Contacts of the helix formed by residues 256 - 269 (chain B) in PDB entry 2I65
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 ASP 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B LYS 5.3 1.2 + - - -
215B ILE* 3.7 25.5 + - + +
251B ARG* 5.9 1.0 + - - -
252B ASP 4.3 0.4 + - - -
253B LEU* 3.2 27.0 + - + +
254B CYS 3.5 0.2 - - - -
255B GLN* 1.3 77.6 - - - +
257B PRO* 1.4 69.9 - - - +
258B THR* 2.8 35.5 + - - +
259B ILE* 2.8 27.3 + - + +
260B LYS* 3.1 9.2 + - - +
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Residues in contact with PRO 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B GLN 3.5 6.2 - - - +
256B ASP* 1.4 93.2 - - - +
258B THR* 1.3 58.7 + - + +
260B LYS* 3.3 10.3 + - + +
261B GLU* 3.0 26.5 + - - +
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Residues in contact with THR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B LYS* 4.0 24.7 - - + -
215B ILE* 3.4 4.3 + - - +
216B PHE* 3.0 51.4 + - - +
256B ASP* 2.8 21.1 + - - +
257B PRO* 1.3 79.2 - - + +
259B ILE* 1.3 59.2 + - - +
261B GLU* 3.3 18.0 - - - +
262B LEU 3.0 20.1 + - - -
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Residues in contact with ILE 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B LEU* 3.7 30.1 - - + -
215B ILE* 3.7 19.7 - - + -
216B PHE* 4.3 8.3 - - + -
240B ALA* 5.2 0.4 - - + -
242B VAL* 4.0 7.9 - - + -
253B LEU 3.4 19.5 - - - +
254B CYS 3.4 21.8 - - - +
256B ASP* 2.8 19.8 + - + +
258B THR* 1.3 70.2 + - - +
260B LYS* 1.3 54.0 + - - +
261B GLU 3.1 1.6 - - - -
262B LEU* 3.1 8.3 + - + +
263B GLU* 2.7 33.8 + - + +
273B PHE* 3.7 24.0 - - + -
275B CYS* 4.0 10.8 - - - -
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Residues in contact with LYS 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B CYS 3.1 25.1 + - - -
255B GLN* 3.5 28.3 + - - +
256B ASP 3.1 11.3 + - - +
257B PRO* 3.7 10.3 - - + +
259B ILE* 1.3 75.6 - - - +
261B GLU* 1.3 56.9 + - - +
263B GLU* 3.4 33.4 + - - +
264B SER* 2.9 32.1 + - - -
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Residues in contact with GLU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B PHE* 4.2 12.3 - - + +
218B LYS* 3.4 39.2 - - - +
257B PRO 3.0 12.9 + - - +
258B THR* 3.3 22.8 - - - +
259B ILE 3.1 0.2 - - - -
260B LYS* 1.3 75.1 - - - +
262B LEU* 1.3 59.9 + - - +
264B SER* 3.2 6.8 + - - -
265B ILE* 2.9 39.8 + - + +
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Residues in contact with LEU 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B LEU* 4.0 26.7 - - + -
216B PHE* 3.8 28.4 - - + -
222B PHE* 4.2 6.5 - - + -
227B VAL* 3.7 30.3 - - + -
238B LEU* 3.9 6.7 - - + -
240B ALA* 4.4 2.0 - - + -
258B THR 3.0 14.2 + - - +
259B ILE* 3.4 10.1 - - + +
261B GLU* 1.3 74.8 - - - +
263B GLU* 1.3 56.6 + - - +
265B ILE* 3.2 4.1 + - + +
266B ILE* 2.9 46.9 + - + +
273B PHE* 3.5 29.6 - - + -
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Residues in contact with GLU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B CYS 5.0 1.2 - - - +
259B ILE 2.7 19.7 + - - +
260B LYS* 3.4 42.3 + - - +
262B LEU* 1.3 73.6 - - - +
264B SER* 1.3 51.4 + - - +
266B ILE* 4.0 1.6 - - - +
267B SER* 2.8 50.0 + - - +
273B PHE* 3.6 35.6 - - + -
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Residues in contact with SER 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B LYS 2.9 17.7 + - - -
261B GLU* 3.6 8.0 - - - -
263B GLU* 1.3 75.7 + - - +
265B ILE* 1.3 66.4 + - - +
267B SER* 3.8 6.0 - - - -
268B LYS* 2.9 43.4 + - - +
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Residues in contact with ILE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B PHE* 3.6 36.6 - - + -
218B LYS* 5.0 7.0 - - + -
223B GLY 5.0 0.2 - - - +
227B VAL* 4.3 13.7 - - + -
228B HIS* 3.9 36.3 - - + +
261B GLU* 2.9 27.4 + - + +
262B LEU* 3.2 8.0 + - + +
264B SER* 1.3 79.8 - - - +
266B ILE* 1.3 63.1 + - + +
268B LYS* 3.2 12.8 + - - +
269B ARG* 3.2 28.4 + - - +
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Residues in contact with ILE 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B VAL* 4.8 9.2 - - + +
230B LEU* 5.2 4.7 - - + -
238B LEU* 3.4 42.2 - - + -
262B LEU* 2.9 24.8 + - + +
263B GLU 4.0 2.2 - - - +
265B ILE* 1.3 76.8 - - + +
267B SER* 1.3 65.4 + - - +
269B ARG* 3.2 11.8 + - - -
271B ILE* 2.9 44.6 + - + +
272B GLN 3.1 35.9 - - - +
273B PHE* 3.5 22.7 - - + -
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Residues in contact with SER 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B GLU* 2.8 39.0 + - - +
264B SER* 3.8 6.3 - - - -
266B ILE* 1.3 73.1 - - - +
268B LYS* 1.3 58.1 + - - +
270B ASN* 3.0 21.7 + - - -
271B ILE 3.6 10.0 + - - +
273B PHE* 4.8 5.0 + - - +
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Residues in contact with LYS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B SER* 2.9 33.7 + - - +
265B ILE* 3.2 8.9 + - - +
267B SER* 1.3 72.9 - - - +
269B ARG* 1.3 58.2 + - + +
270B ASN* 3.0 9.7 + - - +
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Residues in contact with ARG 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B VAL 3.4 18.2 + - - -
228B HIS* 3.2 35.5 + - - +
230B LEU 2.4 31.5 + - - -
231B GLN* 4.3 9.3 - - - +
232B PRO* 3.1 38.7 - - - +
265B ILE* 3.2 27.1 - - + +
266B ILE* 3.2 11.2 + - - +
268B LYS* 1.3 76.9 - - + +
270B ASN* 1.3 66.4 + - - +
271B ILE* 3.2 17.1 + - + +
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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