Contacts of the helix formed by residues 375 - 383 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B LEU* 4.2 14.6 - - + -
371B HIS 2.6 30.3 - - - +
372B PRO* 3.6 15.0 - - + +
374B ASN* 1.3 84.2 - - - +
376B GLN* 1.3 67.8 + - - +
377B PRO* 3.4 1.6 - - - -
378B VAL* 3.1 10.9 + - + +
379B ILE* 3.0 25.4 + - + +
388B LEU* 4.7 17.9 - - + -
390B LEU* 4.2 11.9 - - + -
408B VAL* 5.0 8.7 - - + +
411B ALA* 3.9 24.9 - - + -
412B ILE* 4.6 16.4 - - + -
415B ILE* 4.3 10.5 - - + -
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Residues in contact with GLN 376 (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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372B PRO 5.0 1.8 + - - +
373B GLY 6.3 0.2 - - - -
374B ASN* 5.8 0.7 - - - +
375B ILE* 1.3 81.5 - - + +
377B PRO* 1.3 86.0 - - + +
378B VAL 3.2 0.3 + - - -
379B ILE* 3.3 2.8 + - - +
380B GLU* 2.8 43.3 + - - +
415B ILE* 3.5 31.9 - - + +
421B LEU* 6.0 7.2 - - + +
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Residues in contact with PRO 377 (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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318B ALA* 5.5 0.8 - - - +
320B ALA* 5.0 9.9 - - + -
374B ASN* 3.7 20.2 - - + +
375B ILE 3.4 2.7 - - - -
376B GLN* 1.3 110.8 - - + +
378B VAL* 1.3 60.9 + - + +
380B GLU* 3.6 5.6 - - + +
381B ALA* 3.1 25.5 + - - +
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Residues in contact with VAL 378 (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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317B THR* 4.0 20.9 - - - +
318B ALA* 5.0 4.0 - - - -
320B ALA* 4.3 7.0 - - + -
366B SER* 3.5 19.1 - - - +
370B LEU* 4.6 12.6 - - + -
374B ASN 3.7 20.0 - - - +
375B ILE* 3.2 12.8 - - + +
376B GLN 3.1 0.4 - - - -
377B PRO* 1.3 77.1 - - - +
379B ILE* 1.3 53.9 + - + +
381B ALA* 3.2 2.2 + - - -
382B LEU* 2.7 64.8 + - + +
386B ILE* 4.2 9.2 - - + -
388B LEU* 4.7 4.7 - - + -
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Residues in contact with ILE 379 (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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156B PRO* 4.1 15.0 - - + -
375B ILE* 3.0 13.4 + - + +
376B GLN 4.0 2.7 - - - +
378B VAL* 1.3 73.0 - - - +
380B GLU* 1.3 63.1 + - - +
383B GLY* 2.9 45.7 + - - +
384B THR* 4.5 13.0 - - + -
386B ILE* 4.1 17.5 - - + -
388B LEU* 4.1 24.7 - - + -
412B ILE* 5.1 6.3 - - + -
415B ILE* 4.0 41.5 - - + -
416B MET* 5.8 1.8 - - - -
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Residues in contact with GLU 380 (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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327B ARG* 4.9 4.0 + - - +
376B GLN* 2.8 34.5 + - - +
377B PRO* 3.6 8.7 - - + +
379B ILE* 1.3 78.5 - - - +
381B ALA* 1.3 59.4 + - + +
383B GLY* 4.9 0.3 + - - -
415B ILE* 5.9 0.4 - - - +
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Residues in contact with ALA 381 (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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318B ALA* 4.8 4.3 - - + -
327B ARG* 3.7 46.4 + - + +
331B LEU* 3.2 25.0 - - + +
377B PRO 3.1 17.1 + - - +
378B VAL 3.9 1.8 - - - +
380B GLU* 1.3 78.7 - - - +
382B LEU* 1.3 70.2 + - + +
383B GLY 3.6 0.4 - - - -
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Residues in contact with LEU 382 (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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315B VAL* 4.9 1.8 - - + -
316B GLY 4.4 0.9 - - - +
318B ALA* 4.3 12.3 - - + -
327B ARG 5.1 0.2 - - - +
330B THR* 3.9 27.6 - - + -
331B LEU* 3.9 19.9 - - + +
334B VAL* 3.5 26.9 - - + +
338B ARG* 2.6 40.6 + - - -
366B SER* 3.1 28.5 - - - +
378B VAL* 2.7 34.0 + - + +
381B ALA* 1.3 77.9 - - + +
383B GLY* 1.3 53.0 + - - +
386B ILE* 4.0 17.5 - - + -
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Residues in contact with GLY 383 (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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338B ARG* 4.5 3.8 - - - -
379B ILE* 2.9 33.8 + - - +
380B GLU 4.9 0.4 + - - -
381B ALA 3.6 1.2 - - - -
382B LEU* 1.3 81.1 - - - +
384B THR* 1.3 66.2 + - - -
385B ASP 3.5 1.6 - - - -
386B ILE* 3.8 13.0 - - - +
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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