261K GLN* 2.9 31.3 + - - +
262K THR* 3.0 18.4 + - + +
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Residues in contact with ALA 259 (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* 3.6 33.9 - - + +
235K VAL* 3.3 30.6 - - + +
236K ASN* 3.9 12.0 - - - +
255K PHE* 4.4 1.1 - - + -
256K SER* 3.3 8.1 + - - +
258K PHE* 1.3 78.2 - - - +
260K LEU* 1.3 63.3 + - - +
262K THR* 3.3 11.9 + - - +
263K LEU* 3.0 18.5 + - - +
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Residues in contact with LEU 260 (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* 3.9 8.9 - - - +
249K LEU* 5.4 0.4 - - + -
255K PHE* 3.9 19.3 - - + -
256K SER 3.3 13.8 + - - +
257K GLU* 3.8 3.4 - - - +
258K PHE 3.1 0.6 - - - -
259K ALA* 1.3 78.7 - - - +
261K GLN* 1.3 57.4 + - - +
263K LEU* 3.2 8.7 + - + +
264K LEU* 2.8 65.1 + - + +
275K LEU* 3.8 32.5 - - + -
281K PHE* 4.5 1.8 - - + -
285K HIS* 3.7 39.7 - - + +
288K VAL* 4.2 5.8 - - + -
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Residues in contact with GLN 261 (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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257K GLU 3.1 17.5 + - - +
258K PHE* 2.9 29.4 + - - +
260K LEU* 1.3 74.6 - - - +
262K THR* 1.3 60.4 + - + +
264K LEU* 4.0 2.3 - - - +
265K SER* 2.7 36.7 + - - +
288K VAL* 3.5 17.8 - - + +
292K HIS* 3.1 41.4 + - + +
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Residues in contact with THR 262 (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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236K ASN* 3.5 27.4 + - - +
239K ALA* 3.9 13.3 - - - +
258K PHE 3.0 17.9 + - - +
259K ALA* 3.6 4.3 - - - +
261K GLN* 1.3 76.7 - - + +
263K LEU* 1.3 63.3 + - - +
265K SER* 3.9 5.5 - - - -
266K SER* 2.9 26.3 + - - -
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Residues in contact with LEU 263 (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* 3.8 16.6 + - + +
238K LEU* 3.5 42.4 - - + +
239K ALA* 3.8 5.6 - - - +
244K LEU* 4.7 0.7 - - + -
247K LEU* 3.6 28.5 - - + -
249K LEU* 3.9 18.2 - - + -
259K ALA 3.0 14.4 + - - +
260K LEU* 3.5 14.6 - - + +
262K THR* 1.3 81.6 + - - +
264K LEU* 1.3 63.8 + - + +
266K SER* 3.5 1.0 - - - -
267K CYS* 2.9 48.2 + - - -
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Residues in contact with LEU 264 (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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247K LEU* 5.6 0.9 - - + -
260K LEU* 2.8 47.8 + - + +
263K LEU* 1.3 82.1 - - + +
265K SER* 1.3 64.4 + - - +
267K CYS* 3.4 20.2 + - - +
268K SER* 5.0 0.7 - - - -
270K LEU* 4.8 9.4 - - + -
273K LEU* 3.8 30.3 - - + -
275K LEU* 4.8 2.0 - - + -
288K VAL* 4.0 6.5 - - + +
289K ALA* 3.6 36.8 - - + +
292K HIS* 3.3 27.2 - - + +
293K VAL* 4.2 8.3 - - + +
294K SER* 4.5 3.1 + - - -
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Residues in contact with SER 265 (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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261K GLN* 2.7 31.2 + - - +
262K THR* 3.9 6.5 - - - -
264K LEU* 1.3 74.1 - - - +
266K SER* 1.3 60.9 + - - +
268K SER* 4.3 11.1 + - - -
292K HIS* 3.2 29.7 + - - -
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Residues in contact with SER 266 (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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239K ALA* 2.6 38.1 + - - +
242K SER* 3.4 19.9 - - - -
262K THR 2.9 19.4 + - - -
263K LEU 3.5 3.6 - - - -
265K SER* 1.3 78.5 - - - +
267K CYS* 1.3 58.1 + - - +
268K SER* 3.1 10.3 + - - -
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Residues in contact with CYS 267 (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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238K LEU 4.6 1.6 - - - -
239K ALA 4.8 1.6 - - - -
241K ASN 3.8 12.8 - - - -
242K SER 4.0 6.1 - - - +
244K LEU* 3.5 38.6 - - + +
247K LEU* 5.2 1.6 - - - -
263K LEU* 2.9 33.0 + - - +
264K LEU* 3.4 11.7 + - - +
266K SER* 1.3 75.3 - - - +
268K SER* 1.3 56.9 + - - +
269K ARG 3.2 10.1 + - - -
270K LEU* 3.4 32.2 + - + +
294K SER* 3.5 7.6 + - - -
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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