Contacts of the helix formed by residues 379 - 392 (chain B) in PDB entry 1OI4
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 379 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363B GLU* 3.2 33.2 - - - +
374B SER* 3.7 7.4 - - - -
375B ARG* 2.8 59.9 + - - +
376B THR* 2.8 22.0 + - - +
378B ASP* 1.3 79.9 - - - +
380B LEU* 1.3 65.0 + - - +
381B PRO* 3.3 2.9 - - - -
382B ALA* 3.1 7.6 + - - +
383B PHE* 2.9 20.5 + - - +
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Residues in contact with LEU 380 (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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237B SER* 3.6 29.6 - - - +
238B GLU* 4.6 3.1 - - + +
241B SER* 3.6 22.7 - - - +
242B PRO* 3.8 31.4 - - + -
324B ILE* 3.8 19.5 - - + +
376B THR 3.8 0.6 + - - -
377B PRO* 3.1 30.3 + - + +
379B ASP* 1.3 76.6 - - - +
381B PRO* 1.3 61.5 - - + +
383B PHE* 3.8 8.3 - - + -
384B ASN* 2.7 45.7 + - - +
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Residues in contact with PRO 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B PRO 4.3 1.1 - - - +
378B ASP 3.6 14.6 - - - +
379B ASP 3.4 4.0 - - - -
380B LEU* 1.3 92.8 - - + +
382B ALA* 1.3 57.2 + - - +
384B ASN* 4.0 6.0 - - + +
385B ARG* 3.0 29.9 + - - +
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B GLU* 3.7 33.2 + - + +
364B VAL* 3.7 22.4 - - + -
379B ASP 3.1 8.5 + - - +
381B PRO* 1.3 76.6 - - - +
383B PHE* 1.3 65.2 - - - +
385B ARG* 3.3 21.6 + - - +
386B GLU* 3.0 28.9 + - - +
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Residues in contact with PHE 383 (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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242B PRO* 4.0 10.8 - - + -
246B PHE* 5.5 0.2 - + - -
291B LEU* 3.8 20.0 - - + -
322B PHE* 3.4 34.5 - + + -
323B ALA 3.7 21.3 - - - -
324B ILE* 3.8 17.3 - - + -
364B VAL* 4.2 4.0 - - - -
372B VAL* 3.7 22.8 - - + +
374B SER* 3.3 32.9 + - - +
379B ASP 2.9 10.1 + - - +
380B LEU* 3.0 22.4 + - + +
382B ALA* 1.3 77.7 - - - +
384B ASN* 1.3 74.7 + - - +
386B GLU* 3.4 2.3 + - - +
387B ALA* 3.0 26.0 + - + +
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Residues in contact with ASN 384 (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 SER* 3.1 25.9 + - - -
242B PRO* 3.2 33.1 - - - +
245B GLU* 3.8 30.2 - - + +
246B PHE* 4.9 2.7 - - + -
380B LEU* 2.7 30.0 + - - +
381B PRO* 4.0 5.3 - - + +
383B PHE* 1.3 75.5 - - - +
385B ARG* 1.3 55.9 + - - +
387B ALA* 3.7 5.3 - - - +
388B LEU* 2.8 40.0 + - + +
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Residues in contact with ARG 385 (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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363B GLU* 4.4 9.1 + - - -
364B VAL* 3.5 27.5 - - - +
381B PRO 3.0 19.6 + - - +
382B ALA* 3.4 22.0 - - - +
384B ASN* 1.3 77.6 - - - +
386B GLU* 1.3 82.6 + - - +
388B LEU* 3.5 8.7 + - - +
389B ARG* 3.0 27.9 + - + +
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Residues in contact with GLU 386 (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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364B VAL* 3.7 15.3 - - + -
366B VAL* 3.5 34.8 - - + +
372B VAL* 3.9 14.4 - - + -
382B ALA 3.0 19.6 + - - +
385B ARG* 1.3 104.7 + - - +
387B ALA* 1.3 67.4 + - - +
389B ARG* 3.2 30.8 + - - +
390B LEU* 3.0 26.3 + - - +
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Residues in contact with ALA 387 (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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246B PHE* 3.7 24.7 - - + -
322B PHE* 3.6 37.9 - - + -
372B VAL* 4.4 1.9 - - + +
383B PHE* 3.0 20.3 + - + +
384B ASN* 3.7 4.3 - - - +
386B GLU* 1.3 75.3 - - - +
388B LEU* 1.3 64.2 + - - +
390B LEU* 3.1 3.6 + - - -
391B LEU* 3.0 27.9 + - - +
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Residues in contact with LEU 388 (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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245B GLU* 3.9 37.0 - - + +
246B PHE* 3.9 25.6 - - + -
249B ALA* 4.0 18.6 - - + -
251B HIS* 4.5 8.3 - - + +
384B ASN* 2.8 25.7 + - + +
385B ARG* 3.7 7.0 - - - +
387B ALA* 1.3 77.0 - - - +
389B ARG* 1.3 62.5 + - - +
391B LEU* 3.0 6.1 + - - +
392B GLY* 3.0 21.1 + - - -
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Residues in contact with ARG 389 (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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366B VAL* 4.2 8.5 - - - +
369B ASP* 2.8 31.9 + - - -
385B ARG* 3.0 16.3 + - + +
386B GLU* 3.3 34.2 + - - +
388B LEU* 1.3 78.5 - - - +
390B LEU* 1.3 82.3 + - + +
392B GLY* 3.3 15.0 + - - +
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Residues in contact with LEU 390 (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 LYS* 5.4 1.2 - - - +
320B PRO* 4.2 26.3 - - + +
322B PHE* 4.5 0.9 - - + -
366B VAL* 4.4 2.2 - - + -
369B ASP* 3.5 45.5 - - + +
370B GLN* 3.6 12.1 - - - +
372B VAL* 3.6 27.1 - - + -
386B GLU 3.0 15.6 + - - +
387B ALA 3.1 6.3 + - - +
389B ARG* 1.3 105.1 - - + +
391B LEU* 1.3 64.3 + - - +
392B GLY 3.5 6.6 - - - +
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU 4.6 1.7 - - - +
224B LYS* 3.0 45.4 - - + +
226B ILE* 4.1 17.9 - - + -
246B PHE* 3.9 29.4 - - + -
251B HIS* 3.4 38.6 + - + +
288B ASP 5.3 1.1 - - - +
289B ALA* 3.7 30.1 - - + -
320B PRO* 5.2 3.1 - - + -
322B PHE* 3.7 9.2 - - + -
387B ALA 3.0 16.0 + - - +
388B LEU* 3.0 9.1 + - - +
390B LEU* 1.3 76.0 - - - +
392B GLY* 1.3 59.6 + - - +
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Residues in contact with GLY 392 (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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221B GLY* 6.3 2.9 - - - -
222B LEU 6.4 0.2 - - - -
224B LYS* 4.9 4.3 - - - -
251B HIS* 5.2 2.2 - - - -
388B LEU 3.0 12.2 + - - -
389B ARG 3.3 10.2 + - - +
390B LEU 3.2 10.0 - - - +
391B LEU* 1.3 83.1 - - - +
393B ALA 1.2 49.0 + - - -
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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