Contacts of the helix formed by residues 384 - 400 (chain B) in PDB entry 4KIS
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 ASN 384 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380B ASP* 2.6 27.6 + - - +
381B SER* 3.0 22.6 - - - +
382B MET 2.8 0.8 - - - -
383B MET* 1.3 77.0 - - - +
385B ASP* 1.3 61.0 + - - +
386B ILE 3.2 1.3 - - - -
387B ASP* 3.2 19.5 - - + +
388B ALA* 3.1 25.8 + - - +
407C LYS* 4.8 2.5 + - - -
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Residues in contact with ASP 385 (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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381B SER 2.7 19.8 - - - +
382B MET* 3.0 20.3 + - - +
384B ASN* 1.3 79.3 - - - +
386B ILE* 1.3 67.0 + - + +
388B ALA* 3.6 6.2 + - - +
389B GLN* 3.0 31.9 + - + +
341C ASN* 5.9 1.0 + - - -
407C LYS* 5.2 6.2 + - - +
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Residues in contact with ILE 386 (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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358B GLU* 3.5 46.9 - - - +
361B LYS* 4.5 25.1 - - + +
362B LYS* 3.2 29.6 + - + +
365B LEU* 5.2 3.6 - - + -
382B MET* 3.3 37.2 + - + +
383B MET* 3.9 4.7 - - - +
384B ASN 3.2 0.4 - - - -
385B ASP* 1.3 84.0 - - + +
387B ASP* 1.3 60.2 + - - +
388B ALA 3.3 0.9 - - - -
389B GLN* 3.7 2.0 - - - -
390B ILE* 2.9 26.2 + - + +
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Residues in contact with ASP 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B LYS* 3.9 10.0 - - - +
383B MET* 2.4 56.2 + - - +
384B ASN* 3.2 22.9 - - + +
385B ASP 3.2 0.4 - - - -
386B ILE* 1.3 79.5 - - - +
388B ALA* 1.3 57.6 + - - +
390B ILE* 2.9 28.4 - - + +
391B ASN* 3.0 13.3 + - - +
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Residues in contact with ALA 388 (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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384B ASN 3.1 15.3 + - - +
385B ASP 3.8 5.4 - - - +
387B ASP* 1.3 76.4 - - - +
389B GLN* 1.3 65.5 + - - +
391B ASN* 2.6 22.0 - - - +
392B TYR* 2.9 21.5 + - - +
407C LYS* 3.5 35.2 - - - +
410C GLN* 5.6 3.4 - - + -
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Residues in contact with GLN 389 (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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358B GLU* 3.1 34.2 - - + +
385B ASP 3.0 22.3 + - - +
386B ILE* 4.0 2.9 - - + +
387B ASP 3.4 0.2 - - - -
388B ALA* 1.3 81.4 + - - +
390B ILE* 1.3 60.8 + - - +
392B TYR* 4.0 13.7 - - - +
393B TYR* 2.8 54.2 + - - -
403C LEU* 4.1 24.3 - - - +
406C ASN* 5.3 4.2 + - - -
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Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LEU* 3.6 16.5 - - + +
358B GLU* 3.8 8.3 - - + +
359B HIS* 3.4 57.4 - - + +
362B LYS* 5.0 10.5 - - + +
386B ILE* 2.9 18.7 + - + +
387B ASP* 2.9 24.7 - - + +
388B ALA 3.2 0.4 - - - -
389B GLN* 1.3 77.0 - - - +
391B ASN* 1.3 80.4 + - + +
392B TYR 3.4 0.2 + - - -
394B GLU* 3.2 31.6 + - - +
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Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ASP 3.0 9.6 + - - +
388B ALA* 2.6 38.9 - - - +
390B ILE* 1.3 81.6 - - + +
392B TYR* 1.3 61.4 + - - +
394B GLU* 3.0 26.3 - - - +
395B ALA* 3.0 27.0 - - - +
410C GLN* 3.6 26.6 + - - +
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Residues in contact with TYR 392 (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 ALA 2.9 22.0 + - - +
389B GLN* 4.0 17.0 - - - +
390B ILE 3.2 0.2 - - - -
391B ASN* 1.3 81.8 + - - +
393B TYR* 1.3 90.6 + + - +
395B ALA* 3.7 2.5 - - - +
396B GLN* 2.6 76.7 + - + +
406C ASN* 5.9 3.4 - - - -
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Residues in contact with TYR 393 (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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351B LEU* 4.2 22.4 - - + -
354B LYS* 3.3 56.2 + - + +
355B LEU* 3.3 36.8 - - + -
358B GLU* 4.1 9.6 - - + -
389B GLN* 2.8 41.1 + - - -
391B ASN 3.4 0.2 - - - -
392B TYR* 1.3 101.7 - + - +
394B GLU* 1.3 60.2 + - - +
395B ALA 2.9 1.6 - - - -
396B GLN* 4.2 8.1 - - - +
397B ILE* 2.6 41.3 + - + +
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Residues in contact with GLU 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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355B LEU* 3.7 12.6 - - + +
390B ILE* 3.2 18.4 + - - +
391B ASN* 3.0 40.6 + - - +
393B TYR* 1.3 77.0 - - - +
395B ALA* 1.3 69.6 + - + +
397B ILE* 4.1 3.7 - - - +
398B GLU* 3.3 30.5 + - - +
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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
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391B ASN* 3.0 19.0 + - - +
392B TYR* 3.7 3.4 - - - +
393B TYR 2.9 0.8 + - - -
394B GLU* 1.3 79.3 - - + +
396B GLN* 1.3 57.8 + - - +
397B ILE 2.8 11.0 + - - -
398B GLU* 3.2 15.4 + - - +
399B ALA* 2.8 25.4 + - - +
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Residues in contact with GLN 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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351B LEU* 3.6 33.9 - - - +
392B TYR* 2.6 64.5 + - + +
393B TYR* 4.2 3.3 - - - +
395B ALA* 1.3 71.8 - - - +
397B ILE* 1.3 55.5 + - - +
399B ALA* 3.6 12.3 - - + +
400B ASN* 3.4 16.3 + - - +
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Residues in contact with ILE 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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348B LEU* 3.7 22.2 - - + +
351B LEU* 3.3 51.6 - - + +
352B ASN* 3.1 27.8 - - - +
355B LEU* 4.2 12.1 - - + -
393B TYR* 2.6 30.7 + - + +
394B GLU* 4.1 4.0 - - - +
395B ALA 2.8 0.8 + - - -
396B GLN* 1.3 71.4 - - - +
398B GLU* 1.3 63.1 + - + +
399B ALA 2.8 9.8 + - - -
400B ASN* 3.2 23.2 + - - +
401B GLU* 4.8 0.2 - - - +
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Residues in contact with GLU 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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394B GLU 3.3 12.4 + - - +
395B ALA* 3.2 20.2 + - - +
397B ILE* 1.3 83.0 - - + +
399B ALA* 1.3 76.4 + - - +
400B ASN 3.5 0.2 - - - -
401B GLU* 3.2 28.0 + - - +
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Residues in contact with ALA 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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395B ALA 2.8 17.0 + - - +
396B GLN* 3.6 19.1 - - + +
397B ILE 2.8 1.6 + - - -
398B GLU* 1.3 90.2 + - - +
400B ASN* 1.3 60.1 + - + +
401B GLU* 3.2 5.9 + - - +
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Residues in contact with ASN 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 4.6 12.8 - - - +
351B LEU* 4.8 4.6 - - - +
396B GLN* 3.4 18.5 + - - +
397B ILE* 3.2 17.6 + - - +
398B GLU 4.0 1.6 - - - -
399B ALA* 1.3 73.7 - - - +
401B GLU* 1.3 56.4 + - - +
402B GLU* 3.2 37.5 + - + +
403B LEU* 5.2 1.0 - - - +
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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