Contacts of the helix formed by residues 368 - 384 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C HIS* 4.1 5.7 - - - -
297C VAL* 4.5 7.7 - - - +
298C LEU* 4.9 1.8 - - - -
367C ASP* 1.3 74.3 - - - +
369C ASN* 1.3 57.2 + - - +
370C GLY 3.6 1.8 - - - -
371C ARG* 3.7 15.8 - - - +
372C THR* 2.7 36.6 + - - -
501C APC 2.9 28.2 + - - -
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Residues in contact with ASN 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C LEU* 5.0 2.7 - - + +
360C VAL* 4.5 8.1 - - - -
363C HIS* 3.1 46.3 + - + +
364C PRO* 3.4 6.5 - - + +
365C PHE* 2.9 54.9 + - - +
366C ILE 4.2 0.8 + - - -
367C ASP* 4.1 4.2 - - - +
368C GLY* 1.3 70.1 - - - +
370C GLY* 1.3 56.8 + - - +
372C THR* 3.4 2.8 + - - -
373C SER* 2.8 38.4 + - - -
501C APC 2.8 28.1 + - - +
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Residues in contact with GLY 370 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C VAL* 4.3 3.1 - - - -
369C ASN* 1.3 79.4 - - - +
371C ARG* 1.4 54.9 + - - +
373C SER* 3.7 1.0 - - - -
374C ARG* 2.9 48.3 + - - +
399C TYR* 4.5 0.2 + - - -
501C APC 3.3 41.7 + - - -
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Residues in contact with ARG 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C THR* 3.7 19.0 + - - +
231C VAL* 4.6 6.1 - - - +
263C GLU* 3.6 41.5 + - - +
267C MET* 4.0 24.4 - - - +
297C VAL* 3.8 27.2 + - + +
298C LEU* 4.4 12.3 - - - +
367C ASP* 3.6 6.1 + - - -
368C GLY* 3.7 12.8 - - - +
369C ASN 3.3 0.2 - - - -
370C GLY* 1.4 73.4 - - - +
372C THR* 1.4 62.6 + - - +
374C ARG* 3.5 21.2 + - - +
375C LEU* 3.1 28.9 + - - +
501C APC 2.7 49.5 + - - +
502C MG 3.6 10.1 - - - -
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Residues in contact with THR 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C VAL* 5.5 3.6 - - - -
293C ILE* 4.7 12.3 - - - +
294C HIS* 3.7 20.5 - - - +
297C VAL* 4.0 10.7 - - - +
359C LEU* 4.4 9.5 - - - +
365C PHE* 4.5 13.7 - - - -
368C GLY 2.7 25.0 + - - -
369C ASN 3.4 3.3 + - - -
371C ARG* 1.4 71.3 - - - +
373C SER* 1.4 60.1 + - - +
375C LEU* 3.4 10.7 + - - +
376C LEU* 2.9 28.6 + - - +
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Residues in contact with SER 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C HIS* 3.7 24.3 - - - +
359C LEU* 3.4 27.1 - - - +
360C VAL* 3.2 27.1 + - - +
369C ASN 2.8 21.4 + - - -
370C GLY 3.7 2.2 - - - -
372C THR* 1.4 71.3 - - - +
374C ARG* 1.4 55.6 + - - +
376C LEU* 2.9 5.8 + - - +
377C MET* 2.7 35.9 + - - +
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Residues in contact with ARG 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C HIS* 4.9 9.3 + - + +
230C THR* 2.8 48.2 + - - +
233C ILE* 3.5 14.9 - - - +
356C HIS* 3.8 7.8 + - + -
370C GLY 2.9 29.4 + - - +
371C ARG* 3.5 15.5 - - - +
372C THR 3.5 0.2 - - - -
373C SER* 1.4 73.6 - - - +
375C LEU* 1.4 57.6 + - + +
377C MET* 3.4 16.0 - - + +
378C ASN* 3.2 30.7 + - - +
391C ILE* 4.2 24.5 - - + +
399C TYR* 3.2 37.8 + - - +
501C APC 3.0 39.2 + - - -
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Residues in contact with LEU 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C HIS* 4.1 16.2 - - + -
267C MET* 3.7 25.4 - - + -
270C ALA* 3.7 21.8 - - + -
271C MET* 4.4 14.1 - - + -
274C ILE* 3.8 24.7 - - + +
293C ILE* 3.6 25.6 - - + -
297C VAL* 3.8 11.0 - - + -
371C ARG 3.1 20.2 + - - +
372C THR 3.7 4.0 - - - +
373C SER 3.2 0.2 - - - -
374C ARG* 1.4 72.9 - - + +
376C LEU* 1.3 61.9 + - - +
377C MET 3.2 0.4 - - - -
378C ASN* 3.3 9.3 + - + +
379C LEU* 3.0 24.9 + - - +
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Residues in contact with LEU 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C VAL* 4.8 15.7 - - + -
290C VAL* 5.0 9.0 - - + -
293C ILE* 5.3 12.3 - - + +
334C PHE* 3.6 34.8 - - + -
338C LEU* 4.8 4.3 - - + -
355C ALA* 4.7 11.9 - - + +
356C HIS 6.1 0.4 - - - +
359C LEU* 3.7 17.7 - - + -
372C THR 2.9 16.6 + - - +
373C SER* 2.9 7.8 + - - +
375C LEU* 1.3 71.7 - - - +
377C MET* 1.3 66.3 + - - +
379C LEU* 3.2 25.2 + - + +
380C ILE* 3.1 44.7 + - + +
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Residues in contact with MET 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352C ALA* 3.6 32.3 - - + +
356C HIS* 3.4 30.0 - - + +
373C SER 2.7 15.4 + - - +
374C ARG* 3.4 20.6 - - + +
376C LEU* 1.3 72.3 - - - +
378C ASN* 1.4 61.8 + - - +
380C ILE* 3.1 10.0 + - - +
381C LEU* 3.0 31.4 + - + +
389C ILE* 3.7 30.5 - - + +
391C ILE* 4.3 14.4 - - + -
418C ILE* 3.9 29.2 - - + -
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Residues in contact with ASN 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C HIS* 3.3 31.3 + - - -
271C MET* 5.8 2.0 - - - +
274C ILE* 6.0 0.2 - - - -
374C ARG 3.2 10.4 + - - +
375C LEU* 3.3 12.4 + - + +
377C MET* 1.4 79.2 - - - +
379C LEU* 1.4 59.1 + - - +
381C LEU* 3.7 7.0 - - - +
382C MET* 2.9 40.8 + - - +
388C PRO* 3.5 21.5 - - + +
389C ILE* 2.9 37.6 + - - +
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Residues in contact with LEU 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ILE* 3.7 21.3 - - + +
278C LEU* 3.8 34.1 - - + +
279C VAL* 4.3 16.4 - - + +
285C VAL* 5.2 13.9 - - + -
289C ASP* 6.1 0.4 - - + -
293C ILE* 4.7 6.5 - - + -
375C LEU 3.0 12.9 + - - +
376C LEU* 3.2 28.9 + - + +
378C ASN* 1.4 74.3 - - - +
380C ILE* 1.4 56.0 + - + +
382C MET* 4.0 3.4 - - - +
383C GLN* 3.0 64.2 + - + +
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Residues in contact with ILE 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C VAL* 5.8 5.6 - - + -
338C LEU* 4.0 22.0 - - + -
348C PRO* 4.1 6.7 - - + +
351C PHE* 3.3 44.4 - - + -
352C ALA* 3.7 21.5 - - + +
355C ALA* 4.3 13.7 - - + -
376C LEU* 3.2 26.9 - - + +
377C MET 3.1 6.7 + - - +
379C LEU* 1.4 77.1 - - + +
381C LEU* 1.3 63.6 + - - +
383C GLN* 3.5 15.8 + - - +
384C ALA* 3.4 18.5 + - - +
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Residues in contact with LEU 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C PRO* 4.1 11.2 - - - +
349C VAL* 4.3 18.2 - - + -
352C ALA* 3.9 17.9 - - + -
377C MET* 3.0 22.2 + - + +
378C ASN* 3.7 14.4 - - - +
379C LEU 3.4 0.2 - - - -
380C ILE* 1.3 73.9 - - - +
382C MET* 1.3 58.1 + - + +
384C ALA* 2.9 21.7 + - - +
385C GLY 3.2 0.5 + - - -
386C TYR* 3.1 41.8 + - + +
387C PRO 4.2 6.3 - - - +
389C ILE* 3.8 41.3 - - + -
418C ILE* 5.8 1.1 - - + -
422C THR* 4.2 8.3 - - + -
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Residues in contact with MET 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C ILE* 6.2 1.6 - - - -
275C ASN* 3.7 26.7 - - - +
279C VAL* 4.6 23.2 - - + +
378C ASN* 2.9 27.9 + - - +
379C LEU* 4.1 3.8 - - - +
381C LEU* 1.3 72.0 - - - +
383C GLN* 1.3 60.8 + - - +
385C GLY* 3.1 13.0 + - - -
386C TYR 3.3 19.5 - - - +
387C PRO* 4.8 0.2 - - + -
388C PRO* 3.7 43.7 - - + -
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Residues in contact with GLN 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C LEU 4.0 4.9 - - - +
279C VAL* 3.3 28.4 - - - +
281C ARG 3.9 12.6 - - - +
283C GLY 5.6 1.7 - - - +
285C VAL* 4.5 17.5 - - - +
379C LEU* 3.0 44.5 + - + +
380C ILE* 3.8 15.1 - - - +
381C LEU 3.3 0.2 - - - -
382C MET* 1.3 75.3 - - - +
384C ALA* 1.3 57.4 + - + +
385C GLY 3.3 0.9 + - - -
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Residues in contact with ALA 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C MET* 5.2 3.1 - - - +
348C PRO* 3.8 32.9 - - + +
380C ILE* 3.4 7.5 + - + +
381C LEU 2.9 10.8 + - - +
383C GLN* 1.3 75.8 - - - +
385C GLY* 1.3 61.4 + - - +
386C TYR* 3.6 9.6 - - - -
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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
------------------------------------------------------------
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