Contacts of the helix formed by residues 277 - 287 (chain D) 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 THR 277 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D PHE* 3.5 4.9 - - - -
275D GLY 3.5 5.8 + - - +
276D VAL* 1.3 74.8 - - - +
278D TYR* 1.3 68.9 + - - +
279D ARG* 3.5 16.5 + - + +
280D LEU* 2.8 38.8 + - + +
281D THR* 2.9 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU* 5.6 6.5 - - - -
254D PRO* 3.8 22.2 + - - +
257D ILE* 3.3 38.6 - - + +
258D GLN* 3.7 26.2 - - - +
261D PHE* 3.2 41.9 - + + -
277D THR* 1.3 72.8 + - - +
279D ARG* 1.3 58.7 + - - +
281D THR* 2.7 24.1 + - - -
282D GLN* 3.0 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU* 3.4 21.5 + - - +
14C ASP* 4.3 8.8 + - - +
17C LEU* 3.3 40.6 + - - +
18C ARG* 2.6 63.5 + - - +
21C GLY* 4.6 2.6 - - - -
22C ASP* 2.7 42.2 + - - +
277D THR* 3.1 14.3 + - + +
278D TYR* 1.3 80.6 - - - +
280D LEU* 1.3 57.0 + - - +
282D GLN* 3.4 8.9 + - - +
283D GLY 3.0 7.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ARG* 4.9 3.1 - - - +
225D PRO* 3.7 19.5 - - + -
226D GLU* 3.9 21.3 - - + +
229D ILE* 3.6 15.0 - - + -
275D GLY 3.5 23.3 - - - +
277D THR* 2.8 25.3 + - + +
279D ARG* 1.3 75.1 - - - +
281D THR* 1.3 67.8 + - - +
282D GLN 3.0 1.8 - - - -
283D GLY* 2.9 4.5 + - - +
284D VAL* 2.8 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D ILE* 3.2 22.8 - - + +
257D ILE* 4.0 11.7 - - + -
260D ILE* 3.7 20.2 - - + +
261D PHE* 3.0 58.6 - - + +
276D VAL* 4.2 2.4 - - - +
277D THR 2.9 6.0 + - - -
278D TYR 2.7 11.3 + - - -
280D LEU* 1.3 72.9 - - - +
282D GLN* 1.3 60.6 + - - +
285D VAL* 3.0 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 282 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ASP* 3.5 20.4 - - - +
18C ARG* 3.5 6.5 + - - +
257D ILE* 3.5 38.2 - - + +
278D TYR* 3.0 34.2 + - + +
279D ARG* 3.5 11.8 - - - +
281D THR* 1.3 75.1 - - - +
283D GLY* 1.3 59.6 + - - +
285D VAL* 3.1 4.2 + - - -
286D LYS* 2.7 48.6 + - + +
288D ILE* 3.5 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 283 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ARG* 3.7 13.9 - - - -
279D ARG 3.0 5.1 + - - -
280D LEU* 2.9 9.9 + - - -
282D GLN* 1.3 79.1 - - - +
284D VAL* 1.3 56.8 + - - +
287D ARG* 2.8 32.2 + - - -
288D ILE* 3.3 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D PHE* 5.4 2.5 - - + -
226D GLU* 4.2 18.2 - - + +
229D ILE* 3.4 39.3 - - + -
230D GLU* 3.7 32.8 - - + +
233D ARG* 4.6 1.1 - - - -
280D LEU* 2.8 35.2 + - + +
283D GLY* 1.3 73.4 - - - +
285D VAL* 1.3 60.7 + - - +
287D ARG* 2.6 36.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 285 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D ILE* 4.1 6.7 - - + -
233D ARG* 3.9 29.3 + - - +
249D LEU* 4.6 6.3 - - + -
251D GLY* 4.1 26.5 - - - +
257D ILE* 5.1 6.5 - - + -
260D ILE* 3.9 40.4 - - + -
281D THR* 3.0 26.0 + - + +
282D GLN* 3.8 3.4 - - - +
284D VAL* 1.3 78.4 - - - +
286D LYS* 1.3 62.0 + - + +
287D ARG* 3.5 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 286 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ARG* 4.4 22.2 - - - +
6D ATP 5.7 2.5 - - - +
84D ASP* 5.0 4.9 + - - -
86D SER* 5.8 0.4 + - - -
251D GLY* 2.9 37.5 - - - +
252D ASP* 2.7 38.2 + - - +
257D ILE* 4.3 6.5 - - - -
282D GLN* 2.7 33.9 + - + +
285D VAL* 1.3 76.8 - - + +
287D ARG* 1.3 71.5 + - - +
288D ILE* 3.1 14.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D VAL 5.4 6.2 + - - -
212D ASN* 4.9 11.7 - - - +
230D GLU* 2.9 35.9 + - - -
233D ARG* 4.4 18.8 - - - +
234D MET* 5.0 2.4 - - - +
283D GLY 2.8 11.6 + - - -
284D VAL* 2.6 37.6 + - - +
285D VAL 3.3 4.4 - - - +
286D LYS* 1.3 79.5 - - - +
288D ILE* 1.3 63.9 + - - +
289D ILE* 3.9 9.2 + - - +
----------------------------------------------------------
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