Contacts of the helix formed by residues 393 - 406 (chain B) in PDB entry 1ADI
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 GLN 393 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388B ARG* 5.1 1.6 - - - +
391B LEU 3.3 3.8 + - - -
392B PRO* 1.3 69.8 - - - +
394B ALA* 1.3 56.4 + - - +
396B LEU* 3.0 49.7 + - - +
397B ASN* 2.7 56.9 + - - +
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Residues in contact with ALA 394 (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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375B MET* 5.1 0.9 - - - +
376B PRO* 4.4 12.7 - - + +
377B GLY 3.8 22.0 - - - +
378B TRP* 4.1 20.2 - - + -
392B PRO* 2.8 4.2 + - + +
393B GLN* 1.3 80.0 - - - +
395B ALA* 1.3 60.3 + - - +
397B ASN* 3.4 9.4 + - - +
398B TYR* 3.1 23.7 + - - +
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Residues in contact with ALA 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B LEU* 3.9 26.7 - - + -
378B TRP* 4.3 18.7 - - + -
382B THR* 4.5 2.0 - - + -
391B LEU* 4.2 13.2 - - + -
392B PRO* 2.6 28.7 + - + +
394B ALA* 1.3 74.5 - - - +
396B LEU* 1.3 62.4 + - - +
398B TYR* 3.4 2.7 + - - +
399B ILE* 3.0 32.2 + - - +
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Residues in contact with LEU 396 (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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388B ARG* 3.2 60.1 - - + +
389B SER 5.7 0.2 - - - +
391B LEU* 3.5 34.1 - - + +
392B PRO 3.1 12.1 + - - +
393B GLN* 3.0 38.8 + - - +
395B ALA* 1.3 79.1 - - - +
397B ASN* 1.3 55.1 + - - +
399B ILE* 3.2 9.2 + - + +
400B LYS* 2.8 29.2 + - - +
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Residues in contact with ASN 397 (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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375B MET* 3.6 11.6 - - + +
376B PRO* 6.4 0.2 - - - +
393B GLN* 2.7 53.2 + - - +
394B ALA* 4.1 7.1 - - - +
396B LEU* 1.3 71.7 - - - +
398B TYR* 1.3 58.6 + - - +
400B LYS* 3.3 9.8 - - - +
401B ARG* 2.8 29.6 + - - +
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Residues in contact with TYR 398 (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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268B ALA* 3.0 26.4 + - + -
269B TYR* 5.7 0.2 - - - +
309B TRP* 5.7 1.2 - - - -
310B LEU* 3.9 4.9 + - - +
329B LEU* 5.7 0.9 - - + -
332B LEU* 4.1 27.1 - - + -
335B LEU* 3.8 15.4 - - + +
341B VAL* 3.2 31.0 - - + -
342B LYS 4.1 4.9 + - - -
343B LEU* 3.7 38.2 - - + +
375B MET* 3.3 20.0 - - + +
378B TRP* 4.5 10.3 - + + -
394B ALA 3.1 16.6 + - - +
395B ALA 3.8 4.0 - - - +
397B ASN* 1.3 78.9 - - - +
399B ILE* 1.3 63.2 + - + +
401B ARG* 3.4 2.3 + - - +
402B ILE* 3.2 40.8 + - + +
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Residues in contact with ILE 399 (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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329B LEU* 3.6 22.4 - - + -
332B LEU* 4.2 17.0 - - + -
391B LEU* 3.7 28.0 - - + -
395B ALA 3.0 22.9 + - - +
396B LEU* 3.5 8.7 - - + +
398B TYR* 1.3 77.8 - - + +
400B LYS* 1.3 66.7 + - - +
401B ARG 3.4 0.5 + - - -
402B ILE* 3.5 8.6 + - - +
403B GLU* 3.5 23.7 + - - +
410B ILE* 3.5 27.4 - - + +
413B ILE* 4.0 22.4 - - + -
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Residues in contact with LYS 400 (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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396B LEU 2.8 13.9 + - - +
397B ASN* 3.3 15.0 - - - +
398B TYR 3.2 0.2 - - - -
399B ILE* 1.3 79.3 - - - +
401B ARG* 1.3 62.3 + - - +
403B GLU* 2.6 45.5 + - - +
404B GLU* 3.2 31.8 + - - +
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Residues in contact with ARG 401 (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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343B LEU* 3.4 28.7 - - + -
345B VAL* 4.7 2.0 - - - +
373B GLU* 2.8 40.7 + - - +
375B MET* 4.1 8.7 - - + -
397B ASN 2.8 20.3 + - - +
398B TYR 3.7 2.0 - - - +
399B ILE 3.3 0.2 - - - -
400B LYS* 1.3 72.3 - - - +
402B ILE* 1.3 67.4 + - - +
403B GLU 3.0 0.9 + - - -
404B GLU* 2.6 57.9 + - - +
405B LEU* 3.1 39.9 + - + +
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Residues in contact with ILE 402 (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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266B LEU* 4.2 22.4 - - + -
310B LEU* 4.5 14.4 - - + -
312B THR* 4.9 9.6 - - + -
315B VAL* 5.7 1.1 - - + -
327B PHE* 4.8 4.9 - - + -
329B LEU* 4.8 14.8 - - + -
343B LEU* 3.8 22.0 - - + -
398B TYR* 3.2 44.6 + - + +
399B ILE* 3.8 10.5 - - - +
400B LYS 3.4 0.2 - - - -
401B ARG* 1.3 75.0 - - - +
403B GLU* 1.3 58.6 + - - +
405B LEU* 3.5 4.9 + - - +
406B THR* 3.0 41.6 + - + +
410B ILE* 4.7 8.7 - - + -
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Residues in contact with GLU 403 (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 PHE* 6.2 0.2 - - - -
399B ILE* 3.5 19.0 - - - +
400B LYS* 2.6 41.3 + - - +
401B ARG 3.0 0.6 - - - -
402B ILE* 1.3 73.4 - - - +
404B GLU* 1.3 59.8 + - - +
405B LEU 3.1 2.2 - - - -
406B THR* 3.8 6.5 - - - -
407B GLY* 2.9 31.9 + - - -
408B VAL 3.9 16.2 - - - +
409B PRO* 4.1 5.4 - - + +
410B ILE* 3.1 41.7 + - + +
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Residues in contact with GLU 404 (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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400B LYS* 3.2 30.4 + - - +
401B ARG* 2.6 49.0 + - - +
403B GLU* 1.3 80.8 - - - +
405B LEU* 1.3 62.1 + - - +
407B GLY* 4.6 2.1 + - - -
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B THR* 3.7 25.6 - - + +
316B ARG* 2.3 55.3 + - - +
343B LEU* 4.8 4.3 - - + -
345B VAL* 3.4 33.7 - - + +
401B ARG* 3.1 48.9 + - + +
402B ILE 3.8 4.9 - - - +
404B GLU* 1.3 80.5 - - - +
406B THR* 1.3 59.7 - - + +
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Residues in contact with THR 406 (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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312B THR* 4.8 7.4 - - - -
315B VAL* 4.4 20.0 - - + -
316B ARG* 4.1 19.8 - - + +
319B VAL* 4.3 14.9 - - - +
327B PHE* 3.7 15.8 - - + -
402B ILE* 3.0 25.5 + - + +
403B GLU* 3.7 1.0 + - - -
405B LEU* 1.3 87.7 - - + +
407B GLY* 1.3 59.6 + - - +
408B VAL* 3.1 30.6 + - - +
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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