Contacts of the helix formed by residues 256 - 267 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232E ASP* 2.9 28.0 + - - -
255E PHE* 1.3 78.5 - - - +
257E GLU* 1.3 66.0 + - - +
258E PHE* 2.9 23.0 + - - +
259E ALA 3.1 14.2 + - - -
260E LEU* 3.2 22.9 + - - +
285E HIS* 3.4 6.5 - - - -
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Residues in contact with GLU 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E SER* 1.3 76.4 - - - +
258E PHE* 1.3 92.9 + - + +
260E LEU* 4.0 6.1 - - - -
261E GLN* 3.3 15.1 + - - +
282E THR* 5.1 0.8 + - - -
284E LYS* 3.8 35.0 + - + +
285E HIS* 3.3 41.7 + - + +
288E VAL* 3.2 36.2 - - + +
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Residues in contact with PHE 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E ASP* 5.6 0.2 - - - +
256E SER* 2.9 19.7 - - - +
257E GLU* 1.3 108.4 - - + +
259E ALA* 1.3 66.8 + - - +
260E LEU 3.2 0.9 - - - -
261E GLN* 3.0 25.7 + - - +
262E THR* 2.9 23.0 + - + +
284E LYS* 6.2 0.2 - - + -
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Residues in contact with ALA 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E ASP* 3.6 36.1 + - + +
235E VAL* 3.3 29.5 - - + +
236E ASN* 3.9 18.0 - - - +
255E PHE* 4.2 1.6 - - + -
256E SER* 3.1 8.5 + - - +
258E PHE* 1.3 76.7 - - - +
260E LEU* 1.3 64.2 + - - +
262E THR* 3.2 5.2 + - - +
263E LEU 3.0 18.5 + - - -
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Residues in contact with LEU 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E VAL* 3.8 8.6 - - - +
249E LEU* 5.4 0.2 - - + -
255E PHE* 3.9 22.2 - - + -
256E SER 3.2 15.2 + - - +
257E GLU 3.9 3.8 - - - +
259E ALA* 1.3 81.2 - - - +
261E GLN* 1.3 56.1 + - - +
263E LEU* 3.4 9.3 + - + +
264E LEU* 2.9 63.9 + - + +
275E LEU* 4.0 30.7 - - + -
281E PHE* 4.4 1.8 - - + -
285E HIS* 3.8 39.7 - - + +
288E VAL* 4.0 5.4 - - + -
289E ALA 4.5 1.1 - - - +
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Residues in contact with GLN 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257E GLU 3.3 15.4 + - - +
258E PHE* 3.0 26.8 + - - +
260E LEU* 1.3 77.7 - - - +
262E THR* 1.3 57.9 + - + +
264E LEU* 4.1 1.9 - - - +
265E SER* 2.4 40.9 + - - +
288E VAL* 3.5 19.0 - - + +
292E HIS* 3.2 38.7 + - + +
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Residues in contact with THR 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E ASN* 3.5 27.3 + - - +
239E ALA* 3.9 14.0 - - - +
258E PHE* 2.9 21.7 + - + +
259E ALA 3.6 2.5 - - - +
261E GLN* 1.3 73.2 - - + +
263E LEU* 1.3 62.2 + - - +
265E SER* 3.7 6.3 - - - -
266E SER* 2.9 33.1 + - - -
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Residues in contact with LEU 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E VAL* 3.9 20.4 - - + +
238E LEU* 3.6 35.9 - - + +
239E ALA* 3.8 5.8 - - - +
244E LEU* 4.5 0.7 - - + -
247E LEU* 3.7 27.8 - - + -
249E LEU* 3.9 19.1 - - + -
259E ALA 3.0 16.5 + - - +
260E LEU* 3.7 11.9 - - + +
262E THR* 1.3 80.9 + - - +
264E LEU* 1.3 62.5 + - + +
266E SER* 3.4 2.3 - - - -
267E CYS* 3.0 44.9 + - - -
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Residues in contact with LEU 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247E LEU* 5.6 0.9 - - + -
260E LEU* 2.9 46.4 + - + +
263E LEU* 1.3 80.7 - - + +
265E SER* 1.3 68.5 + - - +
266E SER 3.3 0.2 + - - -
267E CYS* 3.3 21.7 + - + +
268E SER* 5.0 0.7 - - - -
270E LEU* 4.8 9.0 - - + -
273E LEU* 3.9 30.1 - - + -
275E LEU* 4.8 2.7 - - + -
288E VAL* 4.3 5.8 - - + +
289E ALA* 3.7 36.6 - - + +
292E HIS* 3.4 24.5 - - + +
293E VAL* 4.1 8.1 - - + +
294E SER* 4.6 2.4 + - - -
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Residues in contact with SER 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261E GLN* 2.4 31.8 + - - +
262E THR* 3.7 7.2 - - - -
264E LEU* 1.3 78.0 - - - +
266E SER* 1.3 61.1 + - - +
268E SER* 4.2 12.6 + - - -
292E HIS* 3.4 27.9 + - - +
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Residues in contact with SER 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E ALA* 2.4 39.2 + - - +
242E SER* 3.3 20.8 - - - -
262E THR 2.9 20.1 + - - -
263E LEU 3.1 4.2 + - - -
265E SER* 1.3 79.9 - - - +
267E CYS* 1.3 57.8 + - - +
268E SER* 3.1 10.2 + - - -
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Residues in contact with CYS 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238E LEU 4.5 1.1 - - - -
241E ASN 3.7 14.4 - - - -
242E SER* 4.0 6.3 - - - -
244E LEU* 3.5 37.9 - - + +
247E LEU* 5.3 0.9 - - - -
263E LEU* 3.0 32.7 + - - +
264E LEU* 3.3 12.2 + - + +
266E SER* 1.3 75.8 - - - +
268E SER* 1.3 55.9 + - - +
269E ARG 3.3 10.1 + - - -
270E LEU* 3.4 32.7 - - + +
294E 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