Contacts of the helix formed by residues 363 - 375 (chain C) in PDB entry 2XSD
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 363 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361C LYS 3.9 2.2 + - - -
362C PRO* 1.3 74.0 - - - +
364C ALA* 1.3 54.4 + - - +
365C HIS* 2.9 17.0 + - - +
366C GLU* 2.9 35.2 + - - +
367C ILE* 2.8 32.5 + - - +
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Residues in contact with ALA 364 (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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202B C 4.3 30.7 - - - +
362C PRO 3.9 0.2 + - - -
363C SER* 1.3 73.1 - - - +
365C HIS* 1.3 64.5 + - + +
367C ILE* 4.0 13.2 - - - +
368C THR* 3.0 27.4 + - - +
378C LYS* 4.1 14.2 + - - +
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Residues in contact with HIS 365 (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 SER* 2.9 11.4 + - - +
364C ALA* 1.3 86.1 - - + +
366C GLU* 1.3 57.3 + - - +
367C ILE 3.1 0.9 - - - -
368C THR* 3.1 10.5 - - - +
369C GLY* 2.7 32.4 + - - -
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Residues in contact with GLU 366 (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 CYS* 5.4 10.5 - - - +
362C PRO* 3.7 16.4 - - + -
363C SER* 2.9 35.5 + - - +
365C HIS* 1.3 76.0 - - - +
367C ILE* 1.3 53.0 + - - +
369C GLY* 3.2 1.0 + - - -
370C LEU* 2.7 38.3 + - - +
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Residues in contact with ILE 367 (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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202B C 5.0 3.1 - - - +
203B C 3.6 18.4 - - - +
362C PRO* 3.6 34.3 - - + +
363C SER 2.8 19.6 + - - +
364C ALA* 4.0 9.2 - - - +
366C GLU* 1.3 74.7 - - - +
368C THR* 1.3 68.0 + - - +
369C GLY 3.1 0.2 + - - -
370C LEU* 3.7 2.7 - - - +
371C ALA* 2.8 24.8 + - - +
378C LYS* 3.8 33.7 - - + +
381C VAL* 4.2 11.6 - - + +
382C ARG* 4.0 29.2 - - + +
385C PHE* 5.7 2.5 - - + -
389C ARG* 5.2 1.3 - - - +
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Residues in contact with THR 368 (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 ALA 3.0 20.9 + - - +
365C HIS* 3.1 20.2 - - + +
367C ILE* 1.3 77.9 - - - +
369C GLY* 1.3 67.1 + - - +
371C ALA* 3.4 7.7 + - - +
372C ASP* 3.3 31.7 + - - +
378C LYS* 4.0 24.0 - - - +
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Residues in contact with GLY 369 (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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365C HIS 2.7 23.2 + - - -
366C GLU* 3.5 1.6 - - - -
368C THR* 1.3 78.0 - - - +
370C LEU* 1.3 59.3 + - - +
372C ASP* 4.3 1.6 - - - +
373C SER* 2.9 24.9 + - - -
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Residues in contact with LEU 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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352C LEU* 3.5 32.1 - - + -
355C HIS* 3.4 46.0 - - + +
366C GLU 2.7 19.9 + - - +
367C ILE* 3.9 2.7 - - - +
369C GLY* 1.3 72.2 - - - -
371C ALA* 1.3 58.4 + - - +
373C SER* 2.8 19.5 + - - +
374C LEU* 2.9 37.7 + - + +
381C VAL* 3.7 16.4 - - + -
385C PHE* 4.3 11.4 - - + -
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Residues in contact with ALA 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 ILE 2.8 17.7 + - - +
368C THR 3.5 7.0 - - - +
369C GLY 3.2 0.2 - - - -
370C LEU* 1.3 78.4 - - - +
372C ASP* 1.3 54.9 + - - +
374C LEU* 3.1 1.6 + - - +
375C GLN 2.7 30.3 + - - -
376C LEU* 2.8 27.6 + - - +
378C LYS* 3.6 24.0 - - + +
381C VAL* 3.6 17.0 - - + -
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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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368C THR* 3.3 23.6 + - - +
369C GLY 4.4 1.6 - - - +
371C ALA* 1.3 78.4 - - - +
373C SER* 1.3 58.9 + - - +
375C GLN* 2.8 26.5 + - - +
376C LEU 4.0 8.5 - - - +
377C GLU* 5.6 0.2 - - - -
378C LYS* 5.2 2.9 + - - +
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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
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369C GLY 2.9 15.4 + - - -
370C LEU* 2.8 26.9 + - - +
372C ASP* 1.3 79.2 - - - +
374C LEU* 1.3 57.9 + - - +
375C GLN* 5.0 1.6 - - - +
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Residues in contact with LEU 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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347C GLY 5.3 0.9 - - - +
348C VAL* 3.3 55.1 - - + +
351C ALA* 4.5 15.0 - - + -
352C LEU* 3.7 26.9 - - + +
355C HIS* 6.1 0.4 - - + -
370C LEU* 2.9 29.4 + - + +
371C ALA 3.7 2.0 - - - +
373C SER* 1.3 76.6 - - - +
375C GLN* 1.3 71.3 + - - +
376C LEU* 4.1 7.4 - - + +
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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 ALA 2.7 5.3 + - - -
372C ASP* 2.8 18.0 + - - +
373C SER 5.3 1.3 - - - +
374C LEU* 1.3 82.2 - - - +
376C LEU* 1.3 67.6 + - - +
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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
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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