Contacts of the helix formed by residues 352 - 365 (chain W) in PDB entry 2Q4G
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 LEU 352 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324W PHE* 4.2 9.2 - - + -
325W THR 3.9 11.2 - - - +
326W ALA* 3.5 9.6 - - - +
328W CYS* 4.8 0.4 - - - -
329W CYS* 3.3 25.6 - - - -
347W ILE* 3.7 32.3 - - + -
350W ASN* 2.6 33.6 + - + +
351W ARG* 1.3 71.2 - - - +
353W GLU* 1.3 73.9 + - - +
356W GLY* 2.7 25.3 + - - -
357W VAL* 4.3 5.8 - - + +
360W LEU* 3.9 20.4 - - + -
376W LEU* 4.0 13.7 - - + -
379W CYS* 3.4 10.0 + - + +
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Residues in contact with GLU 353 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326W ALA* 5.1 4.9 - - + -
351W ARG* 3.0 25.7 - - - +
352W LEU* 1.3 91.3 - - - +
354W ASP* 1.3 65.0 + - - +
355W ALA* 4.0 8.5 - - + +
356W GLY 4.8 0.2 - - - +
357W VAL* 3.1 20.3 + - - +
379W CYS 3.0 8.8 + - - -
380W ASP* 2.6 58.0 - - - +
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Residues in contact with ASP 354 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353W GLU* 1.3 75.3 - - - +
355W ALA* 1.3 58.4 + - - +
357W VAL* 4.5 0.4 - - - -
358W ARG* 2.9 40.1 + - - +
380W ASP 3.8 3.5 + - - +
381W VAL* 3.7 1.7 - - - -
382W SER* 2.6 40.4 + - - -
384W SER* 2.9 28.3 + - - -
385W SER* 2.9 29.4 + - - -
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Residues in contact with ALA 355 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326W ALA* 4.3 13.7 - - + -
352W LEU 4.6 0.2 - - - +
353W GLU* 3.2 5.8 - - + +
354W ASP* 1.3 79.6 - - - +
356W GLY* 1.3 63.1 + - - +
358W ARG* 3.7 6.6 - - - +
359W GLU* 3.2 28.4 + - - +
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Residues in contact with GLY 356 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326W ALA* 3.8 6.6 - - - +
329W CYS* 3.5 33.8 - - - +
352W LEU* 2.7 25.6 + - - -
355W ALA* 1.3 72.4 - - - +
357W VAL* 1.3 64.3 + - - +
359W GLU* 3.1 7.2 + - - +
360W LEU* 3.0 19.6 + - - +
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Residues in contact with VAL 357 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352W LEU* 3.9 12.5 + - + +
353W GLU 3.1 15.1 + - - +
354W ASP 4.0 2.7 - - - +
356W GLY* 1.3 74.8 - - - +
358W ARG* 1.3 64.4 + - - +
360W LEU* 2.9 12.2 + - + +
361W CYS* 2.8 34.1 + - - -
376W LEU* 4.1 29.6 - - + -
379W CYS* 4.8 0.4 - - + -
381W VAL* 3.3 30.3 - - + -
385W SER* 3.8 21.1 - - - +
389W LEU* 4.4 8.5 - - + -
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Residues in contact with ARG 358 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354W ASP* 2.9 29.9 + - - +
355W ALA* 3.7 6.8 - - - +
357W VAL* 1.3 75.7 - - - +
359W GLU* 1.3 64.8 + - + +
361W CYS* 3.2 11.0 + - - +
362W GLN* 3.0 41.8 + - + +
384W SER* 3.0 27.9 + - - -
385W SER* 3.0 19.2 - - - +
387W SER* 4.4 6.3 + - - -
388W SER* 3.2 24.3 + - - +
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Residues in contact with GLU 359 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326W ALA* 3.3 24.1 - - - +
329W CYS* 3.7 14.3 - - - +
330W SER* 3.0 34.6 + - - -
333W SER* 2.6 28.5 + - - -
355W ALA* 3.2 16.8 - - - +
356W GLY* 3.1 8.7 + - - +
358W ARG* 1.3 78.9 - - + +
360W LEU* 1.3 58.9 + - - +
362W GLN* 2.9 25.8 + - - +
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Residues in contact with LEU 360 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329W CYS* 4.0 12.1 - - + +
332W PHE* 3.3 35.0 - - + -
333W SER* 3.9 9.9 - - - +
336W LEU* 4.1 15.4 - - + +
345W LEU* 5.1 2.2 - - + -
347W ILE* 4.5 9.6 - - + -
352W LEU* 3.9 17.3 - - + -
356W GLY 3.0 15.0 + - - +
357W VAL* 2.9 11.7 + - + +
359W GLU* 1.3 75.1 - - - +
361W CYS* 1.3 64.1 + - - +
363W GLY* 3.2 3.1 + - - -
364W LEU* 3.1 23.4 + - - +
374W LEU* 5.0 12.6 - - + -
376W LEU* 3.7 30.7 - - + -
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Residues in contact with CYS 361 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357W VAL* 2.8 23.2 + - - -
358W ARG 3.4 9.0 - - - +
359W GLU 3.2 0.2 - - - -
360W LEU* 1.3 77.3 - - - +
362W GLN* 1.3 56.7 + - - +
364W LEU* 4.6 4.7 - - - +
365W GLY* 2.9 26.0 + - - -
374W LEU* 6.4 1.1 - - - -
388W SER* 4.0 16.2 - - - -
389W LEU* 3.5 48.2 - - - -
392W THR* 3.4 24.8 + - - +
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Residues in contact with GLN 362 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333W SER* 3.5 4.0 + - - +
358W ARG* 3.0 32.2 + - + +
359W GLU* 2.9 27.9 + - - +
361W CYS* 1.3 78.4 - - - +
363W GLY* 1.3 61.1 + - - +
365W GLY* 3.5 4.4 + - - -
366W GLN* 2.9 30.7 + - - +
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Residues in contact with GLY 363 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333W SER* 2.6 43.0 + - - -
336W LEU 3.7 0.2 - - - +
337W ALA* 2.8 31.9 - - - +
360W LEU 3.2 2.9 + - - -
362W GLN* 1.3 74.3 - - - +
364W LEU* 1.3 64.1 + - - +
366W GLN* 3.1 9.4 + - - +
369W SER* 4.1 0.5 - - - -
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Residues in contact with LEU 364 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336W LEU* 4.0 16.1 - - + +
360W LEU 3.1 15.6 + - - +
361W CYS* 4.2 2.0 - - - +
363W GLY* 1.3 75.6 - - - +
365W GLY* 1.3 59.8 + - - +
366W GLN 3.1 0.2 - - - -
369W SER* 2.8 27.9 + - - +
371W LEU* 3.6 36.3 - - + +
374W LEU* 4.9 13.5 - - + -
392W THR* 3.8 21.5 - - + -
396W ASN* 3.2 41.4 + - - +
399W LEU* 4.3 27.4 - - + -
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Residues in contact with GLY 365 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361W CYS 2.9 18.8 + - - -
362W GLN* 3.9 3.8 - - - -
363W GLY 3.1 0.6 - - - -
364W LEU* 1.3 75.8 - - - +
366W GLN* 1.3 66.5 + - - +
367W PRO* 3.5 5.0 - - - +
392W THR* 4.2 11.6 - - - +
395W ALA* 4.2 21.4 - - - +
396W ASN* 4.5 6.2 + - - -
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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