Contacts of the helix formed by residues 334 - 349 (chain A) in PDB entry 1P5Q
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 ALA 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A HIS* 2.8 36.6 + - + +
332A LEU* 4.4 10.1 - - + +
333A GLN* 1.3 76.5 - - - +
335A PHE* 1.3 62.5 + - - +
336A SER 3.4 2.2 - - - -
337A ALA* 3.0 9.9 + - + +
338A ALA 2.9 16.8 + - - -
147B ASP* 3.7 10.1 - - - +
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Residues in contact with PHE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A LEU* 4.0 21.8 - - + -
333A GLN* 3.7 39.7 - - + -
334A ALA* 1.3 72.6 - - - +
336A SER* 1.3 67.6 + - - +
338A ALA* 2.9 15.9 + - - +
339A ILE* 3.0 19.0 + - + +
361A GLU 5.7 0.2 - - - -
362A ALA* 3.9 16.7 - - + +
365A ALA* 3.2 32.5 - - + -
366A VAL* 3.4 32.1 - - + -
147B ASP* 3.0 10.0 + - - +
148B GLY* 3.9 19.1 - - - -
151B ILE* 4.6 7.9 - - + -
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Residues in contact with SER 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ALA 3.4 0.2 - - - -
335A PHE* 1.3 73.0 - - - +
337A ALA* 1.3 62.1 + - - +
339A ILE* 3.4 14.9 + - - +
340A GLU* 3.4 22.0 + - - +
366A VAL* 5.3 0.6 - - - +
147B ASP* 2.9 30.8 + - - -
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A HIS* 3.8 30.3 - - + +
334A ALA* 3.0 15.4 + - + +
336A SER* 1.3 77.6 + - - +
338A ALA* 1.3 63.8 + - - +
339A ILE 3.2 0.4 - - - -
340A GLU* 3.1 18.0 + - - +
341A SER* 3.2 14.9 + - - -
147B ASP* 4.9 0.6 + - - -
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Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ALA* 3.9 10.1 - - + +
329A HIS* 3.8 13.4 - - + +
330A LEU* 3.4 39.3 - - + +
334A ALA 2.9 10.9 + - - +
335A PHE* 2.9 10.3 + - - +
337A ALA* 1.3 76.3 - - - +
339A ILE* 1.3 58.1 + - - +
341A SER* 3.4 2.4 + - - -
342A CYS* 2.9 35.6 + - - -
362A ALA* 3.9 4.7 - - + -
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Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A PHE* 3.0 18.1 + - + +
336A SER* 3.6 15.0 - - - +
338A ALA* 1.3 74.8 - - - +
340A GLU* 1.3 62.1 + - - +
342A CYS* 3.5 6.4 - - - +
343A ASN* 2.8 49.1 + - - +
359A ARG* 4.2 13.0 - - + -
362A ALA* 4.0 17.7 - - + +
363A HIS* 3.7 36.3 - - + +
366A VAL* 6.1 2.2 - - + -
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Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A SER* 3.4 12.0 + - - +
337A ALA* 3.1 13.3 + - - +
339A ILE* 1.3 79.7 - - - +
341A SER* 1.3 58.7 + - - +
343A ASN* 3.2 11.3 + - - +
344A LYS* 2.9 43.4 + - + +
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A HIS* 3.6 28.4 + - - +
325A LEU* 3.4 22.3 - - - +
326A ALA* 3.8 12.1 - - - -
329A HIS* 4.0 10.6 + - - -
337A ALA 3.2 5.6 + - - -
338A ALA 3.8 5.8 - - - -
340A GLU* 1.3 77.2 - - - +
342A CYS* 1.3 61.5 + - - +
344A LYS* 3.2 8.1 + - - +
345A ALA* 2.8 30.5 + - - +
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Residues in contact with CYS 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A LEU* 5.1 0.7 - - - -
326A ALA* 3.8 11.2 - - - -
338A ALA* 2.9 26.3 + - - +
339A ILE 3.5 4.5 - - - +
340A GLU 3.2 0.2 - - - -
341A SER* 1.3 77.6 - - - +
343A ASN* 1.3 52.1 + - - +
345A ALA* 3.0 8.5 + - - +
346A LEU* 2.7 40.3 + - - +
355A GLY* 3.4 15.5 - - - +
358A ARG* 3.8 13.2 - - - -
359A ARG* 3.3 48.2 - - + -
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Residues in contact with ASN 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 2.8 38.9 + - - +
340A GLU* 3.6 10.1 + - + +
342A CYS* 1.3 74.5 - - - +
344A LYS* 1.3 66.1 + - + +
346A LEU* 3.1 9.2 + - - +
347A GLU* 2.8 31.3 + - - +
359A ARG* 2.8 37.9 + - - -
344C LYS* 6.3 0.6 - - - +
347C GLU* 3.6 21.5 - - - +
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Residues in contact with LYS 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A HIS* 3.4 36.2 - - + +
340A GLU* 2.9 27.4 + - + +
341A SER* 3.6 3.8 - - - +
343A ASN* 1.3 76.7 - - - +
345A ALA* 1.3 65.8 + - - +
347A GLU* 3.0 48.7 + - - +
348A LEU* 3.5 8.5 + - - +
343C ASN* 4.2 14.5 - - - +
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Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A LEU* 3.6 15.7 - - + +
322A HIS* 3.7 18.3 - - + +
323A LEU* 3.2 35.0 - - + -
341A SER 2.8 17.5 + - - +
342A CYS 3.3 6.5 - - - +
344A LYS* 1.3 72.3 - - - +
346A LEU* 1.3 54.5 + - - +
348A LEU* 2.7 35.1 + - - +
349A ASP 3.1 4.7 + - - -
352A ASN* 5.6 0.9 - - - -
355A GLY* 5.1 0.9 - - - -
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A CYS 2.7 22.2 + - - +
343A ASN* 3.1 6.0 + - - +
345A ALA* 1.3 74.3 - - - +
347A GLU* 1.3 59.0 + - - +
349A ASP 3.7 16.8 - - - +
350A SER* 2.9 47.3 + - - +
352A ASN* 4.1 11.2 - - + +
355A GLY* 4.5 6.3 - - - -
356A LEU* 3.8 31.2 - - + +
359A ARG* 3.4 46.4 - - - +
346C LEU 3.9 0.5 - - - +
347C GLU* 4.1 16.6 - - + +
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Residues in contact with GLU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A ASN* 2.8 27.9 + - - +
344A LYS* 3.0 40.4 + - - +
346A LEU* 1.3 72.7 - - - +
348A LEU* 1.3 64.1 + - + +
343C ASN* 3.5 54.7 - - - +
344C LYS* 6.0 0.9 - - - +
346C LEU* 4.0 12.9 - - + +
347C GLU* 3.7 21.0 - - + +
350C SER* 3.5 15.7 - - - +
359C ARG* 4.6 6.8 + - - +
378C LYS* 5.3 1.6 + - - -
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A GLN* 4.0 36.8 - - + +
318A ARG* 3.6 25.1 - - + +
319A LEU* 3.2 46.2 - - + +
322A HIS* 4.2 10.1 - - + -
344A LYS 3.9 6.3 - - - +
345A ALA 2.7 14.3 + - - +
347A GLU* 1.3 83.7 - - + +
349A ASP* 1.3 56.4 + - - +
350C SER* 3.0 15.9 + - - -
378C LYS* 4.1 6.2 + - - +
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Residues in contact with ASP 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A LEU* 3.7 22.9 - - + -
345A ALA 3.1 3.4 + - - -
346A LEU* 3.2 7.8 - - - +
348A LEU* 1.3 79.4 - - - +
350A SER* 1.3 58.7 + - - +
351A ASN* 2.9 20.4 + - - +
352A ASN* 2.9 55.4 + - + +
383A TYR* 5.3 0.5 + - - -
350C SER* 3.6 4.0 + - - -
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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