Contacts of the helix formed by residues 339 - 351 (chain D) in PDB entry 2P5G
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 GLN 339 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334D ILE 3.4 1.6 + - - -
335D ASP* 3.1 19.8 + - - +
336D ALA 4.6 4.5 - - - +
337D LYS 3.0 11.1 + - - +
338D ARG* 1.3 79.4 - - - +
340D PHE* 1.3 66.0 + - - +
341D ILE 4.0 0.2 - - - -
342D ASN* 4.5 16.7 + - + -
343D LEU* 3.8 12.3 + - - +
550D VAL* 4.3 18.4 + - - +
553D MSE 5.2 10.3 - - - +
554D THR* 3.7 36.8 + - - +
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Residues in contact with PHE 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273D TYR* 3.3 32.0 + - + +
276D LEU* 4.3 25.8 - - + +
280D PHE* 5.8 6.5 - - + -
335D ASP* 3.2 4.8 + - - -
338D ARG* 3.3 6.6 + - + +
339D GLN* 1.3 71.6 - - - +
341D ILE* 1.3 69.8 + - - +
342D ASN 3.1 1.6 - - - -
343D LEU* 2.7 24.4 + - - +
344D SER* 3.5 4.8 + - - -
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Residues in contact with ILE 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D VAL* 4.7 17.3 - - + -
212D ILE* 4.2 18.6 - - + -
214D THR* 4.2 30.7 - - + +
271D LEU* 4.7 15.9 - - + -
273D TYR* 4.1 12.8 - - + -
276D LEU* 5.9 0.2 - - + -
335D ASP* 2.8 34.6 + - - +
340D PHE* 1.3 73.6 - - + +
342D ASN* 1.3 61.1 + - - +
344D SER* 2.8 22.0 + - - +
345D LEU* 3.1 31.3 + - + +
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Residues in contact with ASN 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D TYR* 3.6 18.2 + - - -
105D HIS* 3.7 27.3 - - - +
335D ASP* 4.4 4.0 + - - +
339D GLN* 4.5 18.8 + - + -
340D PHE 2.8 5.1 + - - +
341D ILE* 1.3 76.1 - - - +
343D LEU* 1.3 55.7 + - - +
345D LEU* 3.6 8.7 + - - +
346D ASP* 3.1 27.9 + - - +
554D THR* 3.1 34.8 + - - +
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Residues in contact with LEU 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D GLN* 3.8 13.1 + - - +
340D PHE* 2.7 18.4 + - - +
342D ASN* 1.3 74.3 - - - +
344D SER* 1.3 56.7 + - - +
346D ASP* 3.4 2.9 + - - +
347D MSE 3.0 24.6 + - - +
554D THR* 3.7 15.8 + - - +
558D ASN* 3.4 23.8 - - + +
561D LEU* 6.2 2.5 - - + -
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Residues in contact with SER 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D LEU* 3.8 22.5 - - - +
340D PHE 3.5 3.4 + - - -
341D ILE* 2.8 29.1 + - - +
343D LEU* 1.3 76.2 - - - +
345D LEU* 1.3 61.6 + - - +
347D MSE 4.1 2.0 - - - -
348D GLY* 3.0 23.6 + - - -
355D ILE* 4.2 3.6 - - - +
358D VAL* 3.2 40.3 - - - +
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Residues in contact with LEU 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D TYR* 4.4 15.0 - - + -
105D HIS* 5.5 7.6 - - + -
108D ILE* 5.3 13.2 - - + -
110D VAL* 6.0 2.2 - - + -
212D ILE* 4.1 29.4 - - + -
341D ILE* 3.1 39.6 + - + +
342D ASN* 3.8 13.9 - - - +
344D SER* 1.3 76.7 + - - +
346D ASP* 1.3 66.0 + - - +
348D GLY* 3.2 11.2 + - - -
349D TYR* 3.1 38.3 + - + +
355D ILE* 5.4 9.6 - - + +
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Residues in contact with ASP 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D TYR* 3.3 38.7 + - - +
342D ASN 3.1 13.9 + - - +
343D LEU 3.5 5.2 - - - +
345D LEU* 1.3 75.3 - - - +
347D MSE 1.3 56.3 - - - +
349D TYR* 3.5 2.1 + - - +
350D TYR* 3.0 33.0 + - - +
551D ALA 5.0 0.9 - - - +
554D THR* 3.1 25.8 - - - +
555D ALA* 3.6 19.0 - - - +
558D ASN* 3.0 17.7 - - - +
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Residues in contact with MSE 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D LEU 3.0 13.5 + - - +
344D SER* 3.5 10.5 - - - +
345D LEU 3.1 0.4 - - - -
346D ASP* 1.3 74.2 - - - +
348D GLY* 1.3 57.9 + - - +
349D TYR 3.0 4.7 + - - -
350D TYR* 4.6 10.8 - - - -
351D ALA* 2.9 36.0 + - + +
358D VAL* 3.7 26.9 - - + +
364D THR* 3.9 28.7 - - + +
368D ILE* 5.6 0.7 - - - -
558D ASN* 3.4 45.9 + - - +
561D LEU* 4.5 16.2 - - + +
562D LEU* 4.3 16.6 - - + +
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Residues in contact with GLY 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D TYR* 2.6 29.2 + - - -
344D SER 3.0 14.3 + - - -
345D LEU* 3.2 5.1 + - - -
347D MSE 1.3 75.9 - - - +
349D TYR* 1.3 54.3 + - - +
351D ALA* 2.7 16.1 - - - +
353D ILE* 3.0 10.9 - - - +
354D GLN 4.0 12.3 - - - -
355D ILE* 4.8 4.7 - - - -
358D VAL* 4.1 2.7 - - - +
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Residues in contact with TYR 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D PHE* 3.3 30.9 - + + -
5D TYR* 2.4 62.2 + + - -
101D ILE* 3.1 50.6 - - + +
103D TYR* 3.7 37.9 - + + -
108D ILE* 5.5 4.5 - - - +
345D LEU* 3.1 37.2 + - + +
346D ASP 4.0 3.1 - - - +
347D MSE 3.0 0.4 - - - -
348D GLY* 1.3 78.8 - - - +
350D TYR* 1.3 66.4 + - - +
351D ALA 3.9 3.6 - - - -
352D LYS* 4.0 4.0 + - - +
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Residues in contact with TYR 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D ASP* 3.0 25.2 + - - +
347D MSE 3.9 10.5 - - - +
349D TYR* 1.3 78.5 - - - +
351D ALA* 1.3 64.5 + - + +
352D LYS* 3.4 3.3 + - - +
368D ILE* 4.2 31.1 - - + +
478D VAL* 4.8 15.8 - - + +
481D GLN* 2.6 42.7 + - + +
485D HIS* 5.9 6.1 - + - -
555D ALA* 6.3 2.9 - - + -
558D ASN* 5.4 1.1 - - - +
559D ARG* 5.8 10.0 - - + +
562D LEU* 6.5 0.4 - - + -
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Residues in contact with ALA 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347D MSE 2.9 17.1 + - + +
348D GLY* 2.7 21.1 - - - +
349D TYR 3.9 0.2 - - - -
350D TYR* 1.3 73.2 - - + +
352D LYS* 1.3 54.5 + - - +
353D ILE* 2.6 20.9 + - + +
364D THR* 4.0 26.5 - - + +
367D ALA* 4.4 5.6 - - + -
368D ILE* 3.7 30.1 - - + +
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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