Contacts of the helix formed by residues 246 - 260 (chain F) in PDB entry 1NZX
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 246 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243F PHE* 3.6 1.8 - - - -
245F GLY* 1.3 72.5 - - - -
247F THR* 1.3 63.7 + - - +
248F GLU* 3.0 31.3 - - - +
249F ILE* 3.3 1.7 + - - +
250F GLY 3.0 17.2 + - - -
269F LEU* 3.3 7.1 - - - +
270F GLY* 4.8 3.1 - - - +
399F GLU* 5.5 5.8 - - - -
6502F NAD 3.0 33.7 + - - -
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Residues in contact with THR 247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E LEU* 3.7 17.7 - - + +
245F GLY 3.9 1.0 + - - -
246F SER* 1.3 69.9 - - - +
248F GLU* 1.3 69.2 + - - +
250F GLY* 3.0 10.2 + - - -
251F ARG* 3.2 16.4 + - - +
269F LEU* 3.7 15.0 - - - +
270F GLY* 3.7 3.1 + - - +
425F TYR* 3.2 34.5 + - + -
470F MET* 3.3 37.6 + - + +
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Residues in contact with GLU 248 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246F SER* 3.0 20.5 + - - +
247F THR* 1.3 81.1 - - - +
249F ILE* 1.3 90.1 + - + +
251F ARG* 3.3 25.4 + - - +
252F VAL* 3.6 9.6 + - - +
6502F NAD 5.9 0.7 - - - -
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Residues in contact with ILE 249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243F PHE* 3.4 28.0 - - + -
246F SER* 3.3 7.0 + - - +
247F THR 3.3 0.2 - - - -
248F GLU* 1.3 94.5 - - + +
250F GLY* 1.3 65.6 + - - +
251F ARG 3.1 2.0 - - - -
252F VAL* 3.0 15.4 + - + +
253F ILE* 3.0 23.4 + - + +
6502F NAD 3.4 74.0 - - + +
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Residues in contact with GLY 250 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E LEU* 3.9 6.5 - - - -
243F PHE* 3.8 10.1 - - - -
246F SER 3.0 6.7 + - - -
247F THR 3.0 9.5 + - - -
249F ILE* 1.3 77.4 - - - +
251F ARG* 1.3 62.6 + - - +
253F ILE* 3.3 4.1 + - - +
254F GLN* 3.1 18.5 + - - +
267F LEU* 3.7 15.6 - - - +
269F LEU* 3.8 21.8 - - - -
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Residues in contact with ARG 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E GLU* 4.9 4.4 + - - -
258E GLY 3.2 22.2 - - - +
259E SER* 3.0 27.6 + - - +
260E SER 2.8 21.0 + - - -
262E LEU* 3.7 15.7 - - + +
247F THR* 3.2 14.3 + - - +
248F GLU* 3.4 16.8 - - - +
249F ILE 3.1 0.4 - - - -
250F GLY* 1.3 76.1 - - - +
252F VAL* 1.3 63.9 + - + +
254F GLN* 3.2 3.1 + - - +
255F VAL* 2.9 30.9 + - + +
470F MET* 3.3 23.2 - - - +
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Residues in contact with VAL 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F ALA* 6.2 1.6 - - + -
248F GLU 3.7 14.1 - - - +
249F ILE* 3.0 23.5 + - + +
251F ARG* 1.3 77.2 - - + +
253F ILE* 1.3 57.5 + - + +
255F VAL* 3.4 7.0 + - - +
256F ALA* 2.9 31.6 + - + +
6502F NAD 4.0 26.0 - - - +
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Residues in contact with ILE 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F ILE* 3.8 13.2 - - + -
233F ALA* 3.7 22.4 - - + +
241F VAL* 3.9 28.3 - - + -
243F PHE* 3.8 24.9 - - + -
249F ILE* 3.0 19.7 + - + +
250F GLY 3.5 7.2 - - - +
252F VAL* 1.3 77.0 - - + +
254F GLN* 1.3 57.7 + - - +
256F ALA* 3.1 6.6 + - - +
257F ALA* 2.9 27.4 + - - +
265F VAL* 4.5 2.9 - - + -
267F LEU* 4.1 16.8 - - + -
6502F NAD 3.7 28.0 - - + +
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Residues in contact with GLN 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E GLN* 3.9 22.4 + - + +
257E ALA* 3.8 14.7 - - - +
258E GLY* 3.8 16.6 - - - -
262E LEU* 3.2 27.8 - - + +
263E LYS 3.5 21.6 + - - -
264E ARG* 5.4 0.4 - - - +
265E VAL* 3.8 11.7 - - - +
250F GLY 3.1 11.0 + - - +
251F ARG 3.8 3.1 - - - +
253F ILE* 1.3 81.0 - - - +
255F VAL* 1.3 62.4 + - - +
257F ALA* 3.4 7.2 + - - +
258F GLY* 3.1 18.2 + - - -
265F VAL* 4.7 13.9 - - + +
267F LEU* 3.8 12.2 - - + +
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Residues in contact with VAL 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E VAL* 3.8 29.7 - - + +
258E GLY 3.8 10.8 - - - +
259E SER* 3.7 23.6 - - - +
251F ARG* 2.9 22.3 + - + +
252F VAL* 3.7 6.3 - - - +
254F GLN* 1.3 74.6 - - - +
256F ALA* 1.3 57.4 - - - +
258F GLY 3.4 1.0 + - - -
259F SER* 2.7 45.8 + - - +
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Residues in contact with ALA 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F ALA* 6.3 0.9 - - - -
233F ALA* 3.7 20.9 - - + +
234F SER* 3.6 21.6 + - - +
252F VAL* 2.9 21.7 + - + +
253F ILE* 3.5 5.2 - - + +
255F VAL* 1.3 78.8 - - - +
257F ALA* 1.3 56.4 + - - +
259F SER* 3.5 5.8 + - - -
260F SER* 2.9 32.1 + - - -
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Residues in contact with ALA 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254E GLN* 3.3 16.8 - - - +
233F ALA 3.9 2.8 + - - +
241F VAL* 5.0 0.4 - - + -
253F ILE 2.9 12.8 + - - +
254F GLN 3.6 3.1 - - - +
256F ALA* 1.3 78.5 - - - +
258F GLY* 1.3 60.9 + - - +
260F SER* 3.3 11.4 + - - -
262F LEU* 2.9 27.1 + - - -
263F LYS* 3.7 19.3 - - + -
265F VAL* 3.5 26.2 - - + -
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Residues in contact with GLY 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E ARG* 3.1 34.8 - - - +
254E GLN* 3.4 30.6 + - - -
255E VAL* 3.8 10.8 - - - -
254F GLN 3.1 9.0 + - - -
255F VAL 3.9 2.0 - - - -
257F ALA* 1.3 79.5 - - - +
259F SER* 1.3 57.6 + - - +
260F SER 4.6 0.2 - - - +
262F LEU* 4.1 5.5 - - - +
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Residues in contact with SER 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E ARG* 4.0 11.3 + - - +
255E VAL* 3.6 13.1 - - - +
236F GLU* 5.0 0.2 - - - +
255F VAL* 2.7 29.9 + - - +
256F ALA* 3.8 6.7 - - - -
258F GLY* 1.3 76.3 - - - +
260F SER* 1.3 62.9 + - - +
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Residues in contact with SER 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E ARG* 3.2 28.5 + - - -
234F SER* 3.4 28.3 - - - -
235F HIS 4.5 0.2 - - - -
236F GLU* 3.6 21.9 - - - +
256F ALA 2.9 20.6 + - - -
257F ALA 3.3 3.8 + - - -
258F GLY 3.4 1.0 - - - -
259F SER* 1.3 77.0 - - - +
261F ASN* 1.3 66.0 + - - -
262F LEU 3.6 1.1 - - - -
263F LYS* 2.9 20.6 + - - -
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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