Contacts of the helix formed by residues 257 - 267 (chain D) in PDB entry 2FRV
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 TYR 257 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D HIS 3.7 16.6 + - - -
109D LEU* 4.2 11.7 - - + -
112D PHE* 3.1 49.9 - + + +
113D TYR* 3.4 18.7 + + + -
252D PHE* 3.0 10.9 + - - +
253D ILE* 3.7 33.0 - - + +
256D VAL* 1.3 72.9 - - - +
258D ILE* 1.3 61.4 + - + +
260D ASP* 3.8 1.2 - - - +
261D LEU* 2.9 35.8 + - + +
411D THR 4.8 1.9 + - - -
414D ARG* 3.8 16.5 - - - +
415D GLY* 3.7 26.5 + - - -
418D CYS* 4.0 22.7 - - + -
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Residues in contact with ILE 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D ILE* 2.8 41.7 + - + +
254D GLU* 4.1 11.4 - - - +
256D VAL 3.4 0.2 - - - -
257D TYR* 1.3 81.4 - - + +
259D THR* 1.3 58.9 + - + +
261D LEU* 3.2 11.9 + - + +
262D LEU* 3.0 45.0 + - + +
392D LEU* 4.8 14.1 - - + -
393D VAL* 5.5 4.5 - - + -
415D GLY* 3.2 42.0 - - - +
416D ILE* 6.3 0.2 - - + -
419D LEU* 4.6 16.2 - - + -
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Residues in contact with THR 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 3.9 34.6 - - - +
142D SER* 3.9 8.6 + - - -
143D PRO* 5.3 1.6 - - + -
195D HIS* 5.5 0.7 - - - -
254D GLU 3.6 16.4 - - - +
255D GLN* 2.9 28.4 + - - +
256D VAL* 3.1 7.6 + - - -
258D ILE* 1.3 78.5 - - + +
260D ASP* 1.3 67.9 + - - +
262D LEU* 3.4 7.4 + - - +
263D ALA* 3.1 23.7 + - - +
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Residues in contact with ASP 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D PHE* 4.2 10.9 - - + -
113D TYR* 2.9 18.5 + - + +
141D LEU* 5.4 4.5 - - - +
191D ILE* 3.9 13.8 - - - +
192D ALA* 4.6 6.6 - - + -
195D HIS* 2.2 48.7 + - - +
256D VAL 3.0 16.7 + - - +
257D TYR 3.9 0.9 - - - +
259D THR* 1.3 78.2 + - - +
261D LEU* 1.3 67.6 + - - +
263D ALA* 3.8 5.3 - - - +
264D VAL* 3.0 32.3 + - + +
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Residues in contact with LEU 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D PHE* 3.9 25.5 - - + -
257D TYR* 2.9 27.1 + - + +
258D ILE* 3.4 17.3 - - + +
259D THR 3.2 0.2 - - - -
260D ASP* 1.3 80.2 - - - +
262D LEU* 1.3 68.7 + - + +
264D VAL* 4.0 1.4 - - - +
265D ALA* 3.0 30.0 + - + +
393D VAL* 6.4 1.8 - - + -
411D THR* 3.6 34.3 - - + +
412D ALA* 4.2 17.3 - - + +
415D GLY* 3.6 31.9 - - - -
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Residues in contact with LEU 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D ILE* 3.0 31.0 + - + +
259D THR* 3.4 5.6 + - - +
260D ASP 3.3 0.2 - - - -
261D LEU* 1.3 82.2 - - + +
263D ALA* 1.3 53.8 - - - +
265D ALA* 3.5 1.1 + - + -
266D GLY* 2.9 28.8 + - - -
392D LEU* 4.7 8.5 - - + -
393D VAL* 3.7 45.5 - - + +
396D THR* 3.5 37.6 - - + +
397D LEU* 3.4 23.6 - - + +
412D ALA* 5.4 2.7 - - + -
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Residues in contact with ALA 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D LEU* 3.7 28.7 - - + -
188D VAL* 5.5 5.8 - - + -
259D THR 3.1 16.6 + - - +
260D ASP* 3.8 7.0 - - - +
261D LEU 3.2 0.2 - - - -
262D LEU* 1.3 74.6 - - - +
264D VAL* 1.3 68.1 + - + +
266D GLY* 3.2 8.7 + - - -
267D PHE* 3.0 28.3 - - + -
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Residues in contact with VAL 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D PHE* 5.3 12.6 - - + -
120D TRP* 3.9 32.3 - - + -
121D VAL* 4.8 9.0 - - + -
184D LEU* 4.1 19.1 - - + -
188D VAL* 4.3 10.8 - - + -
192D ALA* 5.2 7.0 - - + -
260D ASP* 3.0 18.8 + - + +
261D LEU* 4.2 2.2 - - - +
263D ALA* 1.3 75.3 - - + +
265D ALA* 1.3 65.3 + - - +
267D PHE* 2.9 20.4 + - - +
268D TYR* 3.4 21.9 - - + -
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Residues in contact with ALA 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261D LEU* 3.0 23.7 + - + +
262D LEU* 3.8 5.6 - - + +
264D VAL* 1.3 77.7 - - - +
266D GLY* 1.3 63.6 + - - +
268D TYR* 2.9 17.0 + - - +
269D LYS* 3.4 12.6 + - - +
397D LEU* 3.9 18.6 - - + -
408D LEU* 4.0 31.3 - - + +
411D THR* 6.4 0.7 - - + -
412D ALA* 6.1 3.8 - - + -
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Residues in contact with GLY 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D LEU 2.9 15.7 + - - -
263D ALA* 3.6 7.2 - - - -
264D VAL 3.0 1.2 - - - -
265D ALA* 1.3 77.3 - - - +
267D PHE* 1.3 59.7 + - - +
268D TYR 3.3 1.2 + - - -
269D LYS* 3.8 23.2 - - - +
397D LEU* 3.9 9.8 - - - +
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Residues in contact with PHE 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D LEU* 6.3 0.2 - - + -
183D VAL* 3.5 20.9 - - + +
184D LEU* 3.2 33.0 - - + -
185D PRO* 3.7 30.3 - - + -
188D VAL* 3.9 24.5 - - + -
263D ALA* 3.0 33.0 - - + -
264D VAL 2.9 9.9 + - - +
266D GLY* 1.3 72.9 - - - -
268D TYR* 1.3 63.6 + - + +
269D LYS 3.7 1.3 - - - -
270D ASN* 5.4 0.9 + - - -
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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