Contacts of the helix formed by residues 245 - 255 (chain D) in PDB entry 3NJ4
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 ASP 245 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392C GLU* 4.4 2.9 - - - +
406C LEU* 3.9 1.6 - - - -
425C PHE* 3.4 16.6 - - + +
426C LYS* 3.0 44.0 + - - +
432C TYR* 3.9 5.4 + - - -
243D GLU* 2.9 7.2 + - - +
244D ILE* 1.3 79.8 - - - +
246D PRO* 1.3 67.6 - - - +
247D ILE* 2.8 24.9 + - - +
248D ASN* 3.2 19.5 + - - +
249D ALA* 2.9 30.0 + - - +
504D NAD 3.7 1.6 - - - +
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Residues in contact with PRO 246 (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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392C GLU* 3.4 29.6 - - + +
395C ALA* 3.5 4.8 - - - +
396C GLU* 3.6 35.9 - - + +
399C LEU* 3.7 8.9 - - + +
406C LEU* 3.9 18.1 - - + -
425C PHE* 3.9 15.0 - - + -
244D ILE 3.6 8.4 - - - +
245D ASP* 1.3 90.7 - - - +
247D ILE* 1.3 57.1 + - - +
250D LEU* 3.0 29.5 + - - +
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Residues in contact with ILE 247 (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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184C VAL* 3.6 18.2 - - + -
185C THR* 4.0 10.3 - - + -
189C PHE* 3.8 15.9 - - + -
388C LYS* 5.2 0.4 - - + -
391C ASP* 4.2 7.9 - - + +
392C GLU* 3.8 32.8 - - + +
395C ALA* 3.8 19.3 - - + -
432C TYR* 3.3 47.8 - - + +
245D ASP* 2.8 16.6 + - - +
246D PRO* 1.3 69.6 - - - +
248D ASN* 1.3 65.0 + - - +
250D LEU* 3.1 5.0 + - - +
251D GLN* 2.9 24.9 + - - +
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Residues in contact with ASN 248 (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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426C LYS* 3.5 7.5 - - - +
430C TYR* 4.1 8.5 + - - -
432C TYR* 3.5 16.5 - - - -
221D TYR* 3.0 28.9 - - - +
222D GLY* 4.0 2.9 - - - -
226D LYS* 3.6 7.1 + - - -
243D GLU* 3.5 23.8 - - + +
245D ASP* 3.2 27.5 + - - +
247D ILE* 1.3 74.8 - - - +
249D ALA* 1.3 63.6 + - - +
251D GLN* 3.0 18.0 + - - +
252D ALA* 3.0 19.2 + - - +
504D NAD 3.2 14.7 + - - -
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Residues in contact with ALA 249 (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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399C LEU* 4.6 2.2 - - + -
404C VAL* 4.4 8.3 - - + +
406C LEU* 3.5 24.2 - - + -
243D GLU* 3.9 14.3 - - + +
245D ASP 2.9 17.9 + - - +
246D PRO* 3.8 4.5 - - + +
248D ASN* 1.3 77.4 - - - +
250D LEU* 1.3 59.9 + - - +
252D ALA* 3.4 2.3 + - - +
253D ALA* 3.2 21.5 + - - +
259D VAL* 3.7 23.8 - - + +
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Residues in contact with LEU 250 (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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189C PHE* 3.8 21.5 - - + -
356C PHE* 4.6 5.6 - - + -
360C ASN* 3.8 23.1 - - - +
395C ALA* 4.0 24.0 - - + +
398C HIS* 4.4 11.4 - - + -
399C LEU* 3.9 16.7 - - + +
402C LEU* 3.6 30.1 - - + -
246D PRO 3.0 18.4 + - - +
247D ILE* 3.1 5.1 + - - +
249D ALA* 1.3 74.5 - - - +
251D GLN* 1.3 60.7 + - - +
253D ALA* 4.3 2.7 - - + -
254D MET* 3.0 41.7 + - + +
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Residues in contact with GLN 251 (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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184C VAL* 5.6 0.2 - - - +
188C LYS* 4.7 14.1 - - - +
189C PHE* 3.6 20.8 - - + -
193C TYR* 3.7 15.7 + - + +
432C TYR* 3.0 33.1 + - - +
221D TYR* 3.8 7.6 - - + -
226D LYS* 2.9 32.5 - - - +
247D ILE* 2.9 15.8 + - - +
248D ASN* 3.1 24.6 + - - +
250D LEU* 1.3 78.9 - - - +
252D ALA* 1.3 62.2 + - - +
254D MET* 3.2 4.0 + - - +
255D GLU* 3.0 29.0 + - - +
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Residues in contact with ALA 252 (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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221D TYR* 3.7 25.3 - - + -
241D ILE* 4.1 10.5 - - + -
248D ASN 3.0 11.8 + - - +
249D ALA* 3.8 3.1 - - - +
250D LEU 3.3 0.2 - - - -
251D GLN* 1.3 76.5 - - - +
253D ALA* 1.3 60.8 + - - +
255D GLU 3.3 5.0 + - - -
257D TYR* 2.9 45.8 + - + +
259D VAL* 3.8 21.8 - - + -
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Residues in contact with ALA 253 (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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213A GLY* 3.2 19.1 - - - +
236A GLY 3.4 0.7 - - - +
402C LEU* 3.9 24.9 - - + -
404C VAL* 3.9 18.4 - - + -
249D ALA 3.2 16.4 + - - +
250D LEU* 3.7 6.5 - - - +
251D GLN 3.2 0.2 - - - -
252D ALA* 1.3 73.8 - - - +
254D MET* 1.3 57.6 + - - +
255D GLU 3.0 5.2 - - - -
256D GLY* 2.9 18.5 + - - -
257D TYR 3.6 13.1 + - - +
259D VAL* 4.3 0.9 - - + +
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Residues in contact with MET 254 (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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210A MET* 3.6 12.6 - - + -
212A ALA* 3.5 28.7 - - + +
213A GLY* 3.9 6.1 - - - +
236A GLY* 3.3 9.1 - - - -
189C PHE* 4.2 9.6 - - + -
193C TYR* 3.4 56.3 - - + -
196C ARG* 3.0 25.6 + - - -
356C PHE* 4.1 24.7 - - + -
357C VAL* 4.9 9.2 - - + -
402C LEU* 4.9 0.4 - - - -
250D LEU* 3.0 34.9 + - + +
251D GLN 3.2 2.4 + - - +
253D ALA* 1.3 75.7 - - - +
255D GLU* 1.3 57.1 - - - +
256D GLY 3.3 0.4 - - - -
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Residues in contact with GLU 255 (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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233A ARG 4.9 2.3 - - - +
236A GLY* 3.6 9.9 - - - -
192C LEU* 5.0 2.3 - - - +
193C TYR* 2.9 29.5 + - - +
196C ARG* 3.3 20.7 + - - -
230C GLN* 4.8 4.8 + - - +
221D TYR* 3.6 17.3 + - + +
233D ARG* 2.8 36.9 + - - +
251D GLN 3.0 21.7 + - - +
252D ALA 3.6 8.5 - - - +
253D ALA 3.0 1.0 - - - -
254D MET* 1.3 79.4 - - - +
256D GLY* 1.3 56.4 + - - +
257D TYR* 3.5 15.5 - - + -
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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