Contacts of the helix formed by residues 375 - 383 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A LEU* 4.2 14.4 - - + -
371A HIS 3.3 16.2 - - - +
372A PRO* 4.2 13.0 - - + +
374A ASN* 1.3 80.2 - - - +
376A GLN* 1.3 58.5 + - - +
377A PRO* 3.1 2.7 - - - -
378A VAL* 2.3 37.5 + - + +
379A ILE* 2.9 26.1 + - + -
388A LEU* 4.7 11.9 - - + -
390A LEU* 4.0 20.6 - - + -
408A VAL* 4.8 8.1 - - + -
411A ALA* 4.2 22.7 - - + -
412A ILE* 4.5 13.7 - - + -
415A ILE* 3.9 13.5 - - + -
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Residues in contact with GLN 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A PRO 5.5 1.1 + - - +
373A GLY 5.7 2.5 - - - -
374A ASN* 4.6 1.5 - - - +
375A ILE* 1.3 83.7 - - - +
377A PRO* 1.3 76.2 - - + +
378A VAL 3.1 0.7 + - - -
379A ILE* 3.3 2.8 + - - +
380A GLU* 3.1 31.6 + - - +
415A ILE* 3.1 41.0 - - + +
421A LEU* 6.2 3.6 - - + -
440A HIS* 6.2 2.7 - - + +
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Residues in contact with PRO 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ALA* 4.8 4.8 - - - +
320A ALA* 4.6 11.2 - - + -
327A ARG* 5.1 1.9 + - - -
373A GLY 5.3 0.7 - - - +
374A ASN* 3.2 22.9 - - + +
375A ILE 3.2 4.7 - - - -
376A GLN* 1.3 108.3 - - + +
378A VAL* 1.3 58.4 + - - +
380A GLU* 4.1 4.0 - - + +
381A ALA* 3.4 24.4 + - - +
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Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A THR 3.5 21.8 - - - +
318A ALA* 4.8 4.7 - - - -
320A ALA* 3.8 6.3 - - + -
366A SER* 3.4 32.1 - - - +
370A LEU* 4.5 9.0 - - + -
374A ASN 3.6 15.9 - - - +
375A ILE* 2.3 36.7 + - + +
377A PRO* 1.3 65.6 - - - +
379A ILE* 1.3 60.2 + - - +
380A GLU 3.0 4.9 - - - -
381A ALA 3.2 1.4 + - - -
382A LEU* 3.0 38.4 + - + +
386A ILE* 4.1 10.3 - - + -
388A LEU* 4.3 5.6 - - + -
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Residues in contact with ILE 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PRO* 4.1 21.8 - - + -
375A ILE* 2.9 20.0 + - + +
376A GLN 4.0 4.5 - - - +
378A VAL* 1.3 76.1 - - + +
380A GLU* 1.3 57.9 + - - +
383A GLY* 3.2 34.5 + - - +
384A THR* 4.1 20.5 - - + +
386A ILE* 4.4 5.4 - - + -
388A LEU* 4.1 22.0 - - + -
412A ILE* 4.8 9.0 - - + +
415A ILE* 3.8 43.3 - - + -
416A MET* 5.7 2.9 - - - -
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Residues in contact with GLU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A ARG* 4.7 6.5 + - - +
376A GLN* 3.1 29.7 + - - +
377A PRO* 4.2 5.2 - - + +
378A VAL 3.0 0.8 - - - -
379A ILE* 1.3 79.6 - - - +
381A ALA* 1.3 61.6 + - - +
382A LEU 3.3 0.8 + - - -
383A GLY* 4.1 3.8 + - - -
415A ILE* 6.4 0.7 - - + -
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Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A ALA* 4.4 3.6 - - + -
327A ARG* 3.3 46.0 - - + +
331A LEU* 3.2 25.4 - - + +
377A PRO 3.4 15.8 + - - +
378A VAL 3.2 1.8 + - - -
380A GLU* 1.3 79.3 - - - +
382A LEU* 1.3 79.0 + - + +
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Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A VAL* 5.0 2.5 - - + -
316A GLY 4.6 1.6 - - - +
318A ALA* 3.9 14.1 - - + -
327A ARG 5.0 0.7 - - - +
330A THR* 3.3 28.5 - - + -
331A LEU* 4.2 15.7 - - + +
334A VAL* 3.5 20.9 - - + -
338A ARG* 2.7 37.3 + - - +
366A SER* 4.5 10.3 - - - +
378A VAL* 3.0 31.3 + - + +
381A ALA* 1.3 116.0 - - + +
383A GLY* 1.3 60.7 + - - +
386A ILE* 3.9 14.0 - - + +
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Residues in contact with GLY 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A ARG* 4.4 3.1 - - - -
379A ILE* 3.2 24.4 + - - +
380A GLU 4.1 4.1 + - - -
381A ALA 3.8 0.6 - - - -
382A LEU* 1.3 80.7 - - - +
384A THR* 1.3 63.2 + - - -
385A ASP 3.3 3.1 + - - -
386A ILE* 3.5 18.4 - - - +
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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