Contacts of the helix formed by residues 335 - 348 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175B PRO 3.7 6.9 + - - -
176B GLY* 3.6 20.4 - - - -
177B THR 4.6 0.2 - - - -
298B LEU* 3.5 17.9 - - - -
299B PRO* 4.1 5.2 - - - -
334B TYR* 1.3 76.0 - - - +
336B GLY* 1.3 67.0 + - - +
337B SER* 3.1 9.0 + - - -
338B ASP* 2.7 46.0 + - - -
339B ILE* 3.0 12.5 + - - +
416B THR* 4.5 1.3 - - - -
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Residues in contact with GLY 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B GLY 3.1 11.1 + - - -
177B THR* 4.8 0.4 - - - +
299B PRO* 4.0 5.7 - - - +
307B MET* 3.1 41.4 - - - +
311B ASN* 5.1 2.4 - - - +
335B SER* 1.3 73.6 - - - +
337B SER* 1.3 63.8 + - - +
339B ILE* 3.5 4.4 + - - +
340B ALA* 3.2 16.3 + - - +
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Residues in contact with SER 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLY* 3.1 22.3 + - - -
335B SER* 2.9 8.9 + - - -
336B GLY* 1.3 75.2 - - - +
338B ASP* 1.3 58.7 + - - -
340B ALA* 2.6 36.7 + - - +
341B VAL* 3.0 11.7 + - - +
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Residues in contact with ASP 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B GLY 4.7 0.7 - - - +
334B TYR* 3.6 22.7 - - + -
335B SER* 2.7 33.2 + - - +
337B SER* 1.3 73.7 - - - +
339B ILE* 1.3 65.0 + - - +
341B VAL* 2.9 15.5 + - - +
342B VAL* 2.8 24.3 + - - +
413B THR* 5.3 3.4 - - + +
414B ARG 5.0 2.5 - - - +
415B PRO* 3.8 6.2 - - - +
416B THR* 3.2 51.0 + - - +
417B VAL* 5.7 0.2 - - - +
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Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B PRO* 4.8 0.7 - - + -
304B ARG* 3.6 50.9 - - + +
307B MET* 4.2 17.7 - - + +
308B PHE* 3.8 48.5 - - + +
311B ASN* 4.6 1.6 - - - +
331B THR* 4.3 1.1 - - - +
334B TYR* 3.9 16.2 - - + -
335B SER 3.0 13.4 + - - +
336B GLY 3.8 7.9 - - - +
338B ASP* 1.3 74.7 - - - +
340B ALA* 1.3 57.9 + - - +
342B VAL* 3.1 8.8 + - - +
343B VAL* 2.8 32.0 + - + +
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Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B ASN* 3.0 30.4 + - - +
336B GLY 3.2 9.2 + - - +
337B SER* 2.6 23.1 + - - +
339B ILE* 1.3 72.4 - - - +
341B VAL* 1.3 57.7 + - + +
343B VAL 3.5 0.5 + - - -
344B LYS* 2.9 29.8 + - - +
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B SER* 3.2 18.4 - - - +
338B ASP* 3.3 15.3 - - - +
340B ALA* 1.3 72.1 - - + +
342B VAL* 1.3 68.9 + - + +
344B LYS* 3.0 8.9 + - + +
345B ASP* 3.0 24.6 + - + +
413B THR* 5.4 9.6 - - + +
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Residues in contact with VAL 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 3.8 19.7 - - + -
334B TYR* 3.4 30.7 - - + -
338B ASP 2.8 16.9 + - - +
339B ILE* 3.2 10.8 - - - +
341B VAL* 1.3 76.8 - - - +
343B VAL* 1.3 63.7 + - - +
345B ASP* 3.2 5.6 + - - +
346B ALA* 3.0 18.9 + - - +
406B PHE* 4.2 3.6 - - + +
409B ALA* 3.6 14.9 - - + +
410B ILE* 3.7 28.9 - - + -
413B THR* 3.9 19.3 + - + +
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Residues in contact with VAL 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B PHE* 3.5 31.4 - - + +
311B ASN* 3.6 22.4 - - + +
312B VAL* 3.4 39.3 - - + +
339B ILE* 2.8 26.5 + - + +
340B ALA 4.0 2.0 - - - +
342B VAL* 1.3 70.3 - - - +
344B LYS* 1.3 66.4 + - - +
346B ALA* 4.3 5.2 - - - -
347B LEU* 3.1 32.3 + - + +
406B PHE* 3.9 5.8 - - + -
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Residues in contact with LYS 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B ASN* 5.4 0.2 - - - +
340B ALA 2.9 19.2 + - - +
341B VAL* 3.0 8.3 + - + +
343B VAL* 1.3 78.0 - - - +
345B ASP* 1.3 63.0 + - - +
346B ALA 3.5 0.2 + - - -
347B LEU* 3.6 13.7 + - - +
348B MET* 3.8 22.7 + - + +
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Residues in contact with ASP 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B VAL* 3.0 11.4 + - + +
342B VAL* 3.3 10.5 - - - +
344B LYS* 1.3 78.3 - - - +
346B ALA* 1.3 63.1 + - - +
348B MET* 3.3 18.1 + - - +
349B GLN* 3.7 19.2 + - - -
409B ALA* 3.7 24.1 - - + +
412B SER* 4.4 11.3 - - - -
413B THR* 5.2 2.6 + - - +
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B VAL 3.0 14.5 + - - +
343B VAL 3.8 3.6 - - - +
344B LYS 3.3 0.2 - - - -
345B ASP* 1.3 72.5 - - - +
347B LEU* 1.3 57.8 + - - +
348B MET 2.9 5.2 - - - -
349B GLN* 2.9 30.0 + - - +
401B LEU* 3.7 11.1 - - - +
405B ASP* 3.9 9.8 - - - +
406B PHE* 3.6 52.3 - - + +
409B ALA* 4.3 1.5 - - + +
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Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A ASN* 4.0 23.6 - - + +
163A ARG* 3.0 48.3 + - + +
311B ASN 4.7 2.0 - - - +
312B VAL* 4.0 17.3 - - + -
315B THR* 3.8 27.1 - - + +
343B VAL* 3.1 29.7 + - + +
344B LYS* 4.0 9.9 - - - +
345B ASP 3.5 0.2 - - - -
346B ALA* 1.3 73.4 - - - +
348B MET* 1.3 59.1 + - + +
349B GLN 3.4 0.2 - - - -
350B PRO* 3.8 3.4 - - - +
401B LEU* 3.7 28.0 - - + -
406B PHE* 4.3 4.9 - - + -
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Residues in contact with MET 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A PHE* 5.1 5.6 - - + -
162A ASN 6.0 0.2 - - - +
163A ARG* 3.9 22.7 - - + -
164A LYS 5.5 5.6 - - - +
344B LYS* 3.8 17.9 + - + +
345B ASP* 3.3 14.1 + - - +
346B ALA 2.9 1.2 - - - -
347B LEU* 1.3 82.3 - - + +
349B GLN* 1.3 54.3 + - - +
350B PRO* 3.5 1.3 - - - -
351B ILE* 3.0 35.8 + - + +
352B ARG* 2.7 38.1 + - + +
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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