Contacts of the helix formed by residues 402 - 406 (chain B) in PDB entry 3OY3
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 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B ARG 5.7 2.9 - - - +
363B ASP* 3.7 13.0 - - - +
367B ARG* 3.2 31.9 - - - +
392B THR 3.1 18.2 - - - +
393B TYR* 3.4 18.6 - - + -
400B LYS 4.4 1.6 - - - +
401B PHE* 1.3 83.3 - - + +
403B ILE* 1.3 59.9 + - - +
404B LYS 3.2 2.5 - - - -
405B TRP* 3.1 20.4 + - + -
406B THR* 2.7 27.5 + - - +
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Residues in contact with ILE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B THR 4.0 4.0 + - - -
394B THR* 3.4 24.0 - - - +
395B ALA 5.3 0.4 - - - +
396B HIS* 4.2 18.4 - - + -
401B PHE* 3.1 20.4 + - + +
402B PRO* 1.3 70.9 - - - +
404B LYS* 1.3 58.1 + - - +
406B THR* 3.0 28.2 + - - +
411B LEU* 3.7 31.0 - - + +
445B LEU* 3.6 41.2 - - + +
448B VAL* 4.2 16.5 - - + +
449B TYR 5.8 0.4 - - - +
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Residues in contact with LYS 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B THR 5.4 0.4 + - - -
402B PRO 3.2 1.6 + - - -
403B ILE* 1.3 78.5 - - - +
405B TRP* 1.3 74.1 + - + +
406B THR 3.6 0.4 - - - -
423B TRP* 5.1 0.9 + - - -
427B VAL* 3.6 14.0 - - - +
438B SER* 5.1 5.1 + - - +
439B PRO* 2.9 37.9 + - + +
440B TYR* 3.1 49.8 + - + +
441B PRO* 5.2 0.2 - - - +
442B GLY 5.1 0.8 - - - +
443B ILE 3.1 29.0 + - - +
445B LEU* 3.7 30.4 - - + +
448B VAL* 4.4 12.1 - - + -
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Residues in contact with TRP 405 (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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324B LEU* 6.1 2.5 - - + -
363B ASP* 5.8 0.2 - - - +
364B LEU 3.6 22.4 - - - +
365B ALA* 3.3 5.0 - - + +
367B ARG* 3.2 35.4 - - - +
392B THR* 4.3 20.9 - - - -
402B PRO* 3.1 21.8 + - + +
403B ILE 3.1 0.6 - - - -
404B LYS* 1.3 99.9 - - + +
406B THR* 1.3 58.5 + - - +
407B ALA 3.7 0.7 + - - -
420B SER 5.1 0.5 - - - +
423B TRP* 3.5 17.7 - - - -
424B ALA* 3.7 20.4 - - + +
427B VAL* 3.6 23.1 - - + +
428B LEU 4.6 0.2 - - - -
431B GLU* 2.9 43.1 + - - -
438B SER* 5.2 2.0 - - - -
439B PRO* 3.5 28.3 - - + -
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Residues in contact with THR 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B PHE* 4.0 15.0 - - + -
402B PRO* 2.7 34.5 + - - +
403B ILE* 3.0 12.6 + - - +
404B LYS 3.6 0.4 - - - -
405B TRP* 1.3 77.2 - - - +
407B ALA* 1.3 65.8 + - - +
408B PRO* 3.8 0.7 - - - +
410B SER* 3.4 28.7 - - - -
411B LEU* 3.6 32.9 - - + +
416B PHE* 4.4 7.8 - - + -
423B TRP* 3.8 7.8 + - - -
452B LEU* 4.8 4.3 - - - +
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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