Contacts of the helix formed by residues 308 - 319 (chain X) in PDB entry 1O1F
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 GLY 308 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219X VAL* 3.0 19.3 - - - +
221X LEU* 4.7 5.8 - - - +
307X PRO* 1.3 73.1 - - - +
309X ILE* 1.3 63.4 + - - +
310X ALA* 3.3 3.5 - - - +
311X ASP* 4.0 21.2 - - - +
312X ARG* 3.3 21.3 + - - +
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Residues in contact with ILE 309 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153X LEU* 5.7 4.9 - - + -
219X VAL* 3.9 14.6 - - + -
261X LEU* 4.3 13.5 - - + -
262X PHE* 4.6 8.8 - - + -
274X ILE* 6.2 2.2 - - + -
299X MET* 4.3 14.4 - - + -
303X THR 3.9 7.2 - - - +
304X THR* 3.2 50.5 - - + +
306X TYR* 3.2 26.5 - - + +
307X PRO 3.2 1.4 - - - -
308X GLY* 1.3 77.6 - - - +
310X ALA* 1.3 73.3 + - + +
312X ARG* 3.8 2.6 + - - +
313X MET* 3.0 33.3 + - + +
335X ARG* 3.5 14.4 - - - +
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Residues in contact with ALA 310 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299X MET* 4.0 22.9 - - + -
308X GLY* 5.2 1.1 - - - +
309X ILE* 1.3 82.0 - - + +
311X ASP* 1.4 53.9 + - - +
313X MET* 3.1 3.3 + - - +
314X GLN* 2.8 38.6 + - + +
329X ILE* 4.1 14.3 - - + +
331X ALA* 4.1 14.1 - - + -
335X ARG* 5.5 0.4 - - - +
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Residues in contact with ASP 311 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221X LEU* 3.8 31.8 - - + +
308X GLY* 3.8 16.5 + - - +
309X ILE 3.5 0.4 - - - -
310X ALA* 1.4 72.9 - - - +
312X ARG* 1.3 66.3 + - - +
314X GLN* 3.1 11.0 - - - +
315X LYS* 3.0 27.0 + - - +
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Residues in contact with ARG 312 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219X VAL* 3.6 11.9 - - + -
220X ALA 3.0 23.6 + - - +
221X LEU* 3.8 12.9 - - - +
222X ASP 4.9 2.5 - - - +
223X PHE* 2.9 41.4 - - - +
262X PHE* 3.3 25.6 - - + +
263X GLN* 3.4 26.7 + - - +
308X GLY 3.3 16.3 + - - +
309X ILE 3.9 3.1 - - - +
311X ASP* 1.3 77.0 - - - +
313X MET* 1.3 50.8 + - - +
315X LYS* 3.3 4.3 + - - +
316X GLU* 2.7 77.3 + - - +
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Residues in contact with MET 313 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153X LEU* 4.5 8.5 - - + -
262X PHE* 4.2 11.4 - - + -
274X ILE* 3.9 17.0 - - + -
275X HIS* 3.4 34.3 - - - -
278X THR* 3.0 37.2 - - + +
297X ASN* 4.4 11.4 - - - +
299X MET* 4.8 8.7 - - - -
309X ILE* 3.0 23.6 + - + +
310X ALA* 3.1 5.1 + - - +
312X ARG* 1.3 73.3 - - - +
314X GLN* 1.3 59.4 + - - +
316X GLU* 3.6 1.9 - - - +
317X ILE* 2.9 40.3 + - + +
329X ILE* 4.1 17.5 - - + -
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Residues in contact with GLN 314 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310X ALA* 2.8 12.7 + - + +
311X ASP* 3.1 17.5 - - - +
313X MET* 1.3 75.9 - - - +
315X LYS* 1.3 62.9 + - + +
318X THR* 2.8 34.5 + - - +
327X ILE* 3.5 32.3 + - - +
328X LYS* 4.3 2.2 - - - +
329X ILE* 3.5 30.3 + - + +
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Residues in contact with LYS 315 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221X LEU* 6.3 4.3 - - + -
311X ASP 3.0 12.3 + - - +
312X ARG* 4.0 3.8 - - - +
314X GLN* 1.3 82.1 - - + +
316X GLU* 1.3 67.2 + - + +
318X THR* 3.1 34.0 + - + +
319X ALA* 3.5 29.7 - - - +
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Residues in contact with GLU 316 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262X PHE* 4.6 2.7 - - + -
275X HIS* 3.2 57.7 + - + -
312X ARG* 2.7 60.7 + - - +
313X MET* 3.2 7.6 + - - +
315X LYS* 1.3 81.1 - - - +
317X ILE* 1.3 62.2 + - - +
319X ALA* 3.9 3.6 + - - +
320X LEU* 3.8 17.2 + - - +
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Residues in contact with ILE 317 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275X HIS* 3.8 22.9 - - + +
278X THR* 4.1 16.2 - - + -
279X TYR* 5.1 5.8 - - + +
294X TYR* 4.0 25.1 - - + +
297X ASN* 3.9 13.9 - - - +
313X MET* 2.9 28.6 + - + +
316X GLU* 1.3 77.0 - - - +
318X THR* 1.3 66.4 + - - +
319X ALA 3.2 1.8 - - - -
320X LEU* 3.0 5.8 + - + +
321X ALA* 2.9 25.6 + - - +
327X ILE* 3.7 26.9 - - + -
329X ILE* 3.6 21.1 - - + -
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Residues in contact with THR 318 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314X GLN* 2.8 29.9 + - - +
315X LYS* 3.1 31.3 + - + +
317X ILE* 1.3 74.0 - - - +
319X ALA* 1.3 60.5 + - - +
320X LEU 3.1 5.7 + - - -
321X ALA* 3.1 20.8 + - - +
323X SER* 5.8 0.7 + - - -
325X MET 6.1 0.4 - - - +
327X ILE* 3.7 29.4 - - + -
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Residues in contact with ALA 319 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315X LYS* 3.5 28.9 + - - +
316X GLU 4.0 4.0 - - - +
317X ILE 3.2 0.6 - - - -
318X THR* 1.3 79.7 + - - +
320X LEU* 1.3 58.9 + - - +
321X ALA 4.8 0.9 - - - -
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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