Contacts of the helix formed by residues 361 - 376 (chain C) in PDB entry 3UO8
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 ALA 361 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360C LYS* 1.3 73.8 - - + +
362C PRO* 1.3 70.0 - - - +
363C LEU 3.0 3.7 + - - -
364C VAL* 3.2 9.0 + - - +
365C ASP* 2.9 26.4 + - - +
500C GLU* 3.1 25.8 + - + +
501C ILE 5.9 0.2 - - - +
504C SER* 5.5 3.4 - - - +
507C ALA 3.7 14.1 - - - +
508C ASN 4.1 0.4 - - - -
509C GLY 3.7 24.2 - - - +
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Residues in contact with PRO 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C GLY* 4.0 7.6 - - - -
350C ASN 3.6 11.4 - - - +
351C MET* 3.4 23.3 - - + -
359C LEU* 3.7 13.2 - - + -
360C LYS 3.2 12.3 - - - +
361C ALA* 1.3 90.1 - - - +
363C LEU* 1.3 61.0 - - - +
365C ASP* 4.1 7.6 - - + +
366C VAL* 2.9 28.8 + - - +
384C LEU* 4.8 1.3 - - - -
413C ALA* 3.9 29.6 - - + +
500C GLU* 3.4 12.3 - - - +
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Residues in contact with LEU 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C MET* 3.6 24.7 - - + -
360C LYS 3.8 7.9 - - - +
361C ALA 3.0 0.6 - - - -
362C PRO* 1.3 80.0 - - - +
364C VAL* 1.3 63.1 + - + +
366C VAL 3.4 0.2 + - - -
367C TYR* 3.0 26.8 + - + +
384C LEU* 4.1 21.1 - - + -
607C GLU* 4.2 15.9 - - + +
608C PHE* 3.3 30.2 - - + -
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Residues in contact with VAL 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LYS 5.3 0.7 - - - +
361C ALA* 3.3 14.1 - - - +
363C LEU* 1.3 81.3 - - + +
365C ASP* 1.3 68.9 + - - +
367C TYR* 4.3 7.2 - - + -
368C GLU* 3.0 51.2 + - + +
506C LEU* 3.6 29.8 - - + +
507C ALA 3.3 29.4 - - - +
508C ASN* 3.9 7.0 - - - +
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Residues in contact with ASP 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C ALA* 2.9 21.5 + - - +
362C PRO* 3.8 7.9 - - + +
364C VAL* 1.3 78.5 - - - +
366C VAL* 1.3 62.2 + - - +
369C LEU* 3.1 26.7 + - - +
411C TYR* 3.4 23.2 + - + +
413C ALA* 4.8 2.1 - - - +
462C ASP* 3.8 7.4 - - - +
508C ASN* 3.1 20.8 - - - +
509C GLY* 2.9 35.7 + - - -
512C MET* 3.5 19.4 - - + +
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Residues in contact with VAL 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C LEU* 3.7 13.7 - - + +
348C ILE 3.9 3.6 - - - -
349C GLY* 3.7 28.3 - - - +
362C PRO 2.9 20.8 + - - +
363C LEU 4.0 1.8 - - - +
365C ASP* 1.3 73.0 - - - +
367C TYR* 1.3 67.9 + - - +
370C THR* 2.8 31.3 + - - +
382C SER* 3.7 23.8 - - - -
383C LEU 4.7 4.0 - - - +
384C LEU* 5.9 2.0 - - + -
411C TYR* 3.8 25.4 - - + -
413C ALA* 4.7 0.4 - - + -
608C PHE* 3.6 19.1 - - + -
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Residues in contact with TYR 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C LEU* 3.0 21.0 + - + +
364C VAL* 3.8 9.4 - - + +
365C ASP 3.4 0.2 - - - -
366C VAL* 1.3 80.7 - - - +
368C GLU* 1.3 71.0 + - + +
370C THR* 3.3 5.9 + - - -
371C ASN* 3.2 47.6 + - - -
606C ALA 5.0 4.6 + - - -
607C GLU* 3.4 39.0 - - + -
608C PHE* 3.6 14.8 - + + -
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Residues in contact with GLU 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C VAL* 3.0 32.3 + - + +
365C ASP 4.3 1.3 - - - +
367C TYR* 1.3 83.7 - - + +
369C LEU* 1.3 65.6 + - - +
371C ASN* 3.4 7.7 + - - +
372C LEU* 3.1 32.4 + - + +
506C LEU 4.8 2.3 - - - +
508C ASN* 2.6 29.4 + - - +
512C MET* 4.8 4.2 - - + +
516C LYS* 3.0 34.2 + - + +
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Residues in contact with LEU 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C LEU* 3.9 9.2 - - + -
365C ASP 3.1 19.0 + - - +
366C VAL* 4.7 0.2 - - - -
368C GLU* 1.3 73.9 - - - +
370C THR* 1.3 67.3 + - - +
372C LEU* 3.3 4.2 + - + -
373C LEU* 2.9 36.8 + - + +
411C TYR* 3.3 49.1 - - + -
460C LEU* 4.7 8.1 - - + -
512C MET* 3.7 22.7 - - + -
515C LEU* 4.1 9.0 - - + -
519C LEU* 3.2 33.9 - - + -
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Residues in contact with THR 370 (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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347C LEU* 3.1 13.6 - - - +
366C VAL 2.8 23.8 + - - -
367C TYR* 3.4 7.0 - - - -
369C LEU* 1.3 78.1 - - - +
371C ASN* 1.3 61.2 + - - +
373C LEU* 3.8 2.0 - - - +
374C ARG* 2.9 64.9 + - - +
380C VAL* 3.8 14.7 - - + +
382C SER* 3.1 28.8 - - - +
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Residues in contact with ASN 371 (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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367C TYR* 3.2 45.0 + - - +
368C GLU* 3.7 8.4 - - - +
369C LEU 3.3 0.2 - - - -
370C THR* 1.3 89.3 - - - +
372C LEU* 1.3 62.1 + - + +
374C ARG* 3.3 16.4 + - - +
375C GLN* 3.0 31.9 + - - +
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Residues in contact with LEU 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C GLU* 3.1 26.8 + - + +
369C LEU* 3.3 6.9 + - + +
371C ASN* 1.3 75.0 - - + +
373C LEU* 1.3 63.8 + - - +
375C GLN* 3.1 30.3 + - - +
376C LEU* 3.1 16.3 + - - +
512C MET* 5.2 0.7 - - - -
516C LYS* 3.7 43.3 - - + +
519C LEU* 3.5 27.6 - - + -
520C LEU* 3.8 25.3 - - + +
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Residues in contact with LEU 373 (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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345C ALA* 3.9 12.1 - - + -
347C LEU* 3.8 30.3 - - + -
369C LEU* 2.9 29.5 + - + +
372C LEU* 1.3 76.0 - - - +
374C ARG* 1.3 58.0 + - - +
376C LEU* 3.0 28.4 + - + +
378C PHE* 3.0 54.2 + - + +
380C VAL* 3.6 15.5 - - + -
409C LEU* 3.9 21.5 - - + -
519C LEU* 4.4 11.4 - - + -
560C LEU* 4.5 3.1 - - + -
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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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370C THR* 2.9 42.7 + - - +
371C ASN* 3.7 16.1 - - - +
373C LEU* 1.3 72.6 - - - +
375C GLN* 1.3 65.9 + - - +
377C ASP* 3.0 16.1 + - - +
378C PHE 4.0 10.5 - - - +
380C VAL* 3.1 39.1 + - + +
382C SER* 5.0 2.8 + - - -
584C HIS* 3.6 50.3 + - - +
609C SER* 4.7 9.3 + - - -
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Residues in contact with GLN 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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371C ASN* 3.0 24.3 + - + +
372C LEU* 3.3 24.9 - - - +
374C ARG* 1.3 75.8 - - - +
376C LEU* 1.3 59.2 + - - +
377C ASP* 3.3 11.3 + - - +
520C LEU* 3.5 30.4 - - + +
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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
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343C LYS* 2.7 34.1 + - - -
372C LEU 3.1 13.6 + - - +
373C LEU* 3.0 24.6 + - + +
375C GLN* 1.3 75.6 - - - +
377C ASP* 1.3 63.1 + - - +
378C PHE* 3.2 9.4 - - + -
519C LEU* 3.9 20.9 - - + +
520C LEU* 4.0 20.6 - - + +
560C LEU* 3.8 32.3 - - + +
561C THR* 3.7 31.9 - - + +
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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
------------------------------------------------------------
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