Contacts of the helix formed by residues 258 - 273 (chain A) in PDB entry 6PAU
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 ARG 258 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A PRO* 4.1 5.8 - - + +
256A SER 4.8 4.3 - - - +
257A LYS* 1.3 81.8 - - - +
259A VAL* 1.3 58.9 + - - +
261A PRO* 3.5 30.9 - - + +
262A VAL* 3.3 24.0 - - + +
265A ARG* 5.5 5.8 - - - +
511A 4PS 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 4.6 4.9 - - + -
153A PRO* 4.6 6.5 - - + -
156A PHE* 4.1 26.0 - - + -
214A VAL* 4.4 24.2 - - + -
223A VAL* 5.7 1.1 - - + +
224A GLY* 5.2 2.0 - - - -
250A VAL* 4.3 12.8 - - + -
254A LEU 4.2 3.8 - - - +
257A LYS* 3.9 14.6 - - + +
258A ARG* 1.3 78.6 - - - +
260A ALA* 1.3 68.5 + - - +
261A PRO 3.3 0.2 - - - -
262A VAL* 3.1 8.4 + - - +
263A LEU* 2.9 35.2 + - + +
501A MG 3.1 17.6 - - - -
511A 4PS 3.8 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 4.4 9.8 - - + +
250A VAL* 4.2 2.4 - - + +
259A VAL* 1.3 77.3 - - - +
261A PRO* 1.3 64.5 - - + +
263A LEU* 3.1 14.2 + - - +
264A ILE* 2.9 30.0 + - + +
511A 4PS 3.2 54.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ARG* 3.5 35.7 - - + +
259A VAL 3.4 3.8 - - - -
260A ALA* 1.3 91.1 - - + +
262A VAL* 1.3 56.0 + - - +
264A ILE* 3.3 12.0 + - + +
265A ARG* 3.0 52.0 + - - +
511A 4PS 3.4 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TYR* 4.2 10.8 - - + -
151A SER 3.5 25.4 - - - +
152A LEU* 3.6 10.1 - - + -
153A PRO* 4.6 8.7 - - + -
158A TRP* 3.5 24.9 - - + -
258A ARG* 3.3 21.3 - - + +
259A VAL 3.1 5.8 + - - +
261A PRO* 1.3 72.1 - - - +
263A LEU* 1.3 61.5 + - - +
265A ARG* 3.3 26.2 + - - +
266A GLU* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TRP* 3.9 12.3 - - + -
212A CYS* 3.8 14.1 - - - +
214A VAL* 3.8 25.6 - - + -
224A GLY* 4.3 2.0 - - - -
225A PHE* 3.9 25.1 - - - +
226A ILE* 3.7 30.9 - - + +
248A LEU* 4.0 15.5 - - + -
250A VAL* 4.1 17.9 - - + -
259A VAL* 2.9 20.9 + - + +
260A ALA* 3.4 9.0 - - - +
262A VAL* 1.3 77.2 - - - +
264A ILE* 1.3 60.7 + - - +
266A GLU* 3.9 1.0 - - - +
267A ILE* 3.0 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE* 4.3 5.2 - - + -
248A LEU* 4.1 17.0 - - + -
260A ALA* 2.9 23.7 + - + +
261A PRO* 3.6 10.3 - - + +
263A LEU* 1.3 73.3 - - - +
265A ARG* 1.3 66.7 + - + +
267A ILE* 3.1 9.3 - - - +
268A THR* 2.9 31.4 + - - +
479A TYR* 6.2 0.9 - - + -
1000C MYR 3.8 52.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A TYR* 3.6 41.6 - - + +
151A SER 5.0 3.4 + - - -
258A ARG* 5.5 6.3 - - - +
261A PRO* 3.0 36.4 + - - +
262A VAL* 3.6 30.7 - - - +
264A ILE* 1.3 79.4 - - + +
266A GLU* 1.3 55.9 + - - +
268A THR* 3.2 7.9 + - - -
269A ARG* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PRO* 3.6 11.7 - - - +
150A TYR* 3.0 28.5 + - + -
158A TRP* 3.4 31.0 - - + -
212A CYS* 3.9 4.3 - - - -
262A VAL 2.8 18.5 + - - +
263A LEU 3.9 1.8 - - - +
265A ARG* 1.3 73.2 - - - +
267A ILE* 1.3 63.4 + - - +
269A ARG* 2.7 40.3 + - - +
270A ARG* 2.8 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLN 4.6 1.8 - - - +
210A TRP* 3.8 42.2 - - + +
212A CYS* 4.4 13.2 - - + -
226A ILE* 3.8 30.9 - - + +
227A SER 4.6 0.2 - - - -
228A ALA* 4.0 23.8 - - + +
245A ILE* 4.1 7.4 - - + -
263A LEU 3.0 16.2 + - - +
264A ILE* 3.1 13.2 - - - +
266A GLU* 1.3 77.6 - - - +
268A THR* 1.3 66.0 + - - +
270A ARG* 4.5 2.9 - - + +
271A VAL* 2.9 30.1 + - - +
1000C MYR 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 2.9 21.9 + - - +
265A ARG* 3.4 11.4 - - - -
266A GLU 3.2 0.2 - - - -
267A ILE* 1.3 77.6 - - - +
269A ARG* 1.3 56.4 + - - +
271A VAL* 3.3 1.2 + - - +
272A ASN* 2.9 53.0 + - - +
479A TYR* 3.9 22.2 + - + +
1000C MYR 3.2 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 4.0 9.0 - - + -
146A ARG* 3.1 41.8 + - + +
147A GLN 3.1 25.1 + - - -
148A GLU 3.5 19.6 + - - -
149A PRO* 3.6 15.1 - - - +
150A TYR* 3.9 17.5 - - + +
265A ARG 2.9 12.6 + - - +
266A GLU* 2.7 44.0 + - - +
268A THR* 1.3 76.9 - - - +
270A ARG* 1.3 70.0 + - - +
272A ASN* 3.3 8.5 + - - +
273A LEU* 3.0 50.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PRO* 5.3 3.2 - - - +
158A TRP* 4.3 20.2 - - - +
159A ASP 5.5 0.4 - - - +
160A THR* 3.2 26.2 + - - +
209A GLN* 2.9 38.5 + - + +
210A TRP* 3.3 22.5 + - + -
212A CYS* 3.7 32.2 - - - +
266A GLU* 2.8 50.3 + - - +
267A ILE* 3.9 7.4 - - - +
269A ARG* 1.3 87.5 - - - +
271A VAL* 1.3 61.2 + - - +
273A LEU* 3.7 11.0 + - + +
274A GLU* 3.4 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A TRP* 3.7 21.8 - - + +
228A ALA* 3.9 24.7 - - + -
243A VAL* 3.6 16.2 - - + -
267A ILE* 2.9 24.6 + - + +
268A THR 3.8 0.2 - - - +
270A ARG* 1.3 74.6 - - - +
272A ASN* 1.3 65.5 + - - +
274A GLU* 3.0 14.9 + - - +
275A GLY 3.5 0.2 + - - -
276A ILE* 3.3 45.6 + - + +
1000C MYR 3.6 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 4.0 20.8 - - - +
145A VAL* 3.8 19.8 - - + +
268A THR* 2.9 36.1 + - - +
269A ARG* 3.6 4.8 - - - +
271A VAL* 1.3 76.6 - - - +
273A LEU* 1.3 53.4 + - - +
275A GLY* 2.7 26.9 + - - -
276A ILE 3.0 18.6 - - - +
277A PHE* 3.4 30.0 - - + -
479A TYR* 5.7 0.2 - - - -
1000C MYR 3.7 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A VAL* 3.6 27.1 - - + +
146A ARG 3.7 2.7 - - - +
147A GLN* 3.7 37.7 - - - +
269A ARG* 3.0 49.0 + - - +
270A ARG* 4.0 8.7 - - + +
271A VAL 3.2 0.4 - - - -
272A ASN* 1.3 75.1 - - - +
274A GLU* 1.3 64.3 + - + +
275A GLY 3.3 1.1 + - - -
----------------------------------------------------------
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