Contacts of the helix formed by residues 393 - 406 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A GLU* 5.0 1.2 + - - -
391A LEU 3.4 3.5 + - - -
392A PRO* 1.3 70.7 - - - +
394A ALA* 1.3 61.9 + - - +
396A LEU* 3.5 24.8 + - - +
397A ASN* 3.1 33.3 + - - +
400A LYS* 4.5 8.5 - - - +
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Residues in contact with ALA 394 (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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375A MET* 5.0 2.1 - - - +
376A PRO* 4.2 10.6 - - + +
377A GLY 3.6 26.0 - - - +
378A TRP* 3.8 19.4 - - + -
380A GLU* 5.5 1.5 + - - +
392A PRO* 3.0 2.0 - - + +
393A GLN* 1.3 76.1 - - - +
395A ALA* 1.3 68.1 + - - +
397A ASN* 3.1 14.8 + - - +
398A TYR* 3.5 6.8 + - - +
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Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 4.2 12.5 - - + +
378A TRP* 3.4 31.3 - - + +
382A THR* 5.1 0.2 - - - +
391A LEU* 3.9 14.6 - - + -
392A PRO* 3.0 28.8 + - + +
394A ALA* 1.3 74.9 - - - +
396A LEU* 1.3 56.2 + - - +
398A TYR* 2.6 35.1 + - - +
399A ILE* 3.5 7.2 + - - +
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Residues in contact with LEU 396 (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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388A ARG* 3.6 46.7 - - + +
391A LEU* 3.3 44.6 - - + +
392A PRO 2.9 16.4 + - - +
393A GLN* 3.5 28.5 - - - +
395A ALA* 1.3 76.7 - - - +
397A ASN* 1.3 60.0 + - - +
399A ILE* 3.3 27.6 - - + +
400A LYS* 3.4 18.7 - - + +
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Residues in contact with ASN 397 (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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375A MET* 3.0 22.1 - - + +
393A GLN* 3.1 18.7 + - - +
394A ALA* 3.1 11.5 + - - +
395A ALA 2.7 3.4 + - - -
396A LEU* 1.3 73.4 - - - +
398A TYR* 1.3 63.5 + - - +
399A ILE 3.2 0.7 - - - -
400A LYS* 3.2 32.0 + - - +
401A ARG* 3.6 18.5 + - - +
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Residues in contact with TYR 398 (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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268A ALA* 2.7 26.6 + - + -
309A TRP* 5.6 1.6 - + - -
310A LEU* 4.0 15.3 + - + +
329A LEU* 5.3 1.1 - - + -
332A LEU* 3.4 26.0 - - + -
335A LEU* 3.4 25.6 - - + +
341A VAL* 4.4 12.8 - - + -
342A LYS 4.5 9.3 + - - -
343A LEU* 4.0 30.5 - - + -
375A MET* 3.2 14.4 - - + +
378A TRP* 4.0 17.9 - + + -
394A ALA 3.5 2.0 + - - +
395A ALA 2.6 21.1 + - - +
397A ASN* 1.3 72.5 - - - +
399A ILE* 1.3 60.9 + - - +
401A ARG* 3.4 5.2 + - - +
402A ILE* 3.0 49.7 + - + +
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Residues in contact with ILE 399 (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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329A LEU* 3.7 29.8 - - + -
332A LEU* 5.0 12.8 - - + -
388A ARG* 6.3 0.4 - - - +
391A LEU* 5.8 4.3 - - + -
395A ALA 3.8 8.5 - - - +
396A LEU* 3.3 22.7 - - + +
398A TYR* 1.3 78.3 - - + +
400A LYS* 1.3 60.9 + - + +
402A ILE* 2.6 31.2 + - - +
403A GLU* 2.9 30.9 + - + +
410A ILE* 4.3 14.4 - - + -
413A ILE* 4.4 21.3 - - + -
425A LEU* 6.4 1.1 - - + -
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Residues in contact with LYS 400 (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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388A ARG* 5.0 16.1 - - - +
393A GLN* 4.5 10.5 - - - +
396A LEU* 3.4 20.0 + - + +
397A ASN* 3.2 41.2 + - - +
398A TYR 3.6 0.4 - - - -
399A ILE* 1.3 77.6 - - + +
401A ARG* 1.3 51.5 + - - +
403A GLU* 3.1 17.3 + - - +
404A GLU* 2.8 52.3 + - + +
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Residues in contact with ARG 401 (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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343A LEU* 4.3 8.1 - - + -
373A GLU* 2.6 46.1 + - - -
375A MET* 3.6 30.3 - - + -
397A ASN* 3.6 15.3 + - - +
398A TYR 3.4 9.6 - - - +
400A LYS* 1.3 77.8 - - + +
402A ILE* 1.3 65.3 + - - +
404A GLU* 2.8 35.6 + - - +
405A LEU* 3.1 65.8 + - - +
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Residues in contact with ILE 402 (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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266A LEU* 3.9 23.6 - - + -
310A LEU* 3.9 24.5 - - + -
312A THR* 5.3 3.4 - - + -
315A VAL* 6.2 0.2 - - + -
327A PHE* 4.7 2.5 - - + -
329A LEU* 4.4 22.2 - - + -
343A LEU* 5.2 7.2 - - + -
398A TYR* 3.0 58.0 + - + +
399A ILE* 2.6 17.0 + - - +
401A ARG* 1.3 71.7 - - + +
403A GLU* 1.3 56.2 + - - +
405A LEU* 5.1 1.6 - - - -
406A THR* 3.0 42.0 + - + +
408A VAL 5.0 0.2 - - - -
410A ILE* 4.1 13.2 - - + -
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Residues in contact with GLU 403 (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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399A ILE* 2.9 28.1 + - - +
400A LYS* 3.3 15.6 - - - +
401A ARG 3.1 0.2 - - - -
402A ILE* 1.3 75.4 - - - +
404A GLU* 1.3 55.5 + - + +
406A THR* 3.2 1.2 + - - -
407A GLY* 2.4 40.0 + - - -
408A VAL 3.4 20.1 + - - +
409A PRO* 3.8 7.3 - - + +
410A ILE* 3.0 40.4 + - + +
425A LEU* 5.5 1.4 - - - +
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Residues in contact with GLU 404 (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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400A LYS* 2.8 32.9 + - + +
401A ARG* 2.8 43.6 + - - +
403A GLU* 1.3 74.2 - - + +
405A LEU* 1.3 61.4 + - - +
407A GLY* 3.7 8.9 + - - +
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Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A THR* 3.9 19.7 - - + +
316A ARG* 3.0 34.7 + - - +
343A LEU* 3.1 36.3 - - + -
345A VAL* 3.7 25.8 - - + -
373A GLU* 4.9 1.1 - - - +
401A ARG* 3.1 50.0 + - - +
402A ILE 4.4 2.0 - - - +
404A GLU* 1.3 74.6 - - - +
406A THR* 1.3 63.2 + - - +
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Residues in contact with THR 406 (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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312A THR* 4.8 13.7 - - + -
315A VAL* 4.1 22.7 - - + -
316A ARG* 4.9 12.8 - - - +
319A VAL* 4.3 18.2 - - - +
327A PHE* 3.2 30.4 - - + -
402A ILE* 3.0 27.6 + - + +
403A GLU 3.2 0.8 + - - -
405A LEU* 1.3 77.4 - - + +
407A GLY* 1.3 62.3 + - - +
408A VAL* 3.0 22.3 + - - +
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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