Contacts of the helix formed by residues 260 - 274 (chain B) in PDB entry 1IC8
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 THR 260 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233B VAL* 3.6 9.0 - - - -
258B LEU* 3.1 24.2 - - + +
259B VAL* 1.3 75.9 - - - +
261B GLU* 1.3 67.5 + - - +
262B VAL* 3.8 9.1 + - - +
263B ARG* 2.9 56.6 + - - +
264B VAL* 3.3 7.8 + - - +
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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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226B LYS* 3.7 21.7 + - - +
229B ARG* 3.1 25.0 + - + +
230B GLU* 2.7 46.1 - - + +
233B VAL* 4.1 7.8 - - - +
260B THR* 1.3 72.1 - - - +
262B VAL* 1.3 85.8 + - + +
264B VAL* 2.8 30.1 - - - +
265B TYR 3.2 0.2 + - - -
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Residues in contact with VAL 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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229B ARG* 4.2 2.2 - - - +
260B THR* 3.2 9.3 - - - +
261B GLU* 1.3 90.5 - - + +
263B ARG* 1.3 74.8 + - + +
265B TYR* 3.0 21.0 - - + +
266B ASN* 3.0 23.7 + - - +
316E A 5.9 1.3 - - - +
317E C 5.2 9.0 - - - +
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Residues in contact with ARG 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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204B PHE* 3.7 29.6 - - + +
206B TRP* 3.6 22.2 + - + -
255B GLY 5.3 1.4 + - - -
256B SER* 3.8 20.6 + - - +
258B LEU 3.8 13.9 + - - -
259B VAL 4.2 0.9 - - - -
260B THR* 2.9 48.7 + - - +
262B VAL* 1.3 77.2 - - - +
264B VAL* 1.3 57.4 + - - +
265B TYR 2.6 12.5 + - - -
266B ASN* 2.7 16.2 + - - +
267B TRP* 2.8 10.2 + - - +
316E A 2.8 44.0 + - - +
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Residues in contact with VAL 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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206B TRP* 3.9 9.6 - - + -
214B LEU* 4.6 5.6 - - + -
229B ARG* 3.7 32.5 - - + +
232B LEU* 4.5 8.3 - - + -
233B VAL* 4.3 14.6 - - - +
259B VAL* 3.9 20.9 - - + -
260B THR 3.3 8.7 + - - +
261B GLU* 2.8 29.6 - - - +
263B ARG* 1.3 77.5 - - - +
265B TYR* 1.3 56.6 + - - +
267B TRP* 3.7 9.9 - - - -
268B PHE* 2.9 47.0 + - + -
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Residues in contact with TYR 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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224B PRO* 5.3 2.0 - - + -
229B ARG* 3.1 50.3 - - - +
261B GLU 4.0 0.2 - - - -
262B VAL* 3.0 14.1 + - + +
263B ARG 2.6 4.6 + - - -
264B VAL* 1.3 78.1 - - - +
266B ASN* 1.3 69.4 + - - +
267B TRP 2.9 2.3 + - - -
268B PHE* 3.5 3.7 - - + +
269B ALA* 2.6 37.7 + - + +
272B ARG* 5.5 2.4 + - - -
401F T 3.8 5.8 + - - -
402F C 2.8 80.9 + + - -
403F T 4.6 10.3 - - + -
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Residues in contact with ASN 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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262B VAL* 3.5 25.5 + - - +
263B ARG 2.7 10.0 + - - +
265B TYR* 1.3 85.8 - - - +
267B TRP* 1.3 52.0 + - - +
269B ALA* 3.7 7.3 - - - +
270B ASN* 2.6 50.3 + - - +
315E C 5.3 0.9 - - + -
316E A 3.6 51.4 + - + +
317E C 4.5 12.2 + - - +
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Residues in contact with TRP 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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206B TRP* 3.7 28.8 - + - +
211B GLN* 4.3 17.0 + - - +
214B LEU* 3.1 59.7 - - + +
215B PHE* 3.1 39.4 - + - -
218B TYR* 3.9 20.2 - + + -
263B ARG 2.8 12.7 + - - +
264B VAL* 3.4 13.9 - - - +
265B TYR 2.9 0.4 + - - -
266B ASN* 1.3 77.1 - - - +
268B PHE* 1.3 98.8 + + - +
270B ASN* 3.4 4.9 - - - +
271B ARG* 2.8 37.2 + - + +
315E C 5.3 3.1 + - - -
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Residues in contact with PHE 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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214B LEU* 4.2 11.0 - - + -
217B ALA* 3.2 33.0 - - + -
218B TYR* 3.5 31.8 - + + -
222B LYS 4.0 16.8 - - - -
223B ASN 4.5 7.0 - - - -
224B PRO* 5.0 11.0 - - + -
229B ARG* 5.6 4.0 - - + -
232B LEU* 3.4 33.2 - - + -
264B VAL* 2.9 31.9 + - + +
265B TYR* 3.6 4.7 - - - +
267B TRP* 1.3 90.0 - + - +
269B ALA* 1.3 68.0 + - - +
271B ARG* 3.3 1.3 + - - +
272B ARG* 2.9 39.5 + - - +
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Residues in contact with ALA 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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265B TYR* 2.6 27.0 + - + +
266B ASN* 3.3 11.2 - - - +
268B PHE* 1.3 77.5 - - - +
270B ASN* 1.3 64.7 + - - +
272B ARG* 3.1 19.9 + - - +
273B LYS* 3.0 29.8 + - + +
317E C 6.1 2.7 - - - +
402F C 6.3 0.2 - - - -
403F T 4.5 23.3 + - + -
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Residues in contact with ASN 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 ASN* 2.6 30.6 + - - +
267B TRP* 3.4 5.0 - - - +
269B ALA* 1.3 71.1 - - - +
271B ARG* 1.3 56.1 + - - +
273B LYS* 2.9 19.5 + - - +
274B GLU* 2.7 35.9 + - - +
315E C 4.0 17.0 - - - +
316E A 3.1 47.3 + - - +
317E C 4.6 3.8 - - - +
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Residues in contact with ARG 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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215B PHE* 4.8 21.2 - - + -
218B TYR* 3.7 30.7 - - + -
219B GLU* 4.2 18.2 + - - +
267B TRP* 2.8 46.8 + - + +
268B PHE 3.8 3.1 - - - +
270B ASN* 1.3 71.8 - - - +
272B ARG* 1.3 60.8 + - - +
274B GLU* 2.7 52.2 + - - +
275B GLU* 3.1 38.7 + - - +
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Residues in contact with ARG 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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218B TYR* 3.4 27.1 - - + +
222B LYS* 3.1 44.2 + - + +
224B PRO* 3.8 15.7 - - - +
265B TYR* 5.5 2.0 + - - -
268B PHE* 2.9 26.2 + - - +
269B ALA* 3.2 22.9 - - - +
271B ARG* 1.3 75.9 - - - +
273B LYS* 1.3 54.3 + - + +
274B GLU 2.7 10.7 + - - -
275B GLU* 2.8 27.8 + - - +
402F C 3.3 39.3 + - - -
403F T 3.2 21.9 + - - +
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Residues in contact with LYS 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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152A THR* 5.9 3.1 - - - +
269B ALA* 3.0 17.0 + - + +
270B ASN* 2.9 24.4 + - - +
272B ARG* 1.3 75.1 - - + +
274B GLU* 1.3 57.1 + - - +
275B GLU 3.1 4.4 + - - -
276B ALA* 4.2 13.0 - - - +
316E A 5.0 1.1 - - - +
317E C 5.4 1.6 - - - +
403F T 4.0 23.1 - - + +
404F G 3.1 31.1 + - + +
405F G 2.4 52.0 + - - -
406F T 4.3 3.2 + - - +
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Residues in contact with GLU 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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215B PHE* 5.3 4.7 - - - -
270B ASN 2.7 10.7 + - - +
271B ARG* 2.7 53.8 + - - +
272B ARG 2.7 0.8 + - - -
273B LYS* 1.3 77.5 - - - +
275B GLU* 1.3 57.4 + - - +
276B ALA* 3.1 8.2 + - - +
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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