Contacts of the helix formed by residues 310 - 320 (chain B) in PDB entry 1OL2
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 310 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B GLU* 2.9 38.6 + - - +
233B HIS* 3.7 30.7 - - + +
234B LEU* 3.7 13.0 - - + -
237B ASN* 5.2 2.7 - - + -
308B ALA* 3.5 9.6 - - + +
309B PRO* 1.3 79.6 - - - +
311B VAL* 1.3 65.4 + - - +
312B ASN 3.7 0.4 + - - -
313B GLN* 3.1 12.9 + - - +
314B PHE* 3.1 23.9 + - - -
352B PRO* 3.8 9.4 - - - -
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B HIS* 3.9 16.4 - - + +
310B THR* 1.3 75.1 - - - +
312B ASN* 1.3 57.4 + - - +
314B PHE* 3.2 2.3 + - - -
315B LEU* 2.8 48.2 + - + +
337B GLY* 3.9 19.5 - - - -
340B SER* 4.6 4.5 - - - +
341B LEU* 6.3 1.1 - - + -
352B PRO* 3.4 32.2 - - + +
355B ILE* 3.7 26.9 - - + -
356B ALA* 3.8 14.1 - - - +
359B ALA* 5.4 0.2 - - + -
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Residues in contact with ASN 312 (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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154A VAL* 3.7 16.7 - - - +
229B ASN* 4.5 3.4 + - - +
230B GLU* 2.3 58.1 + - - +
233B HIS* 3.9 20.0 - - + +
310B THR* 3.8 2.5 - - - +
311B VAL* 1.3 80.8 - - - +
313B GLN* 1.3 58.5 + - - +
315B LEU* 3.6 4.7 + - - +
316B THR* 3.1 24.4 + - - -
334B MET* 3.1 36.7 - - + +
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Residues in contact with GLN 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 4.5 5.0 + - - -
153A GLY* 3.7 33.9 - - - +
154A VAL* 4.0 4.0 - - + +
186B LEU* 3.4 30.5 - - + +
230B GLU* 2.7 28.5 + - - +
234B LEU* 4.4 1.2 - - - +
307B ALA 5.6 0.6 - - - -
308B ALA 2.9 25.1 + - - +
309B PRO* 3.6 3.1 - - + +
310B THR* 3.1 22.0 + - - +
312B ASN* 1.3 78.2 - - - +
314B PHE* 1.3 66.9 + - + +
316B THR* 3.4 4.9 + - - -
317B GLN* 3.2 26.4 + - - +
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Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B HIS* 3.8 29.4 - + - -
186B LEU* 3.7 37.0 - - + -
187B ARG* 3.9 5.8 - - + -
190B GLU* 3.1 28.0 - - - -
309B PRO* 4.0 18.4 - - + -
310B THR 3.1 19.7 + - - +
311B VAL 3.2 1.8 + - - +
313B GLN* 1.3 83.3 - - + +
315B LEU* 1.3 55.4 + - - +
317B GLN* 3.3 5.2 + - + +
318B TYR* 2.9 45.5 + + + -
352B PRO* 4.0 2.2 - - + -
353B SER* 3.6 29.8 - - - -
356B ALA* 3.6 19.5 - - + -
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B VAL* 2.8 33.8 + - + +
312B ASN 3.8 4.9 - - - +
314B PHE* 1.3 72.8 - - - +
316B THR* 1.3 60.0 + - - +
318B TYR* 2.9 6.7 + - + +
319B PHE* 2.8 49.6 + - + -
333B ALA* 3.4 41.5 - - + +
334B MET* 4.0 19.3 - - + +
337B GLY* 4.8 0.4 - - - -
356B ALA* 3.2 33.0 - - + +
359B ALA* 4.4 2.2 - - + -
360B PHE* 4.2 15.3 - - + +
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Residues in contact with THR 316 (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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153A GLY 3.7 17.7 - - - +
154A VAL* 3.4 18.3 - - - +
155A PRO* 3.9 23.8 - - + +
312B ASN* 3.1 17.9 + - - -
313B GLN 3.5 3.6 - - - -
314B PHE 3.3 0.2 - - - -
315B LEU* 1.3 74.8 - - - +
317B GLN* 1.3 69.8 + - - +
319B PHE* 3.2 27.8 + - - +
320B LEU* 3.7 14.9 + - + +
334B MET* 5.7 1.2 - - - -
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Residues in contact with GLN 317 (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 PHE 4.8 2.9 - - - +
153A GLY 3.6 15.4 - - - +
179B HIS* 3.3 62.9 + - + +
182B ILE* 4.0 23.4 - - - +
183B HIS* 4.3 13.7 - - + +
186B LEU* 4.3 14.8 - - + -
313B GLN 3.2 14.4 + - - +
314B PHE* 3.5 9.4 - - + +
315B LEU 3.2 0.2 - - - -
316B THR* 1.3 83.2 - - - +
318B TYR* 1.3 67.6 + - + +
319B PHE 3.5 0.3 + - - -
320B LEU* 3.6 12.1 + - - +
321B HIS* 3.8 4.3 - - - -
379B LYS* 4.9 1.0 - - - -
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Residues in contact with TYR 318 (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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183B HIS* 4.3 12.4 + + - -
314B PHE* 2.9 28.9 + + + -
315B LEU* 2.9 11.4 + - + +
317B GLN* 1.3 80.7 - - + +
319B PHE* 1.3 58.3 + - - +
320B LEU 3.1 0.9 - - - -
321B HIS* 2.9 28.1 + - - +
322B GLN 4.1 0.2 + - - -
353B SER* 2.9 30.7 + - - -
356B ALA* 3.6 20.9 - - + -
357B GLY 3.6 22.0 - - - -
360B PHE* 4.1 18.9 - - + -
372B TRP* 3.8 14.8 - + - -
376B LEU* 3.7 27.2 - - + +
379B LYS* 5.0 1.8 - - + -
380B THR* 3.6 31.8 - - + +
382B TYR* 4.4 2.8 - - - -
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Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 2.8 39.7 + - + +
316B THR* 3.2 17.4 + - - +
318B TYR* 1.3 75.7 - - - +
320B LEU* 1.3 65.0 + - + +
321B HIS 3.2 0.6 + - - -
322B GLN* 3.5 17.7 + - - +
325B ALA* 5.7 2.4 - - - +
329B VAL 4.9 0.4 - - - -
330B GLU* 3.6 72.6 - - + +
333B ALA* 4.0 13.7 - - + -
334B MET* 4.4 13.0 - - + -
360B PHE* 3.7 32.1 - + - -
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B PRO* 5.5 10.1 - - + -
179B HIS* 3.5 28.0 - - + +
316B THR* 3.8 16.2 - - + +
317B GLN* 3.7 10.8 - - - +
318B TYR 3.1 0.4 - - - -
319B PHE* 1.3 83.2 - - + +
321B HIS* 1.3 63.8 + - + +
322B GLN 3.3 7.2 + - - +
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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