Contacts of the helix formed by residues 326 - 341 (chain C) in PDB entry 2P82
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 GLU 326 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220C TRP* 3.4 18.2 + - + -
324C CYS 4.1 1.4 - - - -
325C LYS* 1.3 91.1 - - + +
327C GLU* 1.3 67.5 + - - +
328C LYS* 3.2 32.4 + - + +
329C ASP* 2.8 30.0 + - - +
330C PHE 3.4 4.9 + - - -
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Residues in contact with GLU 327 (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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183C LYS* 2.7 34.2 + - - +
187C ARG* 2.8 33.5 + - - +
220C TRP* 3.6 43.0 - - + +
326C GLU* 1.3 74.4 - - - +
328C LYS* 1.3 58.7 + - - +
330C PHE* 3.1 4.0 + - - +
331C ASP* 2.9 33.5 + - - +
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Residues in contact with LYS 328 (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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326C GLU* 3.7 32.0 + - + +
327C GLU* 1.3 78.3 - - - +
329C ASP* 1.3 80.7 + - - +
331C ASP* 3.8 10.0 - - - +
332C ASN* 3.0 29.1 + - - +
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Residues in contact with ASP 329 (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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252C GLN* 3.2 20.5 + - + +
323C PHE 5.0 0.4 - - - +
324C CYS* 3.9 19.3 - - - -
325C LYS* 3.5 11.8 + - - +
326C GLU* 2.8 38.6 + - - +
328C LYS* 1.3 98.0 + - - +
330C PHE* 1.3 59.2 + - - +
332C ASN* 3.6 3.5 + - - -
333C TRP* 3.0 24.6 + - - +
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Residues in contact with PHE 330 (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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179C ILE* 3.8 29.8 - - + -
182C ILE* 3.5 41.7 - - + -
183C LYS* 4.0 14.1 - - - -
220C TRP* 3.8 32.3 - + + -
223C LEU* 4.1 13.5 - - + -
225C LEU* 3.9 4.0 - - + -
324C CYS* 3.7 12.3 - - + +
326C GLU 3.4 2.2 + - - -
327C GLU 3.1 7.0 + - - +
329C ASP* 1.3 75.1 - - - +
331C ASP* 1.3 63.5 + - - +
333C TRP* 3.2 28.4 + + - +
334C CYS* 2.9 48.3 + - - -
351C LEU* 5.0 0.7 - - + -
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Residues in contact with ASP 331 (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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183C LYS* 3.0 34.5 + - - -
327C GLU* 2.9 26.7 + - - +
328C LYS* 3.8 9.0 - - - +
330C PHE* 1.3 78.3 - - - +
332C ASN* 1.3 62.4 + - - +
334C CYS* 3.3 9.9 + - - +
335C SER* 3.2 23.3 + - - -
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Residues in contact with ASN 332 (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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251C PRO* 4.2 6.9 - - - +
252C GLN* 2.9 21.4 + - - +
328C LYS 3.0 19.6 + - - +
329C ASP* 3.8 5.4 - - - +
330C PHE 3.3 0.2 - - - -
331C ASP* 1.3 75.7 - - - +
333C TRP* 1.3 61.3 + - - +
335C SER* 3.2 11.3 + - - -
336C LEU* 3.0 42.7 + - - +
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Residues in contact with TRP 333 (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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177C VAL* 4.0 13.9 - - + -
225C LEU* 3.6 25.6 - - + -
227C VAL* 4.9 0.4 - - + -
250C MET* 3.8 15.0 - - - -
252C GLN* 3.5 24.8 - - + +
322C PHE* 3.2 60.1 - + - -
324C CYS* 4.4 3.8 - - - -
329C ASP 3.0 15.7 + - - +
330C PHE* 3.2 31.2 + + - +
332C ASN* 1.3 74.6 - - - +
334C CYS* 1.3 72.0 + - - +
336C LEU* 3.1 5.9 + - - +
337C VAL* 2.8 54.4 + - + +
349C PHE* 4.0 19.3 - + - -
351C LEU* 3.8 19.7 - - + -
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Residues in contact with CYS 334 (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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179C ILE* 3.2 33.4 - - + -
330C PHE* 2.9 39.8 + - - -
331C ASP* 3.4 13.0 - - - +
333C TRP* 1.3 81.0 - - - +
335C SER* 1.3 56.3 + - - +
337C VAL* 3.3 2.3 + - - +
338C GLN* 2.8 45.2 + - - +
351C LEU* 3.8 13.9 - - + +
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Residues in contact with SER 335 (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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331C ASP 3.2 9.2 + - - -
332C ASN* 3.2 16.0 + - - -
334C CYS* 1.3 77.3 - - - +
336C LEU* 1.3 61.1 + - - +
338C GLN* 3.5 14.8 + - - +
339C LYS* 3.0 29.6 + - - +
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Residues in contact with LEU 336 (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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250C MET* 3.9 23.6 - - + -
251C PRO* 3.7 27.1 - - + -
252C GLN* 3.7 10.5 - - - +
332C ASN* 3.0 40.0 + - - +
333C TRP* 3.6 5.4 - - - +
335C SER* 1.3 74.8 - - - +
337C VAL* 1.3 57.4 + - - +
339C LYS* 3.4 9.8 + - + +
340C GLU* 2.8 45.1 + - + +
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Residues in contact with VAL 337 (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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250C MET* 4.2 9.4 - - + -
333C TRP* 2.8 58.6 + - + +
334C CYS 3.6 3.8 - - - +
336C LEU* 1.3 72.3 - - - +
338C GLN* 1.3 62.5 + - - +
341C ILE* 2.8 41.6 + - + -
342C LEU* 3.0 21.2 + - + -
349C PHE* 3.9 24.9 - - + -
351C LEU* 3.9 18.8 - - + -
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Residues in contact with GLN 338 (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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179C ILE* 5.5 3.4 - - - +
334C CYS* 2.8 34.1 + - - +
335C SER* 3.6 17.3 + - - +
337C VAL* 1.3 72.7 - - - +
339C LYS* 1.3 62.0 + - - +
342C LEU* 3.7 36.4 - - + +
343C LYS* 3.9 6.2 + - - +
351C LEU* 4.1 14.4 + - + +
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Residues in contact with LYS 339 (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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335C SER 3.0 18.1 + - - +
336C LEU* 3.7 11.7 - - + +
338C GLN* 1.3 77.5 - - - +
340C GLU* 1.3 82.8 + - + +
343C LYS* 3.4 28.2 - - - +
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Residues in contact with GLU 340 (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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243C ALA* 4.8 3.5 - - - +
246C GLU* 3.6 46.3 - - + +
250C MET* 4.6 6.3 - - + -
336C LEU* 2.8 27.0 + - + +
339C LYS* 1.3 109.5 + - + +
341C ILE* 1.3 66.4 + - + +
343C LYS* 3.5 35.4 + - - +
344C GLU* 4.5 4.9 - - - +
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Residues in contact with ILE 341 (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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243C ALA* 3.4 34.7 - - + +
246C GLU* 4.2 4.0 - - + -
247C CYS* 4.0 14.1 - - - -
250C MET* 3.9 14.8 - - + -
337C VAL* 2.8 30.4 + - + +
340C GLU* 1.3 83.5 - - - +
342C LEU* 1.3 64.2 + - + +
343C LYS 3.2 5.1 + - - -
344C GLU* 3.4 20.1 + - - +
347C ARG* 4.2 6.6 - - - +
348C MET* 4.4 10.4 + - + +
349C PHE* 3.9 47.3 - - + +
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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
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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