Contacts of the helix formed by residues 244 - 264 (chain A) in PDB entry 1O69
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 VAL 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLY* 5.5 11.0 - - - -
14A GLU* 5.3 1.1 - - - +
186A ILE* 3.9 11.7 - - + -
240A ALA 4.1 9.4 - - - +
241A GLN* 3.0 20.9 + - - +
243A GLU* 1.3 86.7 - - + +
245A LEU* 1.3 62.8 + - - +
246A GLU 3.3 2.5 - - - -
247A GLN* 3.3 29.3 + - - +
248A ARG* 2.9 45.0 + - + +
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Residues in contact with LEU 245 (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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44A TYR* 3.6 35.7 - - + +
160A LEU* 3.6 47.3 - - + +
161A GLY 4.5 0.4 - - - +
185A ILE* 4.0 18.4 - - + -
186A ILE* 3.7 14.6 - - + -
241A GLN 3.3 7.5 + - - +
242A MET* 3.4 36.1 + - + +
243A GLU 3.6 0.2 - - - -
244A VAL* 1.3 75.8 - - - +
246A GLU* 1.3 64.8 + - - +
248A ARG* 3.1 2.8 + - - +
249A VAL* 2.9 29.1 + - + +
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Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TYR* 2.7 40.3 + - + -
163A PHE* 5.0 0.3 - - - -
242A MET 4.9 0.8 + - - -
243A GLU 5.4 0.4 + - - -
244A VAL 3.3 0.6 - - - -
245A LEU* 1.3 81.0 - - - +
247A GLN* 1.3 63.4 + - + +
249A VAL* 3.2 5.2 + - - +
250A LEU* 3.1 39.2 + - + +
277A ARG* 2.9 33.4 + - - -
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Residues in contact with GLN 247 (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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243A GLU 3.4 23.4 + - - -
244A VAL* 3.3 26.1 + - + +
246A GLU* 1.3 78.2 - - + +
248A ARG* 1.3 64.3 + - + +
250A LEU* 3.4 11.5 + - + +
251A LYS* 3.0 23.6 + - - +
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Residues in contact with ARG 248 (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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185A ILE* 3.2 37.5 + - + -
186A ILE* 3.4 10.2 - - + +
187A THR* 5.4 2.6 - - - +
241A GLN* 2.9 36.1 + - - +
244A VAL* 2.9 31.7 + - + +
245A LEU 3.5 7.2 - - - +
247A GLN* 1.3 77.1 - - + +
249A VAL* 1.3 60.2 + - - +
251A LYS* 3.2 3.8 + - - +
252A LYS* 2.8 35.1 + - - +
366A THR* 3.8 31.1 + - + +
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Residues in contact with VAL 249 (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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44A TYR* 4.5 0.9 - - - +
161A GLY* 3.8 28.5 - - - +
185A ILE* 3.6 22.9 - - + +
245A LEU* 2.9 23.1 + - + +
246A GLU* 3.2 7.6 + - - +
248A ARG* 1.3 75.8 - - - +
250A LEU* 1.3 64.0 + - - +
252A LYS* 3.3 3.6 + - - +
253A ARG* 3.1 33.0 + - - +
277A ARG* 3.5 39.3 - - - +
279A ASN* 4.0 10.8 - - + -
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Residues in contact with LEU 250 (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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246A GLU* 3.1 40.1 + - + +
247A GLN* 3.8 10.5 - - - +
248A ARG 3.3 0.2 - - - -
249A VAL* 1.3 76.3 - - + +
251A LYS* 1.3 57.5 + - - +
253A ARG* 3.3 14.0 + - + +
254A GLU* 3.0 31.5 + - + +
277A ARG* 4.1 11.9 - - - +
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Residues in contact with LYS 251 (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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247A GLN 3.0 17.4 + - - +
248A ARG* 3.7 4.7 - - - +
250A LEU* 1.3 75.4 - - - +
252A LYS* 1.3 65.8 + - - +
254A GLU* 3.1 22.5 + - + +
255A ILE* 2.9 28.9 + - + +
258A TRP* 3.9 23.8 - - - -
366A THR* 2.7 49.3 + - + +
367A ALA 4.4 1.6 + - - -
368A MET 2.7 25.4 + - - -
369A SER* 4.9 1.0 - - - +
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Residues in contact with LYS 252 (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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183A ASN 5.6 0.6 + - - -
185A ILE* 3.9 28.8 - - + +
248A ARG 2.8 24.4 + - - +
249A VAL 3.3 1.8 + - - +
251A LYS* 1.3 72.3 - - - +
253A ARG* 1.3 58.2 - - - +
255A ILE* 3.3 8.3 + - - +
256A TYR* 2.9 27.0 + - - +
279A ASN 3.2 24.7 - - - +
280A ARG* 3.5 9.8 - - - +
281A TRP* 2.9 39.2 + - - +
282A LEU* 4.9 2.2 - - - +
283A SER* 4.5 1.0 + - - -
364A SER* 2.7 35.1 + - - +
365A GLY* 4.5 3.8 - - - -
366A THR* 3.9 15.4 - - + +
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Residues in contact with ARG 253 (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 VAL* 3.1 22.7 + - + +
250A LEU* 3.6 12.0 - - - +
251A LYS 3.2 0.2 - - - -
252A LYS* 1.3 73.6 - - - +
254A GLU* 1.3 66.2 + - - +
256A TYR* 3.3 8.0 + - - +
257A GLU* 3.0 29.8 + - + +
272A GLU* 2.8 38.6 + - - -
277A ARG* 3.6 29.8 - - - +
278A SER* 2.8 42.3 + - - +
279A ASN 4.5 0.4 - - - +
280A ARG* 4.2 14.0 - - + +
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Residues in contact with GLU 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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250A LEU* 3.0 16.1 + - + +
251A LYS* 3.1 29.6 + - - +
253A ARG* 1.3 75.7 - - - +
255A ILE* 1.3 59.1 + - - +
257A GLU* 3.3 8.2 + - - +
258A TRP* 2.9 63.1 + - + +
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Residues in contact with ILE 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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251A LYS* 2.9 28.1 + - + +
252A LYS* 3.5 9.6 - - - +
254A GLU* 1.3 77.6 - - - +
256A TYR* 1.3 62.6 + - - +
258A TRP* 3.2 28.8 + - + +
259A TYR* 3.0 46.6 + - + -
283A SER* 4.0 6.3 - - - +
363A PRO 4.3 7.2 - - - +
364A SER* 3.9 17.0 - - - +
365A GLY 3.3 27.4 - - - +
366A THR* 4.0 9.2 - - - -
368A MET* 4.5 5.2 - - + +
373A VAL* 4.1 11.2 - - + +
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Residues in contact with TYR 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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252A LYS 2.9 12.8 + - - +
253A ARG* 3.5 8.5 - - - +
255A ILE* 1.3 76.8 - - - +
257A GLU* 1.3 75.5 + - - +
259A TYR* 3.2 4.7 + - - +
260A LYS* 2.8 43.5 + - + +
269A PHE* 3.4 38.4 + + + +
270A LEU 3.2 23.9 + - - -
271A ASP* 6.3 0.2 - - - -
280A ARG* 3.3 54.7 + - + -
283A SER* 3.3 29.2 - - - +
284A THR 3.7 15.1 + - - -
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Residues in contact with GLU 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 ARG* 3.0 21.5 + - + +
254A GLU* 3.6 7.0 - - - +
256A TYR* 1.3 87.3 - - + +
258A TRP* 1.3 61.0 + - + +
260A LYS* 3.3 38.5 + - - +
261A GLU* 2.9 26.7 + - - +
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Residues in contact with TRP 258 (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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251A LYS* 3.9 31.2 - - - -
254A GLU* 2.9 40.6 + - - +
255A ILE* 3.2 26.2 + - + +
257A GLU* 1.3 76.8 - - + +
259A TYR* 1.3 66.9 + - - +
261A GLU* 3.0 14.1 + - - +
262A PHE* 2.9 34.8 + + + -
368A MET 4.3 0.2 - - - -
369A SER* 3.9 3.8 - - - -
370A LYS* 3.4 70.8 - - + +
373A VAL* 3.8 18.8 - - + -
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Residues in contact with TYR 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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255A ILE* 3.0 34.0 + - + -
256A TYR* 3.5 6.5 - - - +
258A TRP* 1.3 75.0 - - - +
260A LYS* 1.3 58.6 + - - +
262A PHE 3.2 0.4 + - - +
263A LEU* 2.8 48.4 + - + +
269A PHE* 3.8 17.3 - - + -
283A SER* 3.7 19.5 - - - -
362A LEU* 3.8 21.3 - - + -
363A PRO* 2.7 43.8 + - - +
368A MET* 4.3 1.4 - - - +
373A VAL* 3.7 18.5 - - + +
376A ILE* 3.7 28.0 - - + +
377A SER* 3.5 20.0 - - - -
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Residues in contact with LYS 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 TYR* 2.8 26.6 + - + +
257A GLU* 3.3 38.2 + - - +
259A TYR* 1.3 77.0 - - - +
261A GLU* 1.3 63.3 + - - +
264A GLY* 3.0 25.5 + - - -
269A PHE* 3.8 42.2 + - + -
271A ASP* 4.1 18.7 + - - -
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Residues in contact with GLU 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 GLU 2.9 13.5 + - - +
258A TRP* 3.0 20.3 + - - +
260A LYS* 1.3 80.2 - - - +
262A PHE* 1.3 84.3 + - + +
264A GLY* 4.3 2.3 + - - -
370A LYS* 4.8 11.7 + - - -
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Residues in contact with PHE 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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258A TRP* 2.9 34.3 + - + +
259A TYR 4.2 0.2 - - - +
261A GLU* 1.3 105.3 - - + +
263A LEU* 1.3 59.8 + - - +
264A GLY 3.6 0.2 - - - -
265A GLU* 5.2 2.6 + - - +
266A TYR* 5.9 0.2 - - - -
370A LYS* 3.9 32.1 - - + -
373A VAL* 4.0 1.6 - - + -
374A TYR* 3.7 61.5 - + + -
377A SER* 3.6 25.8 - - - +
381A LEU* 3.7 21.2 - - + +
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Residues in contact with LEU 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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259A TYR* 2.8 42.8 + - + +
262A PHE* 1.3 72.6 - - - +
264A GLY* 1.3 56.8 + - - +
265A GLU* 3.0 5.6 - - - -
266A TYR* 2.8 23.4 + - - +
267A PHE* 2.9 30.3 + - + -
269A PHE* 3.9 13.2 - - + -
362A LEU* 4.2 12.3 - - + -
377A SER* 3.6 38.8 - - - +
380A ILE* 3.9 29.8 - - + -
381A LEU* 4.0 17.3 - - + -
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Residues in contact with GLY 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 LYS* 3.0 22.2 + - - -
261A GLU 4.3 1.9 + - - -
262A PHE 3.6 1.4 - - - -
263A LEU* 1.3 76.7 - - - +
265A GLU* 1.3 60.6 + - - +
266A TYR 3.3 0.4 - - - -
267A PHE 3.5 17.3 - - - +
269A PHE* 4.2 6.3 - - - -
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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
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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