Contacts of the helix formed by residues 371 - 383 (chain C) in PDB entry 1C2O
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 SER 371 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364C ARG* 3.6 2.5 - - - +
369C GLN 3.4 4.2 + - - -
370C ALA* 1.3 78.4 - - - +
372C ASP* 1.3 60.2 + - - +
373C LEU* 3.5 3.5 + - - +
374C ALA* 3.2 15.9 + - - +
375C ALA* 2.9 25.8 + - - +
540C LEU* 3.6 6.3 - - - +
543C THR* 2.9 41.3 + - - -
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Residues in contact with ASP 372 (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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364C ARG* 2.9 34.3 + - - +
371C SER* 1.3 71.3 - - - +
373C LEU* 1.3 69.3 + - - +
375C ALA* 2.8 5.0 + - - +
376C GLU* 2.7 31.1 + - - +
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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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373B LEU* 6.1 1.1 - - + -
535B PHE* 4.2 21.4 - - + -
538B LYS* 5.4 13.7 - - + +
539B LEU* 4.7 14.8 - - + -
542B ALA* 4.8 14.4 - - + -
371C SER* 3.5 6.2 + - - +
372C ASP* 1.3 77.6 - - - +
374C ALA* 1.4 59.5 + - - +
376C GLU* 2.9 19.8 + - + +
377C ALA* 2.8 27.0 + - - +
539C LEU* 4.1 19.0 - - + +
543C THR* 4.1 22.4 - - + -
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Residues in contact with ALA 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C ALA* 4.0 5.4 - - + -
371C SER* 3.2 12.3 + - - +
372C ASP 3.1 0.6 - - - -
373C LEU* 1.4 77.8 - - - +
375C ALA* 1.3 63.7 + - - +
377C ALA* 3.1 4.2 + - - +
378C VAL* 2.9 26.8 + - - +
536C LEU* 3.8 15.2 - - + +
539C LEU* 3.7 16.3 - - + +
540C LEU* 3.2 35.2 - - + -
543C THR* 4.9 0.4 + - - +
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Residues in contact with ALA 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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363C VAL* 4.2 9.4 - - + +
364C ARG* 3.4 36.8 - - - +
370C ALA* 4.0 6.9 - - + +
371C SER 2.9 14.5 + - - +
372C ASP 2.8 9.5 + - - +
374C ALA* 1.3 75.1 - - - +
376C GLU* 1.3 65.7 + - - +
378C VAL* 2.9 10.2 + - - +
379C VAL* 2.8 27.2 + - + +
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Residues in contact with GLU 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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535B PHE* 4.8 14.1 - - + -
538B LYS* 4.9 22.0 + - + +
372C ASP* 2.7 21.8 + - - +
373C LEU* 3.0 27.2 - - + +
375C ALA* 1.3 71.2 - - - +
377C ALA* 1.3 64.8 + - - +
379C VAL* 2.8 10.1 + - + +
380C LEU* 2.7 24.6 + - - +
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Residues in contact with ALA 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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535B PHE* 4.7 14.0 - - + -
373C LEU 2.8 9.5 + - - +
374C ALA* 3.2 9.0 - - - +
376C GLU* 1.3 72.7 - - - +
378C VAL* 1.3 58.0 + - - +
380C LEU* 3.1 9.9 + - - +
381C HIS* 2.9 28.6 + - - +
531C PHE* 3.8 22.5 - - + -
535C PHE* 4.7 4.7 - - + -
536C LEU* 4.4 1.1 - - + -
539C LEU* 3.7 26.9 - - + -
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Residues in contact with VAL 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C VAL* 4.1 14.1 - - + -
367C VAL* 4.7 9.0 - - + -
374C ALA 2.9 17.3 + - - +
375C ALA* 3.4 7.9 - - - +
377C ALA* 1.3 74.2 - - - +
379C VAL* 1.3 64.6 + - - +
381C HIS 3.2 1.0 + - - -
382C TYR* 2.9 35.8 + - + +
401C VAL* 3.8 32.3 - - + -
531C PHE* 3.8 15.7 - - + -
532C TRP* 4.0 23.6 - - + -
536C LEU* 4.6 7.0 - - + -
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Residues in contact with VAL 379 (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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356C ARG* 3.4 16.8 - - - +
359C PHE* 3.8 11.0 - - + -
360C LEU* 3.7 26.9 - - + +
363C VAL* 4.2 22.0 - - + -
364C ARG* 6.4 0.4 - - - -
375C ALA* 2.8 26.6 + - + +
376C GLU* 3.6 8.7 - - + +
378C VAL* 1.3 72.3 - - - +
380C LEU* 1.3 55.8 + - - +
382C TYR 4.5 0.2 - - - +
383C THR* 2.6 54.7 + - - +
385C TRP* 5.1 2.5 - - + -
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Residues in contact with LEU 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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381B HIS* 5.7 5.2 - - + +
527B GLN* 4.9 2.8 - - + +
530B ALA* 4.7 0.7 - - + -
531B PHE* 4.1 32.3 - - + +
535B PHE* 3.7 41.7 - - + -
376C GLU 2.7 16.2 + - - +
377C ALA* 3.2 11.9 - - - +
379C VAL* 1.3 74.7 - - - +
381C HIS* 1.3 68.1 + - + +
383C THR 3.6 3.8 + - - +
385C TRP* 3.2 42.9 + - + +
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Residues in contact with HIS 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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380B LEU* 5.5 6.9 - - + +
527B GLN* 6.1 0.5 - - - +
377C ALA 2.9 12.0 + - - +
378C VAL 3.7 3.6 - - - +
380C LEU* 1.3 88.2 - - + +
382C TYR* 1.3 87.5 + + + +
383C THR 4.4 2.4 - - - +
527C GLN* 4.8 7.0 - - + -
528C THR* 3.2 39.5 + - - -
531C PHE* 4.0 31.8 - + + +
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Residues in contact with TYR 382 (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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359C PHE* 4.2 13.5 - - + -
378C VAL* 2.9 27.6 + - + +
381C HIS* 1.3 93.4 - + + +
383C THR* 1.3 64.8 + - - +
393C HIS* 3.3 21.5 + - - -
397C ALA* 3.9 16.8 - - + +
400C ALA* 3.6 17.3 - - + -
401C VAL* 3.6 32.3 - - + -
404C ASP* 2.6 28.9 + - - +
528C THR* 3.2 8.5 - - + +
531C PHE* 4.4 1.6 - + - -
532C TRP* 2.6 45.8 + + - -
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Residues in contact with THR 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B GLN* 4.0 5.5 + - - +
356C ARG* 2.8 44.2 + - - +
359C PHE* 4.5 5.3 - - - -
379C VAL* 2.6 33.2 + - - +
380C LEU 3.6 3.0 + - - +
381C HIS 3.5 2.8 - - - +
382C TYR* 1.3 73.7 - - - +
384C ASP* 1.3 68.7 + - - +
385C TRP* 3.5 48.9 + - + -
388C PRO* 4.0 5.2 - - + -
393C HIS* 4.5 1.6 - - - -
394C LEU* 6.1 2.9 - - - -
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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
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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