Contacts of the helix formed by residues 245 - 255 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C GLU* 2.9 5.1 + - - +
244C ILE* 1.3 78.0 - - - +
246C PRO* 1.3 74.1 - - - +
247C ILE* 2.9 40.2 + - - +
248C ASN* 3.2 22.1 - - - +
249C ALA* 3.0 26.5 + - - +
503C NAD 3.5 13.5 - - - +
392D GLU* 4.6 3.7 - - - +
406D LEU* 3.8 0.9 - - - -
425D PHE* 3.2 22.4 + - + +
426D LYS* 3.1 26.3 + - - +
432D TYR* 4.4 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 246 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ILE 3.4 7.0 - - - +
245C ASP* 1.3 90.5 - - - +
247C ILE* 1.3 55.7 + - - +
249C ALA* 3.3 2.3 + - + +
250C LEU* 2.8 31.2 + - - +
392D GLU* 3.4 33.0 - - + +
395D ALA* 3.8 3.2 - - - +
396D GLU* 3.9 25.1 - - + +
399D LEU* 3.8 5.5 - - + +
406D LEU* 3.5 26.0 - - + -
425D PHE* 3.8 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 247 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C ASP* 2.9 9.6 + - - +
246C PRO* 1.3 72.8 - - - +
248C ASN* 1.3 68.3 + - - +
250C LEU* 2.8 16.1 + - - +
251C GLN* 2.9 14.7 + - - +
184D VAL* 3.7 17.5 - - + -
185D THR* 3.8 15.0 - - + -
189D PHE* 4.0 17.0 - - + -
388D LYS* 5.3 0.2 - - + -
391D ASP* 4.1 13.5 - - + +
392D GLU* 3.7 38.4 - - + +
395D ALA* 3.8 7.6 - - + -
432D TYR* 3.6 45.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 248 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C TYR* 2.9 29.9 - - - +
222C GLY* 3.8 3.3 - - - -
226C LYS* 3.5 8.8 + - - -
243C GLU* 3.3 23.1 - - + +
245C ASP* 3.2 29.2 + - + -
246C PRO 3.5 0.2 - - - -
247C ILE* 1.3 76.3 - - - +
249C ALA* 1.3 57.8 + - - +
251C GLN* 3.0 35.5 + - - +
252C ALA 3.1 6.2 + - - -
503C NAD 3.2 14.0 + - - -
426D LYS* 3.4 17.8 - - - +
430D TYR* 3.9 5.0 + - - -
432D TYR* 3.7 12.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C GLU* 4.0 14.7 - - + +
245C ASP 3.0 20.1 + - - +
246C PRO* 3.5 4.5 - - + +
248C ASN* 1.3 77.2 - - - +
250C LEU* 1.3 61.3 + - - +
252C ALA* 3.3 7.4 + - - +
253C ALA* 3.2 22.9 + - - +
259C VAL* 3.9 17.8 - - + +
399D LEU* 4.6 3.8 - - + -
404D VAL* 4.5 8.4 - - + +
406D LEU* 3.6 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C PRO 2.8 13.2 + - - +
247C ILE 2.8 12.0 + - - +
249C ALA* 1.3 73.0 - - - +
251C GLN* 1.3 59.5 + - - +
253C ALA* 3.9 2.6 - - + +
254C MET* 2.9 38.4 + - + +
189D PHE* 3.3 19.5 - - + -
356D PHE* 4.8 2.7 - - + -
360D ASN* 3.4 33.9 - - - +
395D ALA* 3.5 25.4 - - + +
398D HIS* 4.3 13.0 - - + +
399D LEU* 4.1 17.0 - - + +
402D LEU* 4.1 24.9 - - + -
404D VAL* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 251 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C TYR* 3.9 8.1 - - + -
226C LYS* 2.8 33.3 - - - +
247C ILE* 2.9 9.3 + - - +
248C ASN* 3.0 29.7 + - - +
250C LEU* 1.3 76.8 - - - +
252C ALA* 1.3 63.1 + - - +
254C MET 3.3 1.6 + - - -
255C GLU* 3.1 27.6 + - - +
188D LYS* 4.9 11.2 - - - +
189D PHE* 3.8 22.2 - - + -
193D TYR* 3.6 19.3 + - + +
432D TYR* 2.7 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221C TYR* 3.6 40.1 - - + -
241C ILE* 4.2 7.2 - - + -
248C ASN 3.1 4.4 + - - +
249C ALA 3.3 2.7 + - - +
251C GLN* 1.3 76.5 - - - +
253C ALA* 1.3 64.1 + - - +
255C GLU 3.1 6.2 + - - -
257C TYR* 3.0 38.8 + - + +
259C VAL* 3.9 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B GLY* 3.5 18.2 - - - +
236B GLY 3.5 0.3 - - - +
249C ALA 3.2 16.6 + - - +
250C LEU* 3.9 6.1 - - - +
252C ALA* 1.3 74.2 - - - +
254C MET* 1.3 58.5 + - - +
255C GLU 2.9 5.2 - - - -
256C GLY* 2.9 20.1 + - - -
257C TYR 3.6 14.4 + - - +
259C VAL* 4.2 1.3 - - + +
402D LEU* 3.9 25.1 - - + -
404D VAL* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MET* 4.0 20.0 - - - -
212B ALA* 3.6 35.0 - - + +
213B GLY* 4.0 6.7 - - - +
236B GLY* 3.3 8.4 - - - -
250C LEU* 2.9 27.2 + - + +
251C GLN 3.3 5.6 + - - +
253C ALA* 1.3 75.3 - - - +
255C GLU* 1.3 57.5 + - - +
256C GLY 3.3 0.9 - - - -
189D PHE* 4.1 8.7 - - + -
193D TYR* 3.7 40.8 - - + -
196D ARG* 2.9 25.8 + - - -
356D PHE* 4.1 23.3 - - + -
357D VAL* 4.8 7.4 - - + -
402D LEU* 4.6 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 255 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ARG 5.0 2.3 - - - +
236B GLY* 3.8 7.2 - - - -
221C TYR* 3.9 13.3 + - + +
233C ARG* 3.3 29.6 + - - +
251C GLN* 3.1 16.2 - - + +
252C ALA 3.1 8.2 + - - +
253C ALA 2.9 1.8 - - - -
254C MET* 1.3 79.3 - - - +
256C GLY* 1.3 59.7 + - - +
257C TYR* 3.4 18.7 - - + -
192D LEU* 5.1 2.9 - - - +
193D TYR* 3.5 22.9 + - - +
196D ARG* 2.8 30.1 + - - -
230D GLN* 4.5 8.7 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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