Contacts of the helix formed by residues 262 - 276 (chain G) in PDB entry 1R4N
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 GLU 262 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209G HIS* 3.3 33.4 - - - -
210G SER* 4.4 4.8 + - - -
251G ILE* 3.4 36.9 - - + +
252G LEU* 3.7 20.7 + - - +
260G GLU* 5.0 1.7 - - - +
261G ASP* 1.3 101.1 + - - +
263G GLU* 1.3 65.5 + - - +
264G ASN* 3.3 17.6 + - - +
265G PHE* 3.5 18.4 - - + -
266G GLU* 3.3 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 263 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210G SER* 5.3 3.4 - - - -
261G ASP* 4.8 2.0 - - + +
262G GLU* 1.3 76.3 - - - +
264G ASN* 1.3 57.1 + - - +
266G GLU* 3.1 7.6 + - + +
267G GLU* 2.7 33.2 + - + +
333G ILE* 3.6 27.6 - - + +
214H PRO* 6.0 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 264 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209G HIS 3.2 12.3 - - - +
210G SER* 3.0 40.6 - - - +
212G THR* 3.1 21.5 - - - +
214G TRP* 4.1 7.4 - - + +
217G ILE* 4.4 2.5 - - - +
262G GLU* 3.6 11.5 + - - +
263G GLU* 1.3 88.7 - - - +
265G PHE* 1.3 66.8 + - - +
267G GLU* 3.0 15.4 + - - +
268G ALA* 2.6 35.6 + - - +
333G ILE* 4.0 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 265 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209G HIS* 3.0 41.3 - + - -
217G ILE* 3.5 35.7 - - + -
221G TYR* 4.3 11.0 - + - -
247G ILE* 3.5 31.3 - - + +
250G GLY* 3.6 21.3 - - - -
251G ILE* 4.1 15.7 - - + -
262G GLU* 3.5 24.2 - - + -
263G GLU 3.2 0.2 - - - -
264G ASN* 1.3 95.6 - - - +
266G GLU* 1.3 62.3 + - - +
268G ALA* 3.0 10.2 + - - +
269G ILE* 2.9 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 266 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G ARG* 4.0 17.7 + - - +
262G GLU 3.3 11.2 + - - +
263G GLU* 3.1 12.2 + - + +
265G PHE* 1.3 78.8 - - - +
267G GLU* 1.3 62.6 + - - +
269G ILE* 3.1 33.9 - - - +
270G LYS* 3.0 51.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 267 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214G TRP* 3.7 27.6 - - + +
263G GLU 2.7 13.9 + - - +
264G ASN* 3.0 12.1 + - - +
266G GLU* 1.3 73.3 - - - +
268G ALA* 1.3 63.2 + - - +
270G LYS* 3.1 16.3 + - + +
271G ASN* 2.6 42.5 + - - +
331G ASP 4.6 1.4 - - - +
332G MET* 4.3 7.1 - - - +
333G ILE* 3.2 39.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 268 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214G TRP* 3.9 12.7 - - + +
217G ILE* 3.8 22.2 - - + -
218G ILE* 3.1 31.0 - - + +
247G ILE* 4.7 3.6 - - + -
264G ASN 2.6 15.8 + - - +
265G PHE 3.1 10.1 - - - +
267G GLU* 1.3 71.8 - - - +
269G ILE* 1.3 63.8 + - - +
271G ASN* 2.9 17.9 + - - +
272G VAL* 3.0 11.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 269 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G ARG* 3.2 41.7 + - + +
247G ILE* 4.1 22.4 - - + +
248G ARG* 3.9 36.3 - - + +
251G ILE* 5.9 2.5 - - + -
265G PHE* 2.9 24.2 + - + +
266G GLU* 3.1 38.6 - - - +
268G ALA* 1.3 75.2 - - - +
270G LYS* 1.3 67.2 + - + +
272G VAL* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 270 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G ARG* 4.3 4.3 + - - +
266G GLU* 3.0 40.2 + - - +
267G GLU* 3.5 13.8 - - + +
269G ILE* 1.3 80.5 - - + +
271G ASN* 1.3 61.8 + - - +
272G VAL 3.4 0.2 + - - -
273G ASN* 3.4 18.2 + - - +
274G THR* 5.6 0.2 + - - -
128L GLU* 5.1 4.7 - - - +
131L GLU* 4.9 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 271 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214G TRP* 3.0 66.6 - - + +
218G ILE* 4.0 1.6 - - + -
267G GLU* 2.6 36.5 + - - +
268G ALA 2.9 8.3 + - - +
270G LYS* 1.3 74.0 - - - +
272G VAL* 1.3 55.1 + - - +
273G ASN 2.9 5.4 - - - -
274G THR* 2.8 24.9 + - - -
275G ALA* 3.0 16.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 272 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G ILE* 3.5 17.0 - - + -
240G LYS* 4.2 20.6 - - + +
243G PHE* 3.6 24.2 - - + -
244G ARG* 4.0 12.6 - - + +
247G ILE* 3.7 22.9 - - + -
268G ALA 3.0 11.1 + - - +
269G ILE* 2.8 25.9 + - - +
271G ASN* 1.3 71.4 - - - +
273G ASN* 1.3 60.6 + - - +
274G THR 3.1 1.1 + - - -
275G ALA* 4.4 4.5 - - - -
276G LEU* 3.7 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 273 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240G LYS* 4.4 10.0 + - - +
244G ARG* 3.3 25.7 + - - +
270G LYS 3.4 10.9 + - - +
271G ASN 2.9 1.2 + - - -
272G VAL* 1.3 77.7 - - - +
274G THR* 1.3 59.0 + - - +
128L GLU* 3.0 52.2 + - - +
129L ARG* 5.0 7.1 + - - -
131L GLU* 3.6 16.7 + - - +
132L GLU* 3.6 37.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 274 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180G LEU* 4.0 25.8 - - + -
181G GLU* 5.4 7.6 - - + +
183G LEU* 5.8 3.6 - - + -
240G LYS* 5.5 1.0 + - - -
271G ASN* 2.8 10.0 + - - -
273G ASN* 1.3 81.4 - - - +
275G ALA* 1.3 56.5 + - - +
276G LEU* 2.5 23.9 + - - +
277G ASN 3.5 15.5 + - - +
278G THR* 4.0 11.5 - - + +
131L GLU* 3.7 33.4 + - - +
132L GLU* 5.5 3.1 - - - +
135L GLY* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 275 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G LEU* 4.6 13.8 - - + +
185G LEU* 3.8 31.0 + - + +
214G TRP* 4.7 3.6 - - + +
218G ILE* 4.0 25.4 - - + -
271G ASN* 3.0 19.8 + - + +
272G VAL* 4.4 2.2 - - - -
274G THR* 1.3 74.3 - - - +
276G LEU* 1.3 67.1 + - + +
278G THR* 3.5 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 276 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185G LEU* 5.4 2.7 - - + -
186G ASP* 3.3 26.2 + - - +
218G ILE* 4.8 8.5 - - + -
222G LEU* 4.3 25.6 - - + -
232G ARG 5.1 4.0 - - - +
233G ILE* 3.6 37.0 - - + +
234G PRO* 6.3 0.9 - - + -
240G LYS* 3.7 32.8 - - + +
243G PHE* 4.7 5.6 - - + -
272G VAL* 3.7 26.9 - - + +
274G THR 2.5 8.8 + - - +
275G ALA* 1.3 80.2 - - + +
277G ASN* 1.3 59.6 + - + +
278G THR 3.4 2.4 + - - -
----------------------------------------------------------
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