Contacts of the helix formed by residues 313 - 326 (chain A) in PDB entry 3PEY
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 ASN 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A CYS* 3.3 1.9 - - - +
312A LYS* 1.3 97.3 + - - +
314A GLU* 1.3 68.4 + - - +
315A ALA* 3.3 12.4 + - - +
316A ASP* 2.9 42.6 + - - +
317A LYS* 3.3 13.9 + - - +
441A HIS* 3.7 17.7 - - - +
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Residues in contact with GLU 314 (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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313A ASN* 1.3 75.8 - - - +
315A ALA* 1.3 63.2 + - - +
317A LYS* 2.9 60.1 + - - +
318A PHE* 4.1 1.9 + - - +
405A TYR* 4.1 14.0 + - - -
406A ASP* 4.4 3.7 - - - +
441A HIS* 3.5 27.5 + - + +
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Residues in contact with ALA 315 (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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313A ASN* 3.1 10.6 + - - +
314A GLU* 1.3 78.0 - - - +
316A ASP* 1.3 62.1 + - - +
317A LYS 3.3 0.5 + - - -
318A PHE* 3.5 13.8 + - - +
319A ASP* 3.8 13.5 + - - +
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Residues in contact with ASP 316 (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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311A CYS* 3.5 9.5 - - - +
312A LYS* 2.9 52.7 + - + +
313A ASN* 2.9 25.8 + - - +
315A ALA* 1.3 70.9 - - - +
317A LYS* 1.3 65.6 + - - +
319A ASP* 3.1 18.5 + - - +
320A VAL* 2.9 41.5 + - - +
466A THR* 5.0 3.5 + - - -
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Residues in contact with LYS 317 (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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311A CYS* 4.0 24.7 - - + +
313A ASN 3.3 10.4 + - - +
314A GLU* 2.9 43.9 + - - +
315A ALA 3.1 1.2 - - - -
316A ASP* 1.3 77.5 - - - +
318A PHE* 1.3 57.7 + - - +
320A VAL 3.3 0.2 + - - -
321A LEU* 2.9 25.1 + - - +
405A TYR* 2.8 48.5 + - + +
406A ASP* 3.0 18.0 + - - +
439A PHE* 3.4 20.5 + - + -
441A HIS* 3.6 26.7 + - + +
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Residues in contact with PHE 318 (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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314A GLU 4.1 1.2 + - - +
315A ALA* 3.5 9.8 + - - +
316A ASP 3.2 0.4 - - - -
317A LYS* 1.3 79.8 - - - +
319A ASP* 1.3 69.1 - - - +
321A LEU* 3.2 2.5 + - + +
322A THR* 2.9 56.7 + - + +
346A LEU* 3.6 22.4 - - + -
349A LYS* 3.5 64.2 - - + +
350A LEU* 3.8 16.2 - - + -
353A GLU* 3.3 22.9 - - - -
405A TYR* 3.2 13.2 + - - +
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Residues in contact with ASP 319 (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 ALA 3.8 13.6 - - - +
316A ASP* 3.1 20.9 + - - +
318A PHE* 1.3 87.8 - - - +
320A VAL* 1.3 63.1 + - + +
322A THR* 2.9 22.4 + - - -
323A GLU* 3.3 15.1 + - - +
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Residues in contact with VAL 320 (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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309A MET* 3.6 31.4 - - - -
311A CYS* 3.9 14.8 - - - -
316A ASP* 2.9 41.2 + - - +
317A LYS 3.7 3.4 - - - +
319A ASP* 1.3 76.0 - - + +
321A LEU* 1.3 57.9 + - - +
323A GLU* 3.1 3.4 + - - -
324A LEU* 2.9 25.1 + - - +
439A PHE* 3.8 10.8 - - + -
466A THR* 3.9 24.9 - - + +
469A TRP* 3.6 16.3 - - + -
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Residues in contact with LEU 321 (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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317A LYS 2.9 18.4 + - - +
318A PHE* 3.6 4.7 - - + +
320A VAL* 1.3 76.0 - - - +
322A THR* 1.3 58.0 + - - +
324A LEU* 3.2 6.4 + - + -
325A TYR* 2.8 29.5 + - + +
328A MET* 4.1 15.3 - - + -
335A ILE* 4.0 23.6 - - + -
346A LEU* 3.8 28.5 - - + -
350A LEU* 4.2 16.8 - - + -
403A VAL* 4.4 8.7 - - + -
405A TYR* 3.7 26.2 - - + -
439A PHE* 4.0 17.9 - - + -
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Residues in contact with THR 322 (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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318A PHE* 2.9 57.0 + - + +
319A ASP* 2.9 21.7 + - - -
320A VAL 3.2 0.2 - - - -
321A LEU* 1.3 76.9 - - - +
323A GLU* 1.3 68.6 + - - +
325A TYR* 3.5 14.7 + - - +
326A GLY 4.0 2.8 + - - -
350A LEU* 3.9 13.7 - - + -
353A GLU* 4.0 13.4 + - - +
355A HIS* 4.2 19.1 + - - +
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Residues in contact with GLU 323 (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 ASP 3.5 13.9 - - - +
320A VAL* 3.1 2.5 + - - +
322A THR* 1.3 83.1 + - - +
324A LEU* 1.3 63.0 + - - +
326A GLY* 3.3 7.3 + - - -
327A LEU* 3.1 19.4 - - - +
469A TRP* 3.3 44.8 - - + +
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Residues in contact with LEU 324 (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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309A MET* 4.3 5.8 - - + -
320A VAL 2.9 16.9 + - - +
321A LEU* 3.2 7.8 + - + +
323A GLU* 1.3 73.8 - - - +
325A TYR* 1.3 65.4 + - - +
327A LEU* 2.8 27.2 + - + -
328A MET* 3.5 15.2 + - + +
401A MET* 4.3 11.9 - - + -
403A VAL* 4.0 25.8 - - + -
437A ILE* 3.8 28.7 - - + -
439A PHE* 4.1 24.2 - - + -
469A TRP* 3.7 23.5 - - + -
472A VAL* 4.5 2.2 - - + -
476A VAL* 5.7 0.2 - - + -
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Residues in contact with TYR 325 (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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321A LEU* 2.8 13.6 + - + +
322A THR* 3.5 14.6 - - - +
323A GLU 3.2 0.6 - - - -
324A LEU* 1.3 76.7 - - - +
326A GLY* 1.3 62.2 + - - +
328A MET* 3.0 39.8 + - + +
329A THR* 5.7 0.2 - - - +
335A ILE* 5.7 1.1 - - + -
350A LEU* 5.1 11.2 - - + -
355A HIS* 3.4 44.0 - + + +
356A GLU* 2.7 40.7 + - - +
357A VAL* 4.9 2.0 - - + -
382A LYS* 6.1 0.3 - - - +
383A VAL* 3.6 32.4 - - + +
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Residues in contact with GLY 326 (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 THR 4.0 2.2 + - - -
323A GLU 3.3 9.5 + - - -
324A LEU 3.1 1.6 + - - -
325A TYR* 1.3 84.3 - - - +
327A LEU* 1.3 63.5 + - - +
328A MET 3.4 0.2 - - - -
329A THR* 3.5 18.4 - - - +
355A HIS* 5.8 0.2 - - - -
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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