Contacts of the helix formed by residues 349 - 359 (chain B) in PDB entry 3OX4
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 349 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272B TYR* 2.9 34.0 + - + +
273B TYR* 2.6 33.8 + - + +
346B LYS* 2.8 23.8 + - - +
348B GLU* 1.3 81.1 - - - +
350B VAL* 1.3 66.7 + - - +
351B PRO* 3.3 3.6 - - - -
352B LEU* 3.1 12.2 + - + +
353B LEU* 3.1 26.6 + - + +
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Residues in contact with VAL 350 (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 LYS 3.7 1.2 + - - +
347B LYS* 3.1 25.8 + - - +
349B ASP* 1.3 77.2 - - - +
351B PRO* 1.3 68.8 - - + +
353B LEU* 3.1 10.5 + - + +
354B ALA* 2.9 22.7 + - - +
376B GLU* 3.4 42.8 - - + +
379B PHE* 3.8 11.0 - - + -
380B LEU* 3.6 24.7 - - + -
383B PHE* 3.7 19.7 - - + -
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Residues in contact with PRO 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LYS 3.9 3.8 - - - +
348B GLU* 3.7 12.6 - - - +
349B ASP 3.5 4.5 - - - -
350B VAL* 1.3 92.5 - - + +
352B LEU* 1.3 55.7 + - - +
355B ASP* 3.1 14.6 + - - +
372B GLN* 2.9 21.3 + - - +
376B GLU* 3.6 30.3 - - - +
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Residues in contact with LEU 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B TYR* 3.9 31.6 - - + +
349B ASP* 3.1 11.4 + - - +
351B PRO* 1.3 76.7 - - - +
353B LEU* 1.3 66.2 + - + +
355B ASP* 3.3 9.2 + - + +
356B HIS* 3.0 65.7 + - + +
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Residues in contact with LEU 353 (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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268B GLN* 3.6 41.2 - - + +
269B LEU* 4.2 23.1 - - + +
272B TYR* 4.3 21.3 - - + -
273B TYR* 4.2 7.9 - - + +
346B LYS 5.0 0.9 - - - +
349B ASP* 3.1 35.9 + - + +
350B VAL* 3.6 13.9 - - + +
352B LEU* 1.3 78.2 - - + +
354B ALA* 1.3 56.6 + - - +
356B HIS* 3.5 2.4 + - + -
357B ALA* 2.8 30.0 + - - +
379B PHE* 3.7 24.0 - - + -
383B PHE* 5.5 2.5 - - + -
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Residues in contact with ALA 354 (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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350B VAL 2.9 13.9 + - - +
353B LEU* 1.3 74.2 - - - +
355B ASP* 1.3 67.7 + - - +
357B ALA* 3.1 1.5 + - - +
358B LEU* 2.9 29.2 + - - +
372B GLN* 3.5 22.2 - - - +
375B VAL* 3.6 30.5 - - + +
376B GLU* 3.6 18.2 - - + +
379B PHE* 3.8 2.6 - - + -
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Residues in contact with ASP 355 (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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351B PRO 3.1 16.0 + - - +
352B LEU* 3.5 16.4 - - + +
353B LEU 3.3 0.2 - - - -
354B ALA* 1.3 78.9 - - - +
356B HIS* 1.3 74.3 + - + +
358B LEU* 3.3 11.4 + - - +
359B LYS* 2.9 49.6 + - - +
372B GLN* 3.4 18.7 + - - +
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Residues in contact with HIS 356 (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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268B GLN* 3.1 27.2 + - + +
272B TYR* 6.2 2.5 - + - -
352B LEU* 3.0 55.8 + - + +
353B LEU* 4.1 3.1 - - + +
355B ASP* 1.3 87.1 + - - +
357B ALA* 1.3 65.6 + - - +
359B LYS* 3.0 26.0 + - - +
360B ASP* 3.2 9.7 + - - +
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Residues in contact with ALA 357 (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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264B ALA* 3.6 37.9 - - + +
265B MET* 4.1 17.3 - - + -
268B GLN* 3.8 4.9 - - + +
353B LEU 2.8 20.5 + - - +
354B ALA* 3.1 9.8 + - - +
356B HIS* 1.3 75.8 - - - +
358B LEU* 1.3 63.4 + - - +
360B ASP* 3.2 17.5 + - - +
363B ALA* 3.7 3.9 - - - +
375B VAL* 4.3 5.2 - - + -
379B PHE* 4.4 0.2 - - + -
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Residues in contact with LEU 358 (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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261B TYR* 3.8 21.3 - - + +
354B ALA 2.9 17.7 + - - +
355B ASP* 3.6 7.9 - - - +
356B HIS 3.2 0.2 - - - -
357B ALA* 1.3 76.5 - - - +
359B LYS* 1.3 60.5 + - + +
360B ASP 3.3 1.4 + - - +
363B ALA* 4.1 13.0 - - + +
370B GLY 4.0 8.1 - - - +
371B ASP* 3.8 3.4 - - - -
372B GLN* 3.4 42.8 - - + +
375B VAL* 3.5 26.7 - - + -
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Residues in contact with LYS 359 (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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355B ASP* 2.9 43.7 + - - +
356B HIS* 3.0 23.4 + - - +
358B LEU* 1.3 81.1 - - + +
360B ASP* 1.3 61.0 + - - +
361B ALA* 3.7 1.4 + - - -
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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