Contacts of the helix formed by residues 357 - 372 (chain B) in PDB entry 1B3U
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 LYS 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356B GLY* 1.3 71.1 - - - +
358B ASP* 1.3 69.7 + - - +
360B THR* 3.5 1.9 + - - -
361B ILE* 3.2 26.6 + - + +
393B VAL* 3.2 31.9 + - - +
394B ILE* 3.7 15.7 - - + +
395B GLY* 3.8 27.8 - - - +
397B ARG* 5.4 4.4 - - - +
398B GLN* 4.5 14.0 - - - +
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Residues in contact with ASP 358 (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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39A LEU* 5.0 11.6 - - - +
43A VAL* 6.0 2.9 - - - +
356B GLY 3.3 0.8 + - - -
357B LYS* 1.3 81.4 - - - +
359B ASN* 1.3 64.6 + - - +
361B ILE* 2.8 25.1 - - - +
362B GLU* 3.4 15.0 + - - +
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Residues in contact with ASN 359 (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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77A THR* 3.4 25.7 + - - -
318B GLU* 4.2 5.9 + - - -
322B MET* 3.7 28.7 - - - +
355B LEU* 2.7 43.5 + - + +
356B GLY 3.3 2.0 + - - -
358B ASP* 1.3 77.3 - - - +
360B THR* 1.3 57.7 + - - +
362B GLU* 3.3 3.4 + - - +
363B HIS* 2.8 50.8 + - + +
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Residues in contact with THR 360 (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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349B MET* 5.8 0.2 - - - -
352B SER* 2.9 41.0 + - - +
355B LEU* 4.3 2.1 - - - +
356B GLY 3.0 18.6 + - - -
357B LYS* 3.7 4.5 - - - -
359B ASN* 1.3 76.8 - - - +
361B ILE* 1.3 63.0 + - - +
364B LEU* 2.9 44.8 + - + +
365B LEU* 3.0 15.7 + - + -
390B VAL* 4.0 19.5 - - + -
394B ILE* 4.2 10.8 - - + -
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Residues in contact with ILE 361 (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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357B LYS* 3.2 14.4 + - + +
358B ASP* 2.8 36.6 - - - +
360B THR* 1.3 79.1 - - - +
362B GLU* 1.3 64.6 + - + +
365B LEU* 3.4 40.1 - - + +
366B PRO* 3.9 3.1 - - - +
394B ILE* 4.9 7.6 - - + -
398B GLN* 3.7 24.5 - - + +
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Residues in contact with GLU 362 (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 ASP 3.5 14.7 - - - +
359B ASN* 3.3 4.9 + - - +
360B THR 3.3 0.4 - - - -
361B ILE* 1.3 85.9 - - + +
363B HIS* 1.3 86.9 + - + +
366B PRO* 3.9 12.1 - - - +
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Residues in contact with HIS 363 (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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322B MET* 3.4 33.6 - - + +
326B LEU* 4.0 28.9 - - + +
330B LYS* 5.9 2.0 + - - -
355B LEU* 5.7 3.1 - - + -
359B ASN* 2.8 34.6 + - - +
360B THR 3.3 0.2 + - - -
362B GLU* 1.3 109.3 + - + +
364B LEU* 1.3 67.3 + - + +
366B PRO* 3.2 12.8 - - - +
367B LEU* 3.7 18.6 - - - +
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Residues in contact with LEU 364 (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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326B LEU* 5.2 6.1 - - + -
329B ILE* 6.0 0.9 - - + -
348B ILE* 4.3 20.4 - - + +
349B MET* 3.9 25.5 - - + +
351B LEU* 3.9 13.7 - - + -
352B SER* 3.7 39.3 - - - +
355B LEU* 4.0 22.0 - - + -
360B THR* 2.9 23.5 + - + +
363B HIS* 1.3 75.3 - - + +
365B LEU* 1.3 55.2 + - - +
367B LEU* 3.0 17.4 + - + +
368B PHE* 2.6 36.7 + - - +
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Residues in contact with LEU 365 (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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349B MET* 5.9 1.3 - - - -
360B THR* 3.0 17.5 + - + +
361B ILE* 3.4 34.8 - - + +
364B LEU* 1.3 75.5 - - + +
366B PRO* 1.3 64.3 - - + +
368B PHE* 3.1 17.2 + - + +
369B LEU* 2.9 35.7 + - + +
390B VAL* 4.6 6.1 - - + -
394B ILE* 4.3 23.6 - - + -
398B GLN* 4.8 10.8 - - + +
399B LEU* 5.2 2.7 - - + -
402B SER* 3.9 28.9 - - - +
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Residues in contact with PRO 366 (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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361B ILE 3.9 6.7 - - - +
362B GLU 3.9 13.9 - - - +
363B HIS* 3.2 20.0 - - - +
365B LEU* 1.3 97.0 - - + +
367B LEU* 1.3 61.7 + - + +
369B LEU* 3.4 10.0 + - + +
370B ALA* 3.1 21.5 + - - +
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Residues in contact with LEU 367 (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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326B LEU* 3.9 28.3 - - + -
329B ILE* 4.0 21.1 - - + -
330B LYS* 3.9 37.2 - - + +
333B VAL* 3.8 18.8 - - + +
348B ILE* 4.0 17.9 - - + -
363B HIS 3.7 12.1 - - - +
364B LEU* 3.0 13.7 + - + +
366B PRO* 1.3 76.5 - - + +
368B PHE* 1.3 66.5 + - - +
370B ALA* 3.2 8.0 + - + +
371B GLN* 3.2 27.1 + - - +
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Residues in contact with PHE 368 (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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349B MET* 3.6 36.3 - - + +
364B LEU 2.6 17.2 + - - +
365B LEU* 3.1 24.2 - - + +
367B LEU* 1.3 74.4 - - - +
369B LEU* 1.3 82.3 + - + +
371B GLN* 3.4 5.3 + - - +
372B LEU* 3.1 30.8 + - + +
383B ILE* 3.1 34.3 - - + +
384B ILE* 5.6 0.2 - - + -
387B LEU* 3.7 28.9 - - + -
390B VAL* 5.9 1.3 - - + -
399B LEU* 4.6 15.3 - - + -
402B SER* 5.1 2.2 - - - -
403B LEU* 4.4 19.7 - - + -
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Residues in contact with LEU 369 (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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365B LEU* 2.9 20.9 + - + +
366B PRO* 3.4 8.3 + - + +
368B PHE* 1.3 91.8 - - + +
370B ALA* 1.3 67.5 + - - +
372B LEU* 2.9 24.0 + - + +
373B LYS* 2.9 33.7 + - + +
402B SER* 3.5 41.1 - - - +
406B ALA* 4.7 5.4 - - + -
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Residues in contact with ALA 370 (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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333B VAL* 4.0 21.5 - - + +
366B PRO 3.1 14.3 + - - +
367B LEU* 3.2 12.5 + - + +
369B LEU* 1.3 77.0 - - - +
371B GLN* 1.3 61.2 + - - +
373B LYS* 3.8 16.9 + - - +
374B ASP* 4.0 4.2 + - - +
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Residues in contact with GLN 371 (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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333B VAL* 3.3 29.5 + - + +
341B LYS* 3.1 34.9 + - - +
344B LEU* 3.8 15.8 - - - +
345B ALA* 3.1 28.1 - - - +
348B ILE* 3.4 18.4 - - - +
367B LEU 3.2 10.0 + - - +
368B PHE* 3.9 1.7 - - - +
369B LEU 3.1 0.6 - - - -
370B ALA* 1.3 76.5 - - - +
372B LEU* 1.3 65.1 + - - +
374B ASP* 3.1 21.4 - - - +
379B VAL* 3.9 14.4 - - + +
380B ARG* 4.2 6.2 - - - -
383B ILE* 3.4 17.2 - - + +
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Residues in contact with LEU 372 (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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368B PHE* 3.1 24.6 + - + +
369B LEU* 2.9 13.4 + - + +
371B GLN* 1.3 78.6 - - - +
373B LYS* 1.3 58.8 + - + +
374B ASP 3.0 1.6 + - - -
380B ARG* 3.0 41.5 - - + +
383B ILE* 4.1 14.3 - - + +
384B ILE* 3.4 33.9 - - + -
403B LEU* 3.5 29.4 - - + -
406B ALA* 3.6 24.0 - - + -
407B ILE* 5.1 3.1 - - + +
410B LEU* 4.3 10.0 - - + +
425B TYR* 6.2 0.2 - - + -
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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