Contacts of the helix formed by residues 246 - 260 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C PHE* 3.6 1.6 - - - -
245C GLY* 1.3 73.4 - - - -
247C THR* 1.3 66.0 + - - +
248C GLU* 4.0 12.6 + - - +
249C ILE* 3.2 15.1 + - - +
250C GLY 3.0 17.5 + - - -
269C LEU* 3.4 6.5 - - - +
270C GLY* 4.8 3.1 - - - +
399C GLU* 5.6 3.8 - - - -
3502C NAD 2.8 38.0 + - - -
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Residues in contact with THR 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C GLY 4.0 1.4 + - - -
246C SER* 1.3 72.2 - - - +
248C GLU* 1.3 66.3 + - - +
250C GLY* 3.1 9.7 + - - -
251C ARG* 3.2 23.2 + - - +
269C LEU* 3.6 15.0 - - - +
270C GLY* 3.6 2.6 + - - +
425C TYR* 3.3 29.5 + - + -
470C MET* 3.2 43.4 + - + +
262D LEU* 3.8 16.1 - - + +
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Residues in contact with GLU 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C SER* 4.2 11.8 + - - +
247C THR* 1.3 81.6 - - - +
249C ILE* 1.3 67.2 + - + +
251C ARG* 3.3 26.8 + - - +
252C VAL* 3.6 9.1 + - - +
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Residues in contact with ILE 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C PHE* 3.5 25.8 - - + -
246C SER* 3.2 7.8 + - - +
248C GLU* 1.3 77.0 - - + +
250C GLY* 1.3 66.2 + - - +
251C ARG 3.1 1.8 - - - -
252C VAL* 3.1 13.2 + - + +
253C ILE* 3.0 25.0 + - + +
3502C NAD 3.1 77.6 - - + +
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Residues in contact with GLY 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C PHE* 3.7 18.1 - - - -
246C SER 3.0 13.7 + - - -
247C THR 3.1 5.9 + - - -
249C ILE* 1.3 76.1 - - - +
251C ARG* 1.3 62.2 + - - +
253C ILE* 3.3 4.0 + - - +
254C GLN* 3.1 18.7 + - - +
267C LEU* 3.8 14.2 - - - +
269C LEU* 3.9 11.4 - - - -
262D LEU* 4.0 7.0 - - - -
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Residues in contact with ARG 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C THR* 3.2 25.9 + - - +
248C GLU* 3.4 15.2 - - - +
249C ILE 3.1 0.2 - - - -
250C GLY* 1.3 73.7 - - - +
252C VAL* 1.3 65.9 + - + +
254C GLN* 3.2 3.3 + - - +
255C VAL* 2.9 28.8 + - + +
470C MET* 3.8 25.5 - - - +
236D GLU* 5.2 3.0 + - - -
258D GLY 3.3 18.8 - - - +
259D SER* 3.1 18.5 + - - +
260D SER 3.0 28.7 + - - -
261D ASN* 5.4 0.2 - - - -
262D LEU* 3.8 16.1 - - + +
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Residues in contact with VAL 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ALA* 6.2 2.2 - - + -
248C GLU 3.7 15.3 - - - +
249C ILE* 3.1 22.8 + - + +
251C ARG* 1.3 76.5 - - + +
253C ILE* 1.3 58.2 + - + +
255C VAL* 3.4 8.4 + - + +
256C ALA* 2.8 32.2 + - + +
3502C NAD 4.4 22.2 - - - +
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Residues in contact with ILE 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ILE* 4.0 14.1 - - + -
233C ALA* 3.9 17.2 - - + +
241C VAL* 4.0 29.8 - - + -
243C PHE* 3.9 24.2 - - + -
249C ILE* 3.0 20.2 + - + +
250C GLY 3.5 7.2 - - - +
252C VAL* 1.3 77.4 - - + +
254C GLN* 1.3 57.4 + - - +
256C ALA* 3.2 6.7 + - - +
257C ALA* 2.9 27.0 + - - +
265C VAL* 4.4 3.1 - - + -
267C LEU* 4.0 17.0 - - + -
3502C NAD 3.8 30.3 - - + +
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Residues in contact with GLN 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C GLY 3.1 11.5 + - - +
251C ARG 3.2 0.4 + - - +
253C ILE* 1.3 82.1 - - - +
255C VAL* 1.3 62.2 + - - +
257C ALA* 3.4 6.3 + - - +
258C GLY* 3.0 19.6 + - - -
265C VAL* 4.7 14.3 - - + +
267C LEU* 4.2 9.7 - - + +
254D GLN* 3.9 22.7 + - + +
257D ALA* 3.7 13.3 - - - +
258D GLY* 3.6 19.4 - - - -
262D LEU* 3.0 32.3 - - + +
263D LYS 3.5 21.0 + - - -
264D ARG* 5.5 0.2 - - - +
265D VAL* 3.7 11.1 - - - +
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Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C ARG* 2.9 21.0 + - + +
252C VAL* 3.6 7.2 - - + +
254C GLN* 1.3 72.9 - - - +
256C ALA* 1.3 62.0 + - - +
258C GLY* 3.3 1.4 + - - -
259C SER* 2.8 43.2 + - - +
255D VAL* 3.8 19.7 - - + +
258D GLY 3.8 1.1 - - - +
259D SER* 3.5 39.7 - - - +
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Residues in contact with ALA 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ALA* 5.4 0.9 - - - +
233C ALA* 3.8 27.9 - - + +
234C SER* 4.3 10.6 - - - +
252C VAL* 2.8 21.4 + - + +
253C ILE 3.4 5.6 - - - +
255C VAL* 1.3 78.3 - - - +
257C ALA* 1.3 56.7 + - - +
259C SER* 3.4 5.7 + - - -
260C SER* 2.8 33.8 + - - -
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C ALA 3.9 2.2 + - - +
241C VAL* 4.9 0.2 - - + -
253C ILE 2.9 12.3 + - - +
254C GLN 3.6 3.8 - - - +
255C VAL 3.2 0.2 - - - -
256C ALA* 1.3 77.0 - - - +
258C GLY* 1.3 60.8 + - - +
260C SER* 3.2 11.9 + - - -
262C LEU 3.0 26.3 + - - -
263C LYS* 3.6 20.4 + - + +
265C VAL* 3.5 31.0 - - + -
254D GLN* 3.1 12.8 - - - +
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Residues in contact with GLY 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C GLN 3.0 8.8 + - - -
255C VAL 3.3 2.2 + - - -
257C ALA* 1.3 75.3 - - - +
259C SER* 1.3 60.0 + - - +
260C SER 4.5 0.7 - - - +
262C LEU* 4.2 6.1 - - - +
251D ARG* 3.4 30.9 + - - +
254D GLN* 2.8 34.3 + - - -
255D VAL* 3.8 11.0 - - - -
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Residues in contact with SER 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C VAL* 2.8 29.0 + - - +
256C ALA* 3.9 5.2 - - - -
258C GLY* 1.3 77.1 - - - +
260C SER* 1.3 58.4 + - - +
251D ARG* 3.2 15.7 + - - +
255D VAL* 3.5 15.5 - - - +
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Residues in contact with SER 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C ALA 3.7 0.2 + - - -
234C SER* 3.3 29.4 - - - -
235C HIS 4.6 0.2 - - - -
236C GLU* 3.4 20.3 - - - +
256C ALA 2.8 20.7 + - - -
257C ALA 3.2 4.2 + - - -
258C GLY 3.3 1.0 - - - -
259C SER* 1.3 75.7 - - - +
261C ASN* 1.3 67.4 + - - -
262C LEU 3.6 0.9 - - - -
263C LYS* 2.9 20.5 + - - -
251D ARG* 2.9 31.4 + - - -
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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