Contacts of the helix formed by residues 262 - 274 (chain A) in PDB entry 6FD3
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 THR 262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A MET* 1.3 75.2 - - - +
263A ASP* 1.3 65.8 + - - +
264A GLU* 3.1 9.3 + - - +
265A GLU* 2.7 45.1 + - - +
266A ILE* 2.9 22.8 + - - +
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Residues in contact with ASP 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A MET 4.0 0.2 + - - -
262A THR* 1.3 73.5 - - - +
264A GLU* 1.3 58.0 + - + +
266A ILE* 3.4 8.9 + - - +
267A LEU* 3.0 37.6 + - + +
317A GLN* 2.7 36.1 + - - +
322A LYS* 3.4 28.6 + - - +
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Residues in contact with GLU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A THR* 3.1 8.5 + - - +
263A ASP* 1.3 77.4 - - + +
265A GLU* 1.3 61.3 + - + +
267A LEU* 3.3 8.3 + - + +
268A GLU* 2.8 46.7 + - + +
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Residues in contact with GLU 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A SER 4.1 3.8 - - - +
261A MET* 3.3 30.6 - - + +
262A THR* 2.7 47.8 + - - +
264A GLU* 1.3 76.7 - - + +
266A ILE* 1.3 62.1 + - - +
268A GLU* 3.4 13.7 + - - +
269A LYS* 3.0 19.6 + - - +
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Residues in contact with ILE 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A MET* 3.7 31.6 - - + +
262A THR 2.9 24.2 + - - +
263A ASP* 3.7 6.1 - - - +
265A GLU* 1.3 76.6 - - - +
267A LEU* 1.3 57.9 + - + +
269A LYS* 3.2 3.3 + - - +
270A LEU* 2.9 42.4 + - + +
322A LYS* 3.5 49.6 - - + +
323A GLU* 3.6 24.2 - - + +
326A ILE* 4.0 14.1 - - + -
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ASP* 3.0 23.6 + - + +
264A GLU* 3.9 7.6 - - + +
266A ILE* 1.3 75.7 - - - +
268A GLU* 1.3 58.0 + - + +
270A LEU* 3.4 6.9 + - + +
271A ARG* 2.9 38.9 + - - +
316A LEU* 3.4 32.8 - - + -
322A LYS* 4.6 11.9 - - - +
348A LEU* 4.3 12.5 - - + +
350A GLY 4.2 12.6 - - - +
351A ASP* 3.9 16.4 - - - +
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Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A GLU* 2.8 32.2 + - + +
265A GLU* 3.7 15.5 + - - +
267A LEU* 1.3 77.1 - - - +
269A LYS* 1.3 61.6 + - - +
271A ARG* 3.4 5.9 + - - +
272A SER* 3.2 21.8 + - - -
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Residues in contact with LYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A MET* 4.4 6.1 - - + -
265A GLU 3.0 16.3 + - - +
266A ILE 3.6 4.0 - - - +
268A GLU* 1.3 76.8 - - - +
270A LEU* 1.3 62.3 + - - +
272A SER* 2.7 28.8 + - - +
273A ILE* 3.4 31.5 + - + +
326A ILE* 3.8 40.8 - - + -
330A LEU* 4.4 11.3 - - - +
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A ILE* 2.9 33.7 + - + +
267A LEU* 3.8 6.7 - - + +
269A LYS* 1.3 75.8 - - - +
271A ARG* 1.3 63.0 + - - +
273A ILE* 3.1 7.4 + - + +
274A VAL* 3.1 29.6 + - - +
316A LEU* 4.1 34.3 - - + -
322A LYS* 5.8 0.4 - - + +
325A ILE* 4.3 7.9 - - + +
326A ILE* 3.9 33.2 - - + +
329A ILE* 4.2 22.7 - - + -
348A LEU* 4.4 12.3 - - + -
353A LEU* 4.4 11.7 - - + -
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Residues in contact with ARG 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A LEU* 2.9 26.1 + - - +
268A GLU* 3.7 7.4 - - - +
270A LEU* 1.3 76.8 - - - +
272A SER* 1.3 62.6 + - - +
273A ILE 3.3 0.9 + - - -
274A VAL* 3.8 22.5 + - - +
348A LEU* 3.3 48.3 + - - +
350A GLY* 4.7 15.2 + - - +
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A GLU 3.2 12.1 + - - -
269A LYS* 2.7 31.1 + - - +
271A ARG* 1.3 78.3 - - - +
273A ILE* 1.3 65.7 + - - +
274A VAL 4.8 1.4 - - - +
333A ARG* 5.3 0.2 + - - -
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A LYS* 3.6 23.8 - - - +
270A LEU* 3.4 27.1 - - + +
272A SER* 1.3 93.4 - - - +
274A VAL* 1.3 64.8 + - - +
326A ILE* 4.3 10.3 - - + +
329A ILE* 4.0 26.9 - - + -
330A LEU* 3.9 25.4 - - + -
333A ARG* 2.6 48.4 + - - +
343A TYR* 4.8 0.2 + - - -
346A SER* 4.1 2.6 + - - -
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Residues in contact with VAL 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A LEU 3.2 18.4 - - - +
271A ARG* 3.8 18.7 - - - +
272A SER 3.8 1.6 - - - +
273A ILE* 1.3 81.5 - - - +
275A SER* 1.3 71.9 + - - +
276A VAL* 4.1 3.3 + - - +
329A ILE* 4.0 7.6 - - + -
346A SER* 3.5 26.2 - - - +
347A TYR* 4.0 2.2 - - - +
348A LEU* 3.8 21.8 - - + +
353A LEU* 3.6 29.8 - - + -
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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