Contacts of the helix formed by residues 368 - 384 (chain B) in PDB entry 4U0Z
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 GLY 368 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B HIS* 4.0 5.7 - - - -
297B VAL* 4.5 6.4 - - - +
298B LEU* 4.9 1.8 - - - -
367B ASP* 1.3 73.9 - - - +
369B ASN* 1.3 57.0 + - - +
371B ARG* 3.7 16.7 - - - +
372B THR* 2.7 36.9 + - - -
501B APC 2.9 30.2 + - - -
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Residues in contact with ASN 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LEU* 5.0 2.1 - - + +
360B VAL* 4.5 8.3 - - + -
363B HIS* 3.1 45.8 + - + +
364B PRO* 3.4 6.1 - - + +
365B PHE* 2.8 55.6 + - - +
366B ILE 4.2 2.0 + - - -
367B ASP 4.1 2.8 - - - -
368B GLY* 1.3 73.2 - - - +
370B GLY* 1.3 62.1 + - - +
372B THR* 3.3 4.0 + - - -
373B SER* 2.9 35.1 + - - -
501B APC 2.9 21.9 + - - +
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Residues in contact with GLY 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B VAL* 4.3 3.1 - - - -
369B ASN* 1.3 79.0 - - - +
371B ARG* 1.4 54.3 + - - +
373B SER* 3.5 1.2 + - - -
374B ARG* 3.0 42.8 + - - +
399B TYR* 4.5 0.2 + - - -
501B APC 3.3 47.3 + - - -
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Residues in contact with ARG 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B THR* 3.7 19.0 + - - +
231B VAL* 4.6 6.3 - - - +
263B GLU* 3.6 44.0 + - - +
267B MET* 4.0 24.2 - - - +
297B VAL* 3.8 28.3 + - + +
298B LEU* 4.4 12.1 - - - +
367B ASP* 3.6 11.1 + - - -
368B GLY* 3.7 12.4 - - - +
369B ASN 3.3 0.2 - - - -
370B GLY* 1.4 71.3 - - - +
372B THR* 1.4 63.6 + - - +
374B ARG* 3.5 21.8 + - - +
375B LEU* 3.1 30.4 + - - +
501B APC 2.8 49.1 + - - +
502B MG 4.1 3.0 - - - -
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Residues in contact with THR 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B VAL* 5.5 3.6 - - - -
293B ILE* 4.8 11.6 - - - +
294B HIS* 3.7 20.3 - - - +
297B VAL* 4.0 11.6 - - - +
359B LEU* 4.4 9.6 - - - +
365B PHE* 4.5 14.4 - - - -
368B GLY 2.7 25.2 + - - -
369B ASN 3.3 3.3 + - - -
371B ARG* 1.4 71.1 - - - +
373B SER* 1.3 59.9 + - - +
375B LEU* 3.4 11.2 + - - +
376B LEU* 2.9 28.9 + - - +
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Residues in contact with SER 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B HIS* 3.7 35.3 - - - +
359B LEU* 3.4 27.8 - - - +
360B VAL* 3.3 16.2 + - - +
369B ASN 2.9 20.4 + - - -
370B GLY 3.7 2.5 - - - -
372B THR* 1.3 72.4 - - - +
374B ARG* 1.4 55.1 + - - +
376B LEU* 2.9 5.5 + - - +
377B MET* 2.7 36.6 + - - +
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Residues in contact with ARG 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B HIS* 4.9 9.8 + - + +
230B THR* 2.9 49.8 + - - +
233B ILE* 3.4 15.7 - - - +
356B HIS* 3.8 17.3 - - + -
370B GLY 3.0 28.2 + - - +
371B ARG* 3.5 14.4 - - - +
372B THR 3.4 0.2 - - - -
373B SER* 1.4 73.4 - - - +
375B LEU* 1.4 58.2 + - + +
377B MET* 3.4 16.0 - - + +
378B ASN* 3.2 31.3 + - - +
389B ILE 6.1 0.2 - - - +
391B ILE* 4.2 25.4 - - + +
399B TYR* 3.2 24.5 + - - -
501B APC 2.9 42.6 + - - -
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B HIS* 4.1 16.2 - - + -
267B MET* 3.6 25.6 - - + -
270B ALA* 3.7 22.0 - - + -
271B MET* 4.4 14.4 - - + -
274B ILE* 3.8 25.1 - - + +
293B ILE* 3.6 25.6 - - + -
297B VAL* 3.8 11.0 - - + -
371B ARG 3.1 18.0 + - - +
372B THR 3.6 6.5 - - - +
373B SER 3.1 0.2 - - - -
374B ARG* 1.4 74.7 - - + +
376B LEU* 1.3 60.3 + - - +
377B MET 3.2 0.4 - - - -
378B ASN* 3.4 9.1 + - + +
379B LEU* 3.0 24.9 + - - +
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 4.8 15.3 - - + -
290B VAL* 5.0 9.6 - - + -
293B ILE* 5.2 12.3 - - + +
334B PHE* 3.6 34.8 - - + -
338B LEU* 4.8 4.0 - - + -
355B ALA* 4.7 11.7 - - + +
356B HIS 6.1 0.2 - - - +
359B LEU* 3.8 17.5 - - + -
372B THR 2.9 15.8 + - - +
373B SER* 2.9 8.3 + - - +
375B LEU* 1.3 71.3 - - - +
377B MET* 1.3 64.8 + - - +
379B LEU* 3.2 25.8 + - + +
380B ILE* 3.1 44.9 + - + +
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Residues in contact with MET 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ALA* 3.6 32.7 - - + +
356B HIS* 3.4 29.8 - - + +
373B SER 2.7 15.9 + - - +
374B ARG* 3.4 20.9 - - + +
376B LEU* 1.3 72.0 - - - +
378B ASN* 1.4 61.4 + - - +
380B ILE* 3.1 10.9 + - - +
381B LEU* 3.1 31.3 + - + +
389B ILE* 3.7 30.3 - - + +
391B ILE* 4.3 14.4 - - + -
418B ILE* 3.9 29.4 - - + -
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Residues in contact with ASN 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B HIS* 3.3 31.3 + - - -
271B MET* 5.8 1.8 - - - +
274B ILE* 6.1 0.2 - - - -
374B ARG 3.2 11.1 + - - +
375B LEU* 3.4 12.4 + - + +
377B MET* 1.4 78.3 - - - +
379B LEU* 1.4 59.1 + - - +
381B LEU* 3.7 8.0 - - - +
382B MET* 2.9 41.1 + - - +
388B PRO* 3.5 21.9 - - + +
389B ILE* 2.9 37.1 + - - +
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Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ILE* 3.7 21.1 - - + +
278B LEU* 3.8 34.3 - - + +
279B VAL* 4.3 17.3 - - + +
285B VAL* 5.3 13.9 - - + -
289B ASP* 6.1 0.4 - - + -
293B ILE* 4.7 6.1 - - + -
375B LEU 3.0 13.1 + - - +
376B LEU* 3.2 29.1 + - + +
378B ASN* 1.4 74.3 - - - +
380B ILE* 1.4 56.3 + - + +
382B MET* 4.0 3.4 - - - +
383B GLN* 3.0 64.0 + - + +
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Residues in contact with ILE 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B VAL* 5.8 5.8 - - + -
338B LEU* 4.0 22.0 - - + -
348B PRO* 4.1 6.9 - - + +
351B PHE* 3.3 44.2 - - + -
352B ALA* 3.7 21.8 - - + +
355B ALA* 4.3 13.0 - - + -
376B LEU* 3.1 26.9 + - + +
377B MET 3.1 6.5 + - - +
379B LEU* 1.4 77.5 - - + +
381B LEU* 1.3 63.5 + - - +
383B GLN* 3.5 16.2 + - - +
384B ALA* 3.4 18.5 + - - +
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Residues in contact with LEU 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B PRO* 4.2 11.4 - - - +
349B VAL* 4.3 17.9 - - + -
352B ALA* 3.9 17.5 - - + -
377B MET* 3.1 22.7 + - + +
378B ASN* 3.7 14.8 - - - +
379B LEU 3.4 0.2 - - - -
380B ILE* 1.3 74.1 - - - +
382B MET* 1.3 58.4 + - + +
384B ALA* 3.0 20.8 + - - +
385B GLY 3.3 0.5 + - - -
386B TYR* 3.0 42.6 + - + +
387B PRO 4.2 5.4 - - - +
389B ILE* 3.8 40.6 - - + -
418B ILE* 5.8 1.1 - - + -
422B THR* 4.2 8.1 - - + -
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Residues in contact with MET 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B MET* 5.5 4.0 - - + -
274B ILE* 6.2 1.6 - - - -
275B ASN* 3.7 28.0 - - - +
279B VAL* 4.6 23.6 - - + +
378B ASN* 2.9 27.7 + - - +
379B LEU* 4.2 3.6 - - - +
381B LEU* 1.3 72.1 - - - +
383B GLN* 1.3 60.7 + - - +
385B GLY* 3.1 13.3 + - - -
386B TYR 3.3 19.5 - - - +
388B PRO* 3.7 44.4 - - + -
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Residues in contact with GLN 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B LEU 4.0 4.9 - - - +
279B VAL* 3.4 29.6 - - - +
281B ARG 3.9 13.0 - - - +
283B GLY 5.6 1.9 - - - +
285B VAL* 4.5 17.7 - - - +
379B LEU* 3.0 41.4 + - + +
380B ILE* 3.7 15.1 - - - +
381B LEU 3.3 0.4 - - - -
382B MET* 1.3 76.5 - - - +
384B ALA* 1.3 56.0 + - - +
385B GLY 3.3 1.6 + - - -
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B PRO* 3.8 32.9 - - + +
380B ILE* 3.4 7.5 + - + +
381B LEU 3.0 10.6 + - - +
383B GLN* 1.3 76.2 - - - +
385B GLY* 1.3 61.6 + - - +
386B TYR* 3.6 9.3 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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