Contacts of the helix formed by residues 248 - 270 (chain A) in PDB entry 2O36
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 CYS 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A ASN* 3.4 39.3 - - + -
182A LEU* 3.7 12.1 - - - -
185A ASP* 4.6 10.9 + - - -
246A SER 3.4 1.6 + - - -
247A ARG* 1.3 75.5 - - - +
249A LYS* 1.3 65.3 + - - +
250A GLU 3.4 2.2 - - - -
251A GLU* 3.1 24.9 - - - +
252A ASN* 2.9 44.0 + - - +
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Residues in contact with LYS 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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246A SER* 3.1 24.8 + - - +
247A ARG 2.9 4.6 + - - -
248A CYS* 1.3 77.3 - - - +
250A GLU* 1.3 68.5 + - + +
251A GLU* 4.4 0.4 + - - -
253A SER* 3.0 29.6 + - - -
591A GLY* 2.8 38.3 + - - +
592A THR 4.9 3.6 - - - -
593A ASN* 4.1 19.1 - - + +
596A ALA* 4.2 9.1 - - - +
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Residues in contact with GLU 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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248A CYS 3.4 0.4 - - - -
249A LYS* 1.3 88.5 - - + +
251A GLU* 1.3 74.8 + - + +
253A SER* 3.1 17.2 + - - -
254A ALA* 3.4 12.3 + - - +
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Residues in contact with GLU 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ASN* 4.1 18.4 + - - +
248A CYS* 3.1 31.6 - - - +
249A LYS 4.4 0.2 + - - -
250A GLU* 1.3 90.9 + - + +
252A ASN* 1.3 59.4 + - - +
254A ALA* 3.3 7.6 + - - +
255A ILE* 3.1 31.7 + - + +
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Residues in contact with ASN 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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178A PHE* 3.2 40.6 + - + -
181A ASN* 3.0 29.7 + - - +
182A LEU* 3.5 14.8 - - - +
248A CYS* 2.9 27.3 + - - +
251A GLU* 1.3 72.2 - - - +
253A SER* 1.3 59.8 + - - +
254A ALA 3.2 0.2 - - - -
255A ILE* 3.6 10.2 - - - +
256A LEU* 2.9 29.3 + - - +
596A ALA* 2.9 31.4 + - + +
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Residues in contact with SER 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LYS* 3.0 23.5 + - - -
250A GLU* 3.1 9.9 + - - -
252A ASN* 1.3 77.8 - - - +
254A ALA* 1.3 64.7 + - - +
256A LEU* 3.7 8.2 - - - +
257A LYS* 3.1 22.3 + - - +
572A PRO* 5.7 3.9 - - - +
593A ASN* 3.7 22.0 - - - -
596A ALA* 4.1 5.1 - - - +
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Residues in contact with ALA 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 GLU 3.4 9.6 + - - +
251A GLU* 3.3 11.2 + - - +
252A ASN 3.2 0.4 - - - -
253A SER* 1.3 79.8 + - - +
255A ILE* 1.3 64.9 + - + +
257A LYS* 3.3 10.1 + - - +
258A GLU* 3.3 21.3 + - - +
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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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174A LEU* 3.6 39.0 - - + +
177A ASP* 4.1 11.0 - - + +
178A PHE* 4.0 23.8 - - + +
181A ASN* 3.7 15.3 - - - +
251A GLU* 3.1 12.9 + - + +
252A ASN* 3.6 28.0 - - - +
254A ALA* 1.3 76.5 - - + +
256A LEU* 1.3 60.0 + - - +
258A GLU* 3.1 8.4 + - - +
259A LEU* 2.9 35.4 + - + +
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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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178A PHE* 4.5 6.5 - - + -
252A ASN 2.9 17.5 + - - +
253A SER* 3.7 7.4 - - - +
255A ILE* 1.3 78.4 - - - +
257A LYS* 1.3 62.6 + - - +
259A LEU* 3.3 21.4 + - + +
260A VAL* 3.0 32.5 + - + +
263A ARG* 5.5 2.2 - - - +
564A LEU* 4.1 15.0 - - + -
565A HIS* 6.1 0.9 - - - +
572A PRO* 3.7 36.1 - - + -
593A ASN* 5.5 0.4 - - - +
595A PRO* 3.9 25.4 - - + +
596A ALA* 4.5 4.3 - - + +
601A LEU* 3.9 26.2 - - + -
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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 SER 3.1 14.0 + - - +
254A ALA* 3.6 11.7 - - - +
255A ILE 3.2 0.2 - - - -
256A LEU* 1.3 76.2 - - - +
258A GLU* 1.3 61.1 + - - +
260A VAL* 3.6 6.4 + - - +
261A THR* 3.0 35.1 + - - +
572A PRO* 5.7 6.4 - - + +
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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
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170A LYS* 5.1 6.4 - - - +
174A LEU* 3.1 34.3 - - + +
254A ALA 3.3 9.5 + - - +
255A ILE* 3.1 9.7 + - - +
257A LYS* 1.3 78.2 - - - +
259A LEU* 1.3 65.4 + - - +
261A THR* 3.3 5.4 + - - +
262A LEU* 2.9 45.0 + - + +
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Residues in contact with LEU 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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171A LEU* 3.7 21.4 - - + +
174A LEU* 3.6 25.8 - - + +
175A CYS* 3.9 17.5 - - - -
178A PHE* 4.6 3.8 - - + -
255A ILE* 2.9 33.7 + - + +
256A LEU* 3.6 22.9 - - + +
258A GLU* 1.3 77.2 - - - +
260A VAL* 1.3 58.5 + - + +
263A ARG* 2.9 62.0 + - - +
601A LEU 4.5 2.0 - - - +
602A ALA* 4.5 17.0 - - + -
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Residues in contact with VAL 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* 3.0 25.5 + - + +
257A LYS* 3.7 7.9 - - - +
259A LEU* 1.3 77.7 - - + +
261A THR* 1.3 65.2 + - - +
263A ARG* 3.9 5.8 - - - +
264A ALA* 3.1 24.3 + - + +
564A LEU* 3.4 51.8 - - + +
565A HIS* 5.2 5.3 - - - +
567A GLN 4.3 13.7 - - - +
568A THR* 4.6 11.7 - - - +
570A ALA 5.9 3.6 - - - +
572A PRO* 5.6 2.5 - - + -
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Residues in contact with THR 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* 3.0 23.9 + - - +
258A GLU* 3.3 5.6 + - - -
260A VAL* 1.3 81.5 - - - +
262A LEU* 1.3 62.8 + - + +
264A ALA* 3.3 7.2 + - + +
265A GLN* 3.0 30.7 + - + +
268A ARG* 5.4 0.3 + - - -
568A THR* 5.8 0.8 + - + -
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Residues in contact with LEU 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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166A ARG* 5.4 2.9 - - - +
167A ILE* 3.6 23.6 - - + +
170A LYS* 4.0 29.4 - - + +
171A LEU* 3.5 16.8 - - + -
174A LEU* 3.6 30.7 - - + -
258A GLU* 2.9 29.6 + - + +
261A THR* 1.3 78.0 - - + +
263A ARG* 1.3 60.4 + - - +
265A GLN* 3.2 17.1 + - - +
266A LYS* 2.8 31.7 + - - +
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Residues in contact with ARG 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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171A LEU* 3.9 20.0 - - + +
175A CYS* 3.6 25.9 - - - -
256A LEU* 5.5 1.8 - - - +
259A LEU* 2.9 45.0 + - - +
260A VAL* 3.9 3.5 - - - +
262A LEU* 1.3 75.8 - - - +
264A ALA* 1.3 58.2 + - - +
266A LYS* 3.8 5.6 - - - +
267A SER* 2.9 32.4 + - - -
275A HIS* 3.7 34.8 + - + -
565A HIS* 2.8 46.0 + - + -
601A LEU* 2.8 31.9 + - - +
602A ALA* 4.1 1.0 - - - +
606A ASP* 3.4 22.5 + - - +
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Residues in contact with ALA 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 VAL* 3.1 20.2 + - + +
261A THR* 3.4 8.1 - - + +
263A ARG* 1.3 77.2 - - - +
265A GLN* 1.3 61.9 + - - +
267A SER* 2.6 22.8 + - - -
268A ARG* 3.1 29.1 + - - +
273A HIS 5.5 0.2 - - - +
274A THR* 5.7 1.8 - - - +
275A HIS* 4.5 8.0 - - + +
567A GLN 5.8 3.4 - - - +
568A THR* 6.4 2.2 - - + -
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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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163A ASN* 4.8 4.2 + - - -
166A ARG* 4.1 13.8 + - - +
167A ILE* 3.5 24.3 - - + +
261A THR* 3.0 20.2 + - + +
262A LEU* 3.7 14.8 - - - +
264A ALA* 1.3 76.1 - - - +
266A LYS* 1.3 64.1 + - - +
268A ARG* 3.2 30.5 + - - +
269A LEU* 3.0 34.7 + - + +
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Residues in contact with LYS 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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151A ARG 5.0 1.0 + - - -
164A ILE* 4.1 12.1 - - + -
167A ILE* 4.0 19.2 - - + +
168A LYS* 3.2 41.6 - - + +
171A LEU* 4.1 16.8 - - + -
262A LEU 2.8 18.3 + - - +
263A ARG* 3.8 5.2 - - - +
265A GLN* 1.3 76.0 - - - +
267A SER* 1.3 63.0 + - - +
269A LEU* 3.2 8.6 + - - +
270A LEU* 3.0 48.0 + - + +
275A HIS* 5.8 6.0 - - + +
278A TYR* 3.9 19.2 + - - -
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Residues in contact with SER 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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263A ARG 2.9 15.8 + - - -
264A ALA* 2.6 21.8 + - - -
266A LYS* 1.3 77.5 - - - +
268A ARG* 1.3 60.7 + - - +
270A LEU* 3.2 10.5 + - - +
271A GLY 3.2 5.2 + - - -
272A PHE* 2.8 26.2 + - - +
274A THR* 3.4 13.5 - - - -
275A HIS* 3.3 34.4 + - - -
278A TYR* 4.1 13.5 - - - -
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Residues in contact with ARG 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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261A THR 5.4 0.4 + - - -
264A ALA* 3.1 30.7 + - - +
265A GLN* 3.5 37.9 - - - +
267A SER* 1.3 77.6 + - - +
269A LEU* 1.3 63.0 + - + +
270A LEU 3.0 1.8 - - - -
271A GLY* 2.8 20.4 + - - -
272A PHE 3.2 17.4 + - - +
273A HIS* 4.5 12.9 + - + +
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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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156A LEU* 3.4 21.1 - - - +
160A THR* 3.5 28.7 - - + +
163A ASN* 3.9 23.3 - - + +
164A ILE* 3.9 19.3 - - + -
167A ILE* 3.8 25.6 - - + -
265A GLN* 3.0 30.3 + - + +
266A LYS* 3.6 6.1 - - - +
268A ARG* 1.3 76.8 - - + +
270A LEU* 1.3 59.1 + - - +
271A GLY 3.2 1.0 + - - -
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Residues in contact with LEU 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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150A ARG 3.9 9.8 - - - +
151A ARG* 3.7 17.5 - - - +
152A ASN 4.2 1.1 - - - -
153A GLY* 3.7 20.2 - - - +
155A HIS* 5.6 4.0 + - - -
156A LEU* 4.2 7.8 - - + +
164A ILE* 3.5 26.9 - - + -
266A LYS* 3.0 53.1 + - + +
267A SER* 3.5 6.7 - - - +
268A ARG 3.0 1.2 - - - -
269A LEU* 1.3 75.8 - - - +
271A GLY* 1.3 57.3 + - - +
272A PHE* 3.5 15.9 - - - -
278A TYR* 3.6 30.5 - - + -
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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
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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