Contacts of the strand formed by residues 400 - 407 (chain H) in PDB entry 1OAK
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 LEU 400 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364H LEU* 4.0 2.8 - - - +
365H VAL* 3.0 51.0 + - + +
368H TYR* 3.5 20.3 - - - +
371H GLU* 5.1 1.1 - - - +
373H VAL* 3.5 20.0 - - + +
375H VAL* 4.0 13.9 - - + -
388H THR* 4.1 13.0 - - + -
389H PHE 3.4 20.6 - - - +
390H PRO 4.4 2.2 - - - -
391H ALA* 3.8 14.4 - - + +
399H THR* 1.3 76.6 - - - +
401H SER* 1.3 79.2 + - - +
162L SER* 6.4 0.2 - - - -
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Residues in contact with SER 401 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347H LEU* 4.5 0.3 - - - +
363H CYS 3.5 9.1 + - - -
364H LEU* 3.6 21.1 - - - +
388H THR* 3.6 1.2 - - - -
389H PHE* 2.8 35.4 + - - +
400H LEU* 1.3 81.0 + - - +
402H SER* 1.3 61.0 + - - +
133L VAL* 4.1 12.1 - - - +
135L PHE* 3.7 22.0 - - - -
176L SER* 4.1 11.0 - - - -
178L THR* 4.9 3.0 + - - -
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Residues in contact with SER 402 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362H GLY* 3.1 3.6 - - - -
363H CYS 2.9 34.5 + - - -
375H VAL* 3.5 27.6 - - - +
377H TRP* 2.7 30.4 + - - -
386H VAL* 3.8 1.6 - - - +
387H HIS 3.2 6.4 + - - -
388H THR* 3.1 20.9 + - - -
400H LEU* 4.9 0.4 - - - -
401H SER* 1.3 75.7 - - - +
403H SER* 1.3 61.5 + - - +
135L PHE* 3.5 4.7 - - - -
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Residues in contact with SER 403 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360H THR* 4.3 3.1 - - - +
361H LEU 3.3 6.5 - - - -
377H TRP* 4.4 1.6 - - - -
385H GLY 3.6 1.1 + - - +
386H VAL* 3.1 6.6 - - - +
387H HIS* 2.7 48.8 + - - +
389H PHE* 4.4 1.8 - - - -
402H SER* 1.3 73.0 - - - +
404H VAL* 1.3 63.4 + - - +
405H THR* 4.8 0.7 + - - -
135L PHE* 3.3 38.4 - - - -
137L ASN* 2.9 23.9 + - - -
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Residues in contact with VAL 404 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359H VAL 3.8 0.5 - - - +
360H THR* 3.3 1.6 - - - -
361H LEU* 2.7 49.2 + - + +
377H TRP* 3.7 37.9 - - + -
382H LEU* 4.2 15.3 - - + -
385H GLY* 3.1 8.1 - - - +
386H VAL* 3.5 24.2 - - + -
403H SER* 1.3 76.5 - - - +
405H THR* 1.3 63.2 + - - +
406H VAL* 4.1 17.9 + - + -
416H VAL* 4.2 9.2 - - + -
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Residues in contact with THR 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358H MET* 3.8 29.2 - - + +
359H VAL 3.2 11.9 - - - +
360H THR* 2.8 25.3 + - - +
385H GLY* 2.9 27.9 + - - -
387H HIS* 5.9 1.2 - - - -
403H SER* 4.8 0.5 + - - -
404H VAL* 1.3 73.3 - - - +
406H VAL* 1.3 69.9 + - - +
114L THR* 5.9 0.5 - - - +
137L ASN* 4.7 8.1 + - - +
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Residues in contact with VAL 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358H MET* 3.4 7.5 - - - -
359H VAL* 2.7 51.7 + - + +
361H LEU* 4.2 12.6 - - + -
382H LEU* 3.7 39.0 - - + -
404H VAL* 4.1 10.5 - - + -
405H THR* 1.3 81.2 - - - +
407H PRO* 1.3 71.8 - - + +
410H THR* 3.2 19.3 - - - +
411H TRP* 4.3 4.9 - - + -
416H VAL* 4.5 4.3 - - + -
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Residues in contact with PRO 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357H SER 3.4 9.0 - - - +
358H MET* 3.7 24.9 - - + -
406H VAL* 1.3 91.8 - - + +
408H SER* 1.3 60.4 + - - +
409H SER* 4.0 15.5 - - - +
410H THR* 2.6 43.9 + - + +
411H TRP 3.8 0.5 + - - -
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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