Contacts of the helix formed by residues 386 - 394 (chain B) in PDB entry 1OX4
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 PRO 386 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B ILE 4.7 0.9 - - - +
334B LYS* 4.8 2.7 - - - -
335B ASP* 5.1 8.7 - - - +
346B ALA* 3.6 28.9 - - + -
363B ILE* 4.4 22.7 - - + -
366B ASP* 4.2 33.0 - - + +
370B ALA* 5.7 0.4 - - + -
384B THR 3.9 2.9 - - - +
385B SER* 1.3 89.1 - - - +
387B ILE* 1.3 62.8 + - + +
389B THR* 3.5 8.3 - - - +
390B ILE* 2.9 33.9 + - + +
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Residues in contact with ILE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ILE* 4.6 13.7 - - + -
366B ASP 6.0 0.2 - - - -
367B ALA* 4.2 12.8 - - - -
370B ALA* 4.3 11.7 - - + -
385B SER* 3.7 7.9 - - - +
386B PRO* 1.3 79.5 - - + +
388B GLU* 1.3 52.3 + - - +
391B SER* 2.6 39.8 + - - -
399B VAL* 4.3 9.4 - - + +
401B ILE* 3.5 30.3 - - + -
458B CYS* 3.6 22.4 - - + +
461B LEU* 3.5 27.6 - - + +
462B GLY 4.0 0.2 - - - -
463B ALA* 3.6 25.6 - - - +
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Residues in contact with GLU 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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381B GLY* 3.5 14.0 - - - -
382B ASP* 3.9 4.2 + - - +
383B GLY* 2.7 41.6 + - - -
384B THR 3.4 0.5 + - - -
385B SER* 2.7 37.7 + - - +
387B ILE* 1.3 74.7 - - - +
389B THR* 1.3 60.0 + - - +
391B SER* 3.7 0.9 - - - -
392B LYS* 3.0 52.9 + - - +
461B LEU* 3.5 39.6 - - + +
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Residues in contact with THR 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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346B ALA* 4.7 0.9 - - - +
347B LEU* 3.7 30.9 + - + +
383B GLY 3.9 17.7 - - - +
384B THR* 4.3 9.4 - - - +
385B SER 3.0 11.8 + - - +
386B PRO* 3.2 15.4 + - - +
388B GLU* 1.3 75.0 - - - +
390B ILE* 1.3 74.1 + - - +
392B LYS* 4.1 4.9 - - - +
393B ALA* 3.3 23.2 + - - +
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Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ILE* 4.0 18.2 - - + -
346B ALA 4.3 4.7 - - - +
347B LEU* 4.2 15.0 - - + +
350B ALA* 3.7 22.9 - - + -
354B PHE* 4.2 21.1 - - + -
361B VAL* 4.1 16.8 - - + -
363B ILE* 4.4 7.6 - - + -
386B PRO* 2.9 27.2 + - + +
389B THR* 1.3 85.3 + - - +
391B SER* 1.3 61.9 + - - +
393B ALA 3.3 0.5 + - - -
394B TYR* 2.8 34.7 + - + +
398B ALA* 4.9 0.2 - - + -
399B VAL* 3.7 19.3 - - + -
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Residues in contact with SER 391 (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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52B ASN* 5.3 0.2 - - - +
387B ILE 2.6 25.0 + - - -
388B GLU* 3.3 4.2 + - - -
390B ILE* 1.3 77.3 - - - +
392B LYS* 1.3 63.3 + - - +
395B GLY* 2.6 41.7 + - - -
396B ALA* 3.8 3.0 + - - -
399B VAL* 3.7 8.9 - - - +
461B LEU 3.6 3.5 + - - -
462B GLY* 3.2 37.4 - - - -
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Residues in contact with LYS 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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52B ASN* 3.1 31.0 + - - +
55B HIS* 5.1 0.3 - - - +
383B GLY* 3.9 26.6 + - - +
388B GLU* 3.0 38.2 + - - +
389B THR* 4.1 4.9 - - - +
391B SER* 1.3 81.2 - - - +
393B ALA* 1.3 57.5 + - - +
461B LEU 5.5 2.2 - - - +
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Residues in contact with ALA 393 (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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51B GLY* 3.7 2.3 - - - -
52B ASN* 2.9 18.9 + - - +
55B HIS* 3.3 37.0 - - + +
347B LEU* 3.9 15.9 - - + -
389B THR 3.3 15.0 + - - +
390B ILE 3.3 1.4 + - - -
391B SER 3.3 0.2 - - - -
392B LYS* 1.3 80.4 - - - +
394B TYR* 1.3 77.4 + - + +
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Residues in contact with TYR 394 (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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11B SER* 3.6 25.9 + - - -
12B GLY* 3.9 20.0 + - - -
50B VAL* 4.7 14.4 - - + +
51B GLY* 3.1 29.0 + - - +
55B HIS* 5.9 2.5 - + - -
347B LEU* 3.9 16.2 - - + -
350B ALA* 5.4 0.2 - - + -
351B SER* 2.6 37.0 + - - -
354B PHE* 3.5 35.7 - + - -
390B ILE* 2.8 25.4 + - + +
393B ALA* 1.3 82.7 - - + +
395B GLY* 1.3 59.4 + - - +
397B GLN* 3.2 11.8 + - - +
398B ALA* 3.7 21.2 - - + +
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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