Contacts of the helix formed by residues 375 - 383 (chain H) in PDB entry 3KDO
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 ILE 375 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370H LEU* 4.2 21.3 - - + -
371H HIS 3.2 19.5 - - - +
372H PRO* 4.2 15.5 - - + +
373H GLY 3.8 0.4 - - - -
374H ASN* 1.3 81.9 - - - +
376H GLN* 1.3 63.8 + - - +
377H PRO* 3.2 1.8 - - - -
378H VAL* 3.3 5.9 + - - +
379H ILE* 2.8 43.0 + - + +
388H LEU* 4.7 11.4 - - + -
390H LEU* 4.3 10.8 - - + -
408H VAL* 4.6 9.9 - - + -
411H ALA* 4.2 17.7 - - + -
412H ILE* 4.1 25.6 - - + -
415H ILE* 3.8 12.1 - - + -
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Residues in contact with GLN 376 (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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373H GLY 5.9 2.2 - - - +
375H ILE* 1.3 79.4 - - - +
377H PRO* 1.3 65.8 - - + +
379H ILE* 3.8 0.9 - - - +
380H GLU* 2.9 32.0 + - - +
415H ILE* 3.2 30.8 - - + +
421H LEU* 6.3 3.4 - - + -
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Residues in contact with PRO 377 (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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320H ALA* 5.2 8.1 - - + -
327H ARG* 5.3 0.3 + - - -
373H GLY 5.1 2.0 - - - +
374H ASN* 3.4 24.9 - - + +
375H ILE 3.2 4.7 - - - -
376H GLN* 1.3 95.0 - - + +
378H VAL* 1.3 58.5 - - + +
380H GLU* 3.2 7.0 + - + +
381H ALA* 2.9 31.8 + - - +
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Residues in contact with VAL 378 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317H THR 3.5 21.3 - - - +
318H ALA* 6.0 1.1 - - - -
320H ALA* 3.8 19.1 - - + -
366H SER* 3.7 19.5 - - - +
370H LEU* 4.1 13.7 - - + -
374H ASN 3.8 10.8 - - - +
375H ILE* 3.3 8.8 + - - +
377H PRO* 1.3 74.6 - - - +
379H ILE* 1.3 59.0 + - + +
381H ALA* 3.3 2.4 + - - -
382H LEU* 2.8 56.3 + - + +
386H ILE* 3.9 10.5 - - + -
388H LEU* 4.5 4.9 - - + -
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Residues in contact with ILE 379 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H PRO* 4.2 12.8 - - + -
375H ILE* 2.8 25.1 + - + +
376H GLN 3.9 2.7 - - - +
378H VAL* 1.3 72.1 - - - +
380H GLU* 1.3 58.6 + - - +
383H GLY* 2.7 45.7 + - - +
384H THR* 4.3 16.8 - - + -
386H ILE* 4.4 9.2 - - + -
388H LEU* 4.1 27.4 - - + -
412H ILE* 5.0 7.0 - - + -
415H ILE* 3.5 45.3 - - + -
416H MET* 6.1 1.3 - - - -
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Residues in contact with GLU 380 (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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327H ARG* 5.0 4.4 + - - +
376H GLN 2.9 20.6 + - - +
377H PRO* 3.5 7.0 - - + +
379H ILE* 1.3 78.7 - - - +
381H ALA* 1.3 61.4 + - - +
383H GLY* 4.3 1.9 + - - -
415H ILE* 5.8 0.4 - - - +
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Residues in contact with ALA 381 (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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318H ALA* 5.6 3.1 - - + -
327H ARG* 3.5 44.6 + - + +
331H LEU* 3.4 24.6 - - + +
377H PRO 2.9 16.6 + - - +
378H VAL* 3.9 3.1 - - - +
380H GLU* 1.3 79.1 - - - +
382H LEU* 1.3 70.2 + - + +
383H GLY 3.5 0.2 - - - -
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Residues in contact with LEU 382 (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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315H VAL* 5.1 1.6 - - + -
316H GLY 4.4 1.1 - - - +
317H THR 4.8 3.4 - - - +
318H ALA* 5.0 3.4 - - + -
327H ARG 5.1 0.9 - - - +
330H THR* 3.5 34.3 - - + -
331H LEU* 3.9 17.3 - - + +
334H VAL* 3.7 18.8 - - + -
338H ARG* 2.7 37.1 + - - +
366H SER* 3.3 27.1 - - - +
378H VAL* 2.8 32.6 + - + +
381H ALA* 1.3 83.6 - - + +
383H GLY* 1.3 58.9 + - - +
386H ILE* 3.9 16.9 - - + +
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Residues in contact with GLY 383 (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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338H ARG* 4.3 3.6 - - - -
379H ILE* 2.7 31.6 + - - +
380H GLU 4.3 1.9 + - - -
381H ALA 3.5 2.0 + - - -
382H LEU* 1.3 81.0 - - - +
384H THR* 1.3 63.2 + - - -
385H ASP 3.3 3.0 + - - -
386H ILE* 3.7 12.8 - - - +
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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