Contacts of the helix formed by residues 335 - 347 (chain C) in PDB entry 2QPA
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 335 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175C PRO 4.3 7.0 - - - -
176C GLY* 2.9 28.2 + - - -
177C THR* 5.7 1.6 - - - -
298C LEU* 4.8 10.9 - - - +
299C PRO* 4.4 6.1 - - - -
333C GLY 4.0 2.0 + - - -
334C TYR* 1.3 77.7 - - - +
336C GLY* 1.3 73.5 + - - +
337C SER* 2.9 14.1 + - - -
338C ASP* 2.7 30.8 + - - +
339C ILE* 3.4 14.4 + - - +
416C THR* 5.2 5.2 - - - -
417C VAL* 5.5 4.0 - - - +
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Residues in contact with GLY 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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176C GLY 3.5 9.5 + - - -
177C THR* 5.1 1.0 - - - +
299C PRO* 4.2 7.3 - - - +
307C MET* 3.4 37.9 - - - +
311C ASN* 4.7 1.0 - - - +
335C SER* 1.3 76.3 + - - +
337C SER* 1.3 57.6 + - - -
338C ASP 3.2 0.2 - - - -
339C ILE* 3.7 3.7 + - - +
340C ALA* 3.1 25.5 + - - +
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Residues in contact with SER 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C GLY* 3.3 20.2 + - - -
335C SER* 2.9 8.8 + - - -
336C GLY* 1.3 76.1 - - - +
338C ASP* 1.3 57.1 + - - +
340C ALA* 3.1 10.2 - - - +
341C VAL* 2.7 40.8 + - - +
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Residues in contact with ASP 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334C TYR* 3.6 24.7 - - + -
335C SER* 2.7 36.9 + - - +
336C GLY 3.2 0.2 - - - -
337C SER* 1.3 75.7 - - - +
339C ILE* 1.3 54.6 + - - +
340C ALA 3.0 0.9 - - - -
341C VAL* 2.6 30.1 + - - +
342C VAL* 2.7 22.7 + - + +
413C THR* 5.4 6.1 - - + +
414C ARG 4.9 2.5 - - - +
415C PRO* 4.2 2.0 - - - +
416C THR* 2.5 41.3 + - - -
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Residues in contact with ILE 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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304C ARG* 3.5 49.8 - - + +
307C MET* 3.9 13.9 - - + -
308C PHE* 3.8 48.2 - - + +
311C ASN* 3.6 12.1 - - - +
331C THR* 4.2 10.3 - - + -
334C TYR* 4.2 3.8 - - + +
335C SER 3.4 13.1 + - - +
336C GLY 4.0 7.0 - - - +
338C ASP* 1.3 76.0 - - - +
340C ALA* 1.3 62.4 + - - +
342C VAL* 3.8 8.2 - - - +
343C VAL* 3.0 30.8 + - - +
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Residues in contact with ALA 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C ASN* 3.0 24.3 + - - +
336C GLY 3.1 16.4 + - - +
337C SER* 3.1 18.2 - - - +
338C ASP 3.0 0.2 - - - -
339C ILE* 1.3 77.1 - - - +
341C VAL* 1.3 58.4 + - + +
343C VAL* 4.3 1.0 - - - +
344C LYS* 3.5 22.6 + - - +
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Residues in contact with VAL 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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337C SER* 2.7 25.8 - - - +
338C ASP* 2.6 16.9 + - - +
340C ALA* 1.3 73.3 - - + +
342C VAL* 1.3 66.1 + - + +
343C VAL 3.2 1.3 - - - -
344C LYS* 3.5 4.4 + - - +
345C ASP* 3.3 23.7 + - + +
413C THR* 4.7 19.5 - - + +
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Residues in contact with VAL 342 (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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308C PHE* 4.1 16.2 - - + -
331C THR* 5.8 0.2 - - + -
334C TYR* 4.5 19.5 - - + -
338C ASP 2.7 25.7 + - - +
339C ILE* 3.8 8.1 - - - +
341C VAL* 1.3 71.8 - - - +
343C VAL* 1.3 58.5 + - - +
345C ASP* 3.3 5.9 + - - +
346C ALA* 3.0 24.1 + - - +
406C PHE* 4.3 6.5 - - + +
409C ALA* 3.6 20.2 - - + +
410C ILE* 3.7 35.2 - - + +
413C THR* 4.6 15.7 - - + -
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Residues in contact with VAL 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C PHE* 3.4 32.3 - - + +
311C ASN* 3.4 24.0 - - + +
312C VAL* 3.4 42.8 - - + +
339C ILE* 3.0 17.9 + - + +
342C VAL* 1.3 71.9 - - - +
344C LYS* 1.3 56.6 + - - +
345C ASP 2.6 17.1 + - - -
346C ALA* 2.9 10.9 + - - +
347C LEU* 3.0 21.9 + - + +
406C PHE* 4.2 10.3 - - + -
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Residues in contact with LYS 344 (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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340C ALA 3.5 17.5 + - - +
341C VAL* 3.5 5.4 + - - +
343C VAL* 1.3 77.7 - - - +
345C ASP* 1.3 56.9 + - - +
347C LEU* 3.8 17.6 - - + +
348C MET* 4.0 22.5 - - - +
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Residues in contact with ASP 345 (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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341C VAL* 3.3 18.2 + - + +
342C VAL* 3.4 4.5 - - - +
343C VAL 2.6 5.9 + - - -
344C LYS* 1.3 75.0 - - - +
346C ALA* 1.3 67.6 + - - +
347C LEU 3.3 0.7 - - - -
348C MET* 3.4 13.9 + - - +
349C GLN* 3.6 22.7 + - - +
409C ALA* 3.2 24.2 - - + +
412C SER* 5.3 6.1 - - - -
413C THR* 6.1 1.6 - - - +
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Residues in contact with ALA 346 (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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342C VAL 3.0 9.7 + - - +
343C VAL 2.9 2.1 + - - +
345C ASP* 1.3 75.4 + - - +
347C LEU* 1.3 55.0 + - - +
348C MET 2.6 6.2 + - - -
349C GLN* 2.5 39.3 + - - +
350C PRO* 3.5 4.0 - - - +
401C LEU* 4.3 4.9 - - - +
405C ASP* 3.9 4.9 - - + +
406C PHE* 3.6 55.9 - - + +
409C ALA* 4.2 1.3 - - + -
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Residues in contact with LEU 347 (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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311C ASN 4.7 4.3 - - - +
312C VAL* 4.0 17.0 - - + +
315C THR* 3.3 44.3 - - + +
343C VAL* 3.0 34.9 + - + +
344C LYS* 3.8 18.2 - - + +
346C ALA* 1.3 75.3 - - - +
348C MET* 1.3 64.0 + - + +
350C PRO* 3.4 17.6 - - - +
351C ILE* 5.1 3.5 - - - +
401C LEU* 4.6 14.1 - - + +
406C PHE* 5.3 3.2 - - + -
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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