Contacts of the strand formed by residues 399 - 405 (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 VAL 399 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361B VAL* 3.8 3.4 - - + +
363B ILE* 4.0 25.4 - - + -
387B ILE* 4.3 15.5 - - - +
390B ILE* 3.7 19.3 - - + -
391B SER* 3.7 36.8 - - - +
395B GLY 4.2 1.3 - - - +
396B ALA 2.9 7.3 + - - +
397B GLN 3.4 0.8 - - - -
398B ALA* 1.3 83.6 - - - +
400B VAL* 1.3 63.8 + - - +
401B ILE* 4.5 9.9 - - + -
462B GLY 4.6 0.4 - - - +
463B ALA* 3.9 11.8 - - - -
464B GLY 2.9 27.0 + - - -
465B GLU* 3.3 5.7 + - - +
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Residues in contact with VAL 400 (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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328B THR* 4.6 8.3 - - + -
360B LYS* 3.9 26.0 - - + -
361B VAL 2.8 15.3 + - - +
362B SER* 4.0 12.1 - - - +
363B ILE* 2.7 33.4 + - - +
399B VAL* 1.3 76.8 - - - +
401B ILE* 1.3 63.2 + - - +
465B GLU* 3.5 36.3 - - + +
467B LEU* 3.8 30.3 - - + +
497B ILE* 5.1 3.4 - - + -
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Residues in contact with ILE 401 (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 ILE* 3.5 7.2 - - + -
367B ALA* 3.8 24.5 - - + -
387B ILE* 3.5 37.2 - - + -
399B VAL* 4.5 2.5 - - + -
400B VAL* 1.3 77.9 - - - +
402B SER* 1.3 60.4 + - - +
403B VAL* 3.5 20.3 + - + -
454B LEU* 5.2 2.2 - - + -
455B THR* 6.1 0.2 - - - -
458B CYS* 3.8 15.7 - - + -
463B ALA* 3.4 28.0 - - + -
465B GLU 2.9 9.2 + - - +
466B ILE* 3.6 16.2 - - + +
467B LEU 2.6 31.6 + - - +
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Residues in contact with SER 402 (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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297B LEU* 5.9 1.6 - - - +
362B SER* 3.2 22.0 + - - -
363B ILE 2.8 17.9 + - - +
364B GLY* 3.8 18.2 - - - +
401B ILE* 1.3 73.9 - - - +
403B VAL* 1.3 61.1 + - - +
404B ASP* 4.2 8.8 + - - +
454B LEU* 5.6 0.9 - - - +
467B LEU* 3.5 18.3 - - - +
469B ASN* 3.1 21.3 + - - -
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Residues in contact with VAL 403 (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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401B ILE* 3.8 19.1 - - + +
402B SER* 1.3 76.7 + - - +
404B ASP* 1.3 62.9 + - - +
405B PRO* 3.2 20.5 - - + +
438B CYS* 4.6 1.3 - - - -
451B VAL* 3.6 24.2 - - + -
454B LEU* 3.7 29.6 - - + -
455B THR* 4.2 17.5 - - + -
466B ILE* 4.3 4.7 - - + -
467B LEU 2.9 11.8 + - - +
468B LEU* 4.2 7.6 - - + -
469B ASN* 3.0 31.7 + - - +
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Residues in contact with ASP 404 (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 GLY* 5.9 1.4 - - - -
402B SER* 4.2 9.4 + - - +
403B VAL* 1.3 76.3 - - - +
405B PRO* 1.3 63.7 - - - +
438B CYS* 4.6 1.7 - - - +
439B THR* 2.9 48.8 + - - +
440B ILE* 6.1 0.3 - - - -
442B GLY* 5.5 3.6 - - - -
443B GLY* 5.1 7.6 + - - -
454B LEU* 5.7 0.6 - - - +
469B ASN* 3.1 30.5 + - - +
471B ILE* 3.6 14.2 - - + +
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Residues in contact with PRO 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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403B VAL* 3.2 17.3 - - + +
404B ASP* 1.3 86.1 - - - +
406B LYS* 1.3 61.4 + - - +
436B TYR* 3.7 21.3 - - + -
437B GLN 3.2 11.2 - - - +
438B CYS* 4.4 1.3 - - - -
451B VAL* 4.2 11.7 - - + -
468B LEU* 4.3 4.3 - - + -
469B ASN 3.1 27.1 - - - +
470B CYS* 4.1 2.0 - - - -
471B ILE* 3.2 29.5 + - - +
472B ASP 4.6 0.3 + - - -
484B LEU* 3.8 22.0 - - + -
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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