Contacts of the helix formed by residues 261 - 274 (chain B) in PDB entry 1I09
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 SER 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A ASP* 5.6 2.9 - - - -
217A ILE 4.3 10.1 - - - -
218A CYS 3.7 23.6 - - - -
219A SER* 4.6 2.7 - - - -
259B GLY 3.2 0.4 - - - -
260B ASP* 1.3 78.5 - - - +
262B GLY* 1.3 64.4 + - - +
263B VAL* 3.3 9.8 + - - +
264B ASP* 3.1 30.0 + - - -
265B GLN* 3.1 28.1 + - - +
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Residues in contact with GLY 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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216A TYR* 3.9 19.2 + - - +
218A CYS 4.7 1.4 + - - -
223A ARG* 6.4 0.2 - - - -
223B ARG* 5.5 2.9 - - - -
228B ILE* 3.8 22.9 - - - -
261B SER* 1.3 73.9 - - - +
263B VAL* 1.3 52.5 + - - +
265B GLN* 3.4 11.1 + - - +
266B LEU* 2.7 40.4 + - - +
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Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 3.3 36.1 - - + -
203A SER* 5.3 7.6 - - - +
216A TYR* 3.2 27.1 + - + +
217A ILE* 3.8 25.1 - - + +
261B SER* 3.1 7.6 - - - +
262B GLY* 1.3 74.2 - - - +
264B ASP* 1.3 64.5 + - - +
266B LEU* 2.9 8.7 + - - +
267B VAL* 2.7 28.5 + - + +
293B PHE* 4.0 14.8 - - + -
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Residues in contact with ASP 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 3.5 19.3 + - - +
67A PHE* 4.5 7.6 - - - -
183A LYS* 5.4 5.9 + - - -
258B PRO 4.1 2.9 - - - +
259B GLY* 3.6 17.9 - - - -
260B ASP* 3.8 8.0 + - - +
261B SER* 3.1 25.7 + - - +
263B VAL* 1.3 76.9 - - - +
265B GLN* 1.3 64.5 + - - +
267B VAL* 2.9 14.5 - - + +
268B GLU* 2.8 25.7 + - - +
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Residues in contact with GLN 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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220B ARG* 2.6 46.0 + - - +
221B TYR* 3.7 5.5 - - - +
223B ARG* 4.1 12.3 + - - -
228B ILE* 4.0 19.7 - - + +
257B PHE* 4.0 11.8 + - + +
258B PRO 3.7 8.3 + - - -
259B GLY* 3.4 26.0 + - - +
261B SER 3.1 16.9 + - - +
262B GLY* 3.6 13.2 - - - +
264B ASP* 1.3 77.6 - - - +
266B LEU* 1.3 58.2 + - - +
268B GLU* 3.3 3.3 + - - +
269B ILE* 2.9 35.1 + - + +
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TYR* 3.9 11.2 - - + -
225B PRO* 5.1 3.4 - - + +
228B ILE* 3.5 39.5 - - + -
229B PHE* 3.8 33.7 - - + -
262B GLY 2.7 19.7 + - - +
263B VAL 3.2 5.6 - - - +
265B GLN* 1.3 71.5 - - - +
267B VAL* 1.3 59.0 + - - +
269B ILE* 3.1 11.2 + - + +
270B ILE* 2.8 41.3 + - + +
284B MET* 5.2 0.9 - - + -
293B PHE* 3.3 34.8 - - + -
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Residues in contact with VAL 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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66A SER* 3.7 29.2 - - - -
67A PHE* 4.0 31.6 - - + +
263B VAL 2.7 19.0 + - - +
264B ASP* 2.9 25.8 - - - +
266B LEU* 1.3 72.4 - - - +
268B GLU* 1.3 63.9 + - - +
270B ILE* 3.8 8.5 - - + +
271B LYS* 2.9 40.0 + - - +
293B PHE* 4.2 15.3 - - + -
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Residues in contact with GLU 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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66A SER* 5.0 3.5 - - - -
256B ILE 4.0 7.2 - - - +
257B PHE* 3.7 9.8 - - - -
258B PRO* 3.7 41.6 - - + +
264B ASP* 2.8 16.4 + - - +
265B GLN 3.3 9.9 - - - +
267B VAL* 1.3 87.4 - - - +
269B ILE* 1.3 59.8 + - - +
271B LYS* 3.4 34.9 + - - +
272B VAL* 3.3 21.3 - - - +
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Residues in contact with ILE 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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223B ARG 4.9 2.5 - - - +
225B PRO* 4.4 11.4 - - + -
228B ILE* 4.1 24.5 - - + -
241B TRP* 3.9 22.0 - - + -
257B PHE* 3.4 32.1 - - + -
265B GLN* 2.9 20.1 + - + +
266B LEU* 3.6 10.8 - - + +
268B GLU* 1.3 75.0 - - - +
270B ILE* 1.3 61.3 + - + +
272B VAL* 3.3 3.1 + - - +
273B LEU* 2.8 46.4 + - + +
323B TYR* 3.8 22.0 - - + +
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Residues in contact with ILE 270 (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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266B LEU* 2.8 29.7 + - + +
267B VAL* 3.9 6.5 - - + +
269B ILE* 1.3 74.3 - - + +
271B LYS* 1.3 62.9 + - - +
274B GLY* 2.6 32.4 + - - -
275B THR* 3.6 31.0 - - + +
276B PRO* 4.4 14.8 - - + -
291B PHE* 4.6 6.3 - - + -
293B PHE* 3.9 34.8 - - + -
294B PRO* 5.0 2.5 - - + +
296B ILE 4.4 3.1 - - - +
297B LYS* 3.6 11.7 - - + +
323B TYR* 3.5 18.2 - - + +
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Residues in contact with LYS 271 (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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64A ASN* 5.9 0.6 + - - -
65A GLY 5.3 1.0 + - - -
66A SER* 4.1 28.8 + - - +
267B VAL* 2.9 26.1 + - + +
268B GLU* 3.4 37.4 + - - +
269B ILE 3.2 0.2 - - - -
270B ILE* 1.3 76.0 - - - +
272B VAL* 1.3 60.3 + - + +
297B LYS* 4.8 9.4 - - + -
298B ALA 3.0 25.8 - - - +
299B HIS* 3.0 4.5 - - - -
300B PRO* 3.8 4.0 - - - +
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Residues in contact with VAL 272 (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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256B ILE* 4.6 10.1 - - + +
257B PHE* 3.6 20.0 - - + -
268B GLU 3.3 17.7 - - - +
269B ILE 3.3 0.4 + - - +
271B LYS* 1.3 78.1 - - + +
273B LEU* 1.3 80.5 + - + +
274B GLY 3.3 0.4 - - - -
299B HIS* 3.0 22.3 - - - +
300B PRO* 3.8 12.3 - - + +
301B TRP* 3.6 34.4 + - + -
304B VAL* 4.4 10.5 - - + -
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Residues in contact with LEU 273 (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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241B TRP* 4.0 23.8 - - + -
257B PHE* 4.8 3.1 - - + -
269B ILE* 2.8 26.3 + - + +
272B VAL* 1.3 90.6 - - + +
274B GLY* 1.3 63.7 + - - +
275B THR 4.3 1.6 - - - +
299B HIS* 4.3 2.0 - - - -
301B TRP* 3.8 16.6 - - + +
321B LEU* 3.5 32.1 - - + +
322B GLU* 4.6 0.2 - - - -
323B TYR* 3.6 43.6 - - + +
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Residues in contact with GLY 274 (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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270B ILE* 2.6 23.6 + - - +
272B VAL 3.3 2.8 - - - -
273B LEU* 1.3 79.4 - - - +
275B THR* 1.3 67.9 + - - -
297B LYS 3.3 13.5 - - - -
298B ALA* 3.8 3.6 - - - -
299B HIS 3.6 12.7 - - - +
323B TYR* 2.9 15.2 + - - -
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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