Contacts of the helix formed by residues 375 - 383 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370G LEU* 4.1 27.6 - - + -
371G HIS 3.3 13.0 - - - +
372G PRO* 3.7 15.9 - - + +
373G GLY 3.8 0.2 - - - -
374G ASN* 1.3 80.1 - - - +
376G GLN* 1.3 68.2 + - - +
377G PRO 3.4 0.9 - - - -
378G VAL* 3.0 8.9 + - - +
379G ILE* 2.9 25.3 + - + +
388G LEU* 4.5 19.3 - - + -
390G LEU* 4.2 11.9 - - + -
408G VAL* 4.7 7.6 - - + +
411G ALA* 4.1 12.8 - - + -
412G ILE* 4.1 22.7 - - + -
415G ILE* 3.6 22.7 - - + -
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Residues in contact with GLN 376 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372G PRO 5.0 0.6 + - - -
373G GLY 5.3 4.3 - - - +
374G ASN 4.7 0.2 - - - +
375G ILE* 1.3 81.9 - - - +
377G PRO* 1.3 73.0 - - + +
379G ILE* 3.3 2.9 + - - +
380G GLU* 2.9 40.4 + - - +
415G ILE* 3.9 33.6 - - + +
421G LEU* 4.8 16.0 - - + +
440G HIS* 5.8 4.5 - - + -
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Residues in contact with PRO 377 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318G ALA* 5.3 3.9 - - - +
320G ALA* 5.0 9.6 - - + -
327G ARG* 5.3 1.0 + - - -
373G GLY 5.2 0.9 - - - +
374G ASN* 3.7 19.5 - - + +
375G ILE 3.5 3.1 - - - -
376G GLN* 1.3 104.8 - - + +
378G VAL* 1.3 55.7 + - - +
380G GLU* 3.5 7.9 - - + +
381G ALA* 3.0 30.5 + - - +
440G HIS* 6.3 0.4 - - + -
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Residues in contact with VAL 378 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317G THR* 3.7 13.0 - - - +
318G ALA* 5.0 4.7 - - - -
320G ALA* 3.5 29.4 - - + -
366G SER* 3.6 31.6 - - - +
370G LEU* 4.1 12.8 - - + -
374G ASN 3.8 9.2 - - - +
375G ILE* 3.0 10.4 + - + +
377G PRO* 1.3 73.8 - - - +
379G ILE* 1.3 61.2 + - + +
381G ALA 3.3 0.7 + - - -
382G LEU* 2.8 46.1 + - + +
386G ILE* 4.2 9.6 - - + -
388G LEU* 4.5 4.9 - - + -
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Residues in contact with ILE 379 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156G PRO* 4.2 13.2 - - + -
375G ILE* 2.9 19.4 + - + +
376G GLN 3.9 3.1 - - - +
378G VAL* 1.3 76.2 - - + +
380G GLU* 1.3 58.4 + - - +
383G GLY* 2.8 45.4 + - - +
384G THR* 4.1 16.8 - - + -
386G ILE* 4.4 13.7 - - + -
388G LEU* 4.2 21.5 - - + -
412G ILE* 5.0 4.5 - - + -
415G ILE* 3.7 45.8 - - + -
416G MET* 5.8 1.8 - - - -
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Residues in contact with GLU 380 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327G ARG* 4.5 6.3 + - - +
376G GLN* 2.9 29.2 + - - +
377G PRO* 3.5 10.3 - - + +
379G ILE* 1.3 79.6 - - - +
381G ALA* 1.3 61.5 + - + +
383G GLY* 4.3 2.1 + - - -
415G ILE* 6.0 0.2 - - - +
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Residues in contact with ALA 381 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318G ALA* 4.5 4.9 - - + -
327G ARG* 3.4 51.1 + - + +
331G LEU* 3.4 27.1 - - + +
377G PRO 3.0 16.2 + - - +
378G VAL 4.1 1.3 - - - +
380G GLU* 1.3 76.9 - - - +
382G LEU* 1.3 68.3 + - + +
383G GLY 3.6 0.2 - - - -
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Residues in contact with LEU 382 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315G VAL* 4.9 1.3 - - + -
316G GLY 4.3 1.3 - - - +
318G ALA* 4.2 15.5 - - + -
330G THR* 3.8 24.5 - - + -
331G LEU* 3.9 22.4 - - + +
334G VAL* 3.8 25.3 - - + +
338G ARG* 3.0 33.9 + - - -
366G SER* 3.3 26.5 - - - +
378G VAL* 2.8 27.5 + - + +
381G ALA* 1.3 82.9 - - + +
383G GLY* 1.3 59.1 + - - +
386G ILE* 4.1 16.8 - - + -
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Residues in contact with GLY 383 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338G ARG* 4.6 2.9 - - - -
379G ILE* 2.8 23.2 + - - +
380G GLU 4.3 1.7 + - - -
381G ALA 3.6 1.4 - - - -
382G LEU* 1.3 81.8 - - - +
384G THR* 1.3 63.3 + - - -
385G ASP 3.4 2.5 - - - -
386G ILE* 3.4 22.2 - - - +
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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