Contacts of the helix formed by residues 426 - 433 (chain B) in PDB entry 1OPL
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 ALA 426 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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424B TRP 3.9 0.8 + - - -
425B THR* 1.3 77.4 - - - +
427B PRO* 1.3 77.3 - - + +
428B GLU* 3.4 24.9 - - - +
429B SER* 3.0 14.9 + - - +
430B LEU* 3.0 11.3 + - - +
439B SER* 3.8 17.6 + - - -
442B TRP* 3.7 28.8 - - + -
502B ARG* 3.9 1.6 - - - +
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Residues in contact with PRO 427 (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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425B THR 3.8 0.9 - - - +
426B ALA* 1.3 87.2 - - + +
428B GLU* 1.3 61.3 + - - +
430B LEU* 3.2 4.9 + - + -
431B ALA* 3.0 26.5 + - - +
442B TRP* 3.5 37.9 - - + -
468B TYR* 3.4 19.6 - - + -
471B LEU* 4.2 7.6 - - + -
497B TRP* 3.6 50.5 - - + +
502B ARG* 3.9 2.0 - - - +
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Residues in contact with GLU 428 (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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426B ALA* 3.5 13.4 - - - +
427B PRO* 1.3 74.1 - - - +
429B SER* 1.3 58.3 + - - +
432B TYR* 2.9 41.2 + - + +
433B ASN 3.4 4.0 + - - -
434B LYS* 3.4 29.0 + - + +
436B SER* 4.9 2.1 + - - -
439B SER* 3.8 10.3 + - - -
497B TRP 4.2 1.7 - - - +
499B PRO* 3.7 25.8 - - + +
502B ARG* 2.8 45.7 + - - -
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Residues in contact with SER 429 (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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420B PHE* 3.4 10.9 - - - -
425B THR* 3.3 23.5 - - - +
426B ALA* 3.0 6.2 + - - +
428B GLU* 1.3 78.1 - - - +
430B LEU* 1.3 62.3 + - - +
433B ASN* 2.8 25.5 + - - +
434B LYS 2.8 24.2 + - - +
435B PHE* 3.6 23.3 - - - -
439B SER* 3.6 17.3 - - - -
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Residues in contact with LEU 430 (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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420B PHE* 4.5 9.4 - - + -
422B ILE* 3.5 45.3 - - + +
425B THR* 3.6 34.1 - - + +
426B ALA 3.0 15.0 + - - +
427B PRO* 3.6 8.3 - - + +
429B SER* 1.3 79.2 - - - +
431B ALA* 1.3 58.8 + - - +
433B ASN* 4.5 5.2 - - - +
467B VAL* 5.1 0.9 - - + -
468B TYR* 3.9 36.8 - - + +
471B LEU* 4.7 8.3 - - + -
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Residues in contact with ALA 431 (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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427B PRO 3.0 16.2 + - - +
430B LEU* 1.3 79.9 - - - +
432B TYR* 1.3 88.2 + - + +
433B ASN* 5.1 1.2 - - - +
468B TYR* 3.6 26.5 - - + +
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Residues in contact with TYR 432 (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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413B THR* 4.2 7.4 - - - +
428B GLU* 2.9 25.6 + - + +
431B ALA* 1.3 99.8 - - + +
433B ASN* 1.3 73.4 + - - +
434B LYS* 3.1 37.4 + - + +
468B TYR* 5.1 5.4 + - - -
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Residues in contact with ASN 433 (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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413B THR* 3.3 5.8 - - + -
414B ALA* 2.9 49.8 + - + +
415B HIS 3.4 17.2 + - - -
416B ALA* 3.9 8.7 - - - +
417B GLY 4.5 0.9 + - - +
418B ALA* 4.0 5.1 + - - +
420B PHE* 3.5 28.2 - - - -
429B SER* 2.8 20.0 + - - +
430B LEU 4.5 5.0 - - - +
431B ALA 5.1 0.9 - - - +
432B TYR* 1.3 80.3 - - - +
434B LYS* 1.3 59.2 - - - +
435B PHE* 3.4 12.2 - - - -
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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