Contacts of the helix formed by residues 253 - 272 (chain A) in PDB entry 3R9X
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 GLY 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A ILE* 3.3 23.8 - - - -
250A GLY 3.0 7.5 + - - -
252A LYS* 1.3 75.8 - - - +
254A GLN* 1.3 58.7 + - - +
255A ARG 3.1 3.5 + - - -
256A LEU* 3.5 5.8 + - - +
257A LYS* 3.0 29.1 + - - +
1534C A 3.8 10.3 - - - -
1535C C 3.5 13.9 - - - +
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Residues in contact with GLN 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ILE 3.7 1.0 + - - -
250A GLY 4.4 0.2 - - - -
251A LYS 3.4 18.3 + - - +
252A LYS* 2.8 29.4 + - + +
253A GLY* 1.3 78.0 - - - +
255A ARG* 1.3 56.5 + - - +
257A LYS* 2.8 36.3 + - - +
258A GLU* 3.3 23.0 + - - +
1535C C 3.8 3.4 - - - -
1536C C 3.1 20.3 + - - -
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Residues in contact with ARG 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 3.4 33.4 - - + +
206A THR* 4.8 3.4 - - - -
247A ILE 2.7 22.6 + - - -
248A ILE 3.5 8.7 - - - +
249A ILE 3.0 10.7 + - - +
250A GLY* 4.0 4.3 - - - -
254A GLN* 1.3 76.4 - - - +
256A LEU* 1.3 59.4 + - - +
257A LYS 2.9 9.2 + - - -
258A GLU* 3.0 5.6 + - + +
259A ILE* 3.0 36.2 + - + +
1531C A 2.9 60.3 + - - -
1532C U 3.2 13.8 + - - -
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ILE* 4.4 12.8 - - + -
248A ILE* 3.0 12.6 + - + +
249A ILE* 3.0 22.1 + - + +
253A GLY* 3.8 5.4 - - - +
255A ARG* 1.3 73.5 - - - +
257A LYS* 1.3 56.0 + - - +
259A ILE* 4.1 7.2 - - + -
260A GLY* 3.2 17.5 + - - +
279A LEU* 3.9 34.0 - - + +
281A VAL* 4.2 14.1 - - + -
1534C A 3.5 37.2 - - + +
1535C C 3.6 31.1 - - + +
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Residues in contact with LYS 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A GLY 3.0 15.5 + - - +
254A GLN* 2.8 35.5 + - - +
255A ARG 2.9 0.4 - - - -
256A LEU* 1.3 78.3 - - - +
258A GLU* 1.3 60.5 + - - +
259A ILE 3.3 0.4 - - - -
260A GLY 3.9 0.2 - - - -
261A LYS* 2.9 34.2 + - + +
1535C C 3.7 19.1 - - - +
1536C C 2.8 64.9 + - + +
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Residues in contact with GLU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 3.6 15.9 - - + -
254A GLN 3.3 10.8 + - - +
255A ARG* 3.0 8.6 + - + +
257A LYS* 1.3 77.1 - - - +
259A ILE* 1.3 60.5 + - - +
261A LYS* 3.2 28.5 + - - +
262A ARG* 2.7 70.6 + - - +
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Residues in contact with ILE 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A VAL* 4.2 13.0 - - + +
201A LYS* 3.9 8.1 - - + +
202A ALA* 3.9 40.8 - - + +
205A LEU* 3.4 26.0 - - + -
206A THR* 5.4 2.0 - - + -
237A ILE* 4.8 5.6 - - + -
248A ILE* 4.1 29.4 - - + +
255A ARG* 3.0 25.6 + - + +
256A LEU* 4.0 5.6 - - - +
258A GLU* 1.3 78.1 - - - +
260A GLY* 1.3 65.4 + - - +
262A ARG* 3.3 2.3 + - - +
263A ALA* 3.0 22.4 + - + +
279A LEU* 4.7 11.2 - - + -
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Residues in contact with GLY 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LEU 3.2 14.7 + - - -
259A ILE* 1.3 80.1 - - - +
261A LYS* 1.3 57.2 + - - +
263A ALA* 4.5 0.4 - - - -
264A ARG* 2.8 33.8 + - - +
277A LEU* 3.7 5.1 - - - +
279A LEU* 3.9 18.8 - - - +
1536C C 3.3 19.6 + - - -
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Residues in contact with LYS 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A LYS* 2.9 25.0 + - + +
258A GLU* 3.5 34.2 + - - +
259A ILE 3.2 0.2 - - - -
260A GLY* 1.3 75.4 - - - +
262A ARG* 1.3 73.0 + - - +
264A ARG* 3.7 1.1 - - - +
265A GLN* 3.0 62.8 + - - +
1536C C 3.5 36.4 - - + +
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Residues in contact with ARG 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LYS* 3.7 26.6 + - + +
204A MET* 3.3 28.8 - - - +
205A LEU* 4.1 29.4 - - - +
258A GLU* 2.7 50.8 + - - +
259A ILE 3.8 1.8 - - - +
261A LYS* 1.3 84.8 - - - +
263A ALA* 1.3 65.3 + - - +
265A GLN* 3.7 7.0 + - - +
266A GLU* 3.3 19.2 + - - +
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ILE* 4.0 13.9 - - + -
198A VAL* 3.9 19.3 - - + -
201A LYS* 3.9 11.6 - - + +
259A ILE 3.0 17.2 + - - +
260A GLY* 4.5 0.4 - - - -
262A ARG* 1.3 73.4 - - - +
264A ARG* 1.3 67.9 + - - +
266A GLU* 2.8 14.7 + - - +
267A LEU* 2.9 21.4 + - + +
277A LEU* 3.7 18.2 - - + -
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Residues in contact with ARG 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A GLY 2.8 21.2 + - - +
261A LYS* 3.7 2.5 + - - +
263A ALA* 1.3 73.7 - - - +
265A GLN* 1.3 95.6 + - - +
267A LEU* 3.2 10.9 + - - +
268A GLU* 2.9 57.0 + - - +
275A VAL* 3.5 20.0 - - + +
277A LEU* 3.7 15.1 - - + +
1536C C 3.0 32.7 + - - +
1537C U 3.3 37.3 + - - +
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Residues in contact with GLN 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LYS* 3.0 48.1 + - - +
262A ARG* 4.0 5.5 - - - +
264A ARG* 1.3 103.4 - - - +
266A GLU* 1.3 61.9 + - - +
268A GLU* 3.5 12.6 + - - +
269A LEU* 3.3 30.5 + - + +
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Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS* 3.0 33.0 + - - +
197A ILE* 4.2 17.9 - - + +
200A GLU* 3.9 1.9 - - - +
201A LYS* 3.1 26.6 + - - -
262A ARG 3.3 8.9 + - - +
263A ALA 2.8 14.7 + - - +
265A GLN* 1.3 72.4 - - - +
267A LEU* 1.3 63.0 + - - +
269A LEU* 3.5 15.3 + - + +
270A ILE* 3.2 40.3 + - + +
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU* 5.0 11.0 - - + -
193A LEU* 5.2 2.9 - - + -
194A ALA* 3.8 28.0 - - + +
197A ILE* 3.8 27.4 - - + -
198A VAL* 5.5 2.5 - - + -
233A ILE* 4.2 16.8 - - + -
263A ALA* 2.9 46.8 + - + +
264A ARG* 3.6 9.2 - - - +
266A GLU* 1.3 73.8 - - - +
268A GLU* 1.3 56.9 + - - +
270A ILE* 2.9 5.0 + - + -
271A LEU* 2.7 43.1 + - + +
275A VAL* 4.1 14.1 - - + -
277A LEU* 4.4 9.2 - - + -
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Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A MET* 5.2 0.2 - - - +
264A ARG* 2.9 47.4 + - - +
265A GLN* 3.7 12.4 - - - +
266A GLU 3.4 0.2 - - - -
267A LEU* 1.3 75.2 - - - +
269A LEU* 1.3 58.4 + - + +
272A GLY* 2.7 35.4 + - - +
273A ARG 4.0 11.0 - - - +
274A PRO* 3.7 13.3 - - + +
275A VAL* 3.2 38.7 + - + +
1537C U 4.6 1.9 + - - -
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLN* 3.3 17.4 + - + +
266A GLU* 3.5 17.9 - - + +
267A LEU 3.2 0.4 - - - -
268A GLU* 1.3 83.0 - - + +
270A ILE* 1.3 64.8 + - + +
272A GLY* 3.9 5.2 + - - -
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Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LYS 6.1 0.7 - - - +
193A LEU* 3.8 26.2 - - + -
197A ILE* 3.6 28.9 - - + -
266A GLU* 3.2 24.7 + - + +
267A LEU* 2.9 9.2 + - + +
269A LEU* 1.3 79.6 - - + +
271A LEU* 1.3 72.9 + - + +
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU* 3.6 34.5 - - + -
231A LEU* 3.3 33.4 - - + -
233A ILE* 4.5 12.1 - - + -
267A LEU* 2.7 26.2 + - + +
270A ILE* 1.3 85.6 - - + +
272A GLY* 1.3 57.2 + - - +
273A ARG* 3.2 24.5 + - + +
275A VAL* 4.6 8.7 - - + -
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Residues in contact with GLY 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A GLU 2.7 22.0 + - - -
269A LEU 3.9 4.4 + - - -
270A ILE 3.5 2.0 - - - -
271A LEU* 1.3 71.7 - - - +
273A ARG* 1.3 56.8 + - - +
274A PRO* 4.2 3.5 - - - +
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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
------------------------------------------------------------
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