Contacts of the helix formed by residues 348 - 359 (chain D) in PDB entry 3PRJ
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 348 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311D ARG* 4.1 0.4 - - - -
336D PHE 2.8 27.9 + - - -
337D ALA 3.7 4.3 + - - -
338D PHE* 3.5 24.3 - - - -
345D THR 2.8 16.0 + - - -
346D ARG 3.2 0.8 - - - -
347D GLU* 1.3 77.4 - - - +
349D SER* 1.3 54.8 + - - +
350D SER* 2.8 18.6 + - - -
351D ILE* 2.8 36.5 + - - +
352D TYR* 3.6 4.9 - - - -
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Residues in contact with SER 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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270D VAL* 3.7 25.7 + - - -
271D GLY* 2.7 32.9 + - - -
273D GLY* 4.7 2.8 - - - -
311D ARG* 2.9 33.1 + - - +
338D PHE* 5.1 1.8 + - - +
347D GLU 3.4 3.6 + - - -
348D SER* 1.3 71.7 + - - +
350D SER* 1.3 63.0 + - - +
352D TYR* 3.0 4.2 + - - +
353D ILE* 2.9 27.1 + - - +
414D CYS 5.7 0.9 - - - -
442D ARG* 5.5 4.0 - - - +
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Residues in contact with SER 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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333D ILE* 5.1 0.8 - - - +
335D GLY 2.8 22.9 + - - -
336D PHE* 3.3 30.5 - - - -
337D ALA 4.4 0.3 + - - -
348D SER* 2.8 16.0 + - - -
349D SER* 1.3 78.0 - - - +
351D ILE* 1.3 56.9 + - - +
353D ILE* 4.0 0.7 - - - +
354D SER* 2.6 35.5 + - - -
414D CYS* 3.1 25.6 + - - +
415D THR* 3.8 2.4 + - - -
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Residues in contact with ILE 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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336D PHE* 3.7 28.5 - - + -
345D THR* 3.3 25.8 - - - +
346D ARG* 5.2 0.4 - - - -
347D GLU* 4.2 7.9 - - - +
348D SER* 2.8 21.3 + - - +
350D SER* 1.3 72.8 - - - +
352D TYR* 1.3 70.4 + - + +
354D SER* 3.5 2.8 + - - -
355D LYS* 3.0 42.5 + - - +
379D ASP* 3.7 39.5 - - + +
380D LEU* 4.1 4.2 - - + +
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Residues in contact with TYR 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D GLN* 4.5 5.9 + - - -
308D ASP* 6.0 1.1 - - - -
311D ARG* 3.2 48.9 - - - -
347D GLU* 2.8 34.4 + - - -
348D SER 3.6 12.6 - - - -
349D SER 3.0 5.6 + - - +
351D ILE* 1.3 86.1 - - + +
353D ILE* 1.3 67.0 + - - +
355D LYS* 3.0 20.9 + - + +
356D TYR* 3.0 37.6 + + + -
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Residues in contact with ILE 353 (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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270D VAL* 3.7 29.4 - - + -
311D ARG* 3.6 32.5 - - + +
314D PHE* 3.8 8.3 - - + -
315D ALA* 4.4 8.7 - - + -
318D ILE* 4.5 8.5 - - + -
333D ILE* 5.3 2.2 - - + -
349D SER* 2.9 23.9 + - - +
350D SER 4.1 2.9 - - - +
352D TYR* 1.3 72.5 - - - +
354D SER* 1.3 63.0 + - - +
356D TYR* 3.3 7.0 + - + +
357D LEU* 3.1 40.1 + - + +
412D VAL* 4.4 18.4 - - + -
414D CYS* 4.6 13.2 - - - -
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Residues in contact with SER 354 (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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333D ILE* 4.3 15.5 - - - +
336D PHE* 3.7 11.9 - - - -
350D SER 2.6 24.6 + - - -
351D ILE 3.5 4.3 - - - -
353D ILE* 1.3 77.2 - - - +
355D LYS* 1.3 58.5 + - - +
357D LEU* 3.1 8.6 + - - +
358D MET* 2.8 31.2 + - - +
364D LEU* 3.7 23.7 - - - +
366D ILE* 4.5 1.0 - - - +
380D LEU* 3.9 17.5 - - - -
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Residues in contact with LYS 355 (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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351D ILE* 3.0 26.5 + - - +
352D TYR* 3.0 15.9 + - + +
354D SER* 1.3 72.6 - - - +
356D TYR* 1.3 64.4 + - + +
358D MET* 3.3 18.6 + - + +
359D ASP* 3.0 32.6 + - - +
379D ASP 4.0 16.8 + - - -
380D LEU* 4.3 8.4 - - + +
381D SER* 3.9 28.7 - - - +
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Residues in contact with TYR 356 (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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98B MET* 4.6 12.1 - - + -
308D ASP 4.9 2.9 + - - -
311D ARG* 4.8 5.2 - - + +
312D ARG* 3.7 46.6 + - + +
315D ALA* 3.8 28.5 - - + -
319D ILE* 4.7 5.9 - - + +
352D TYR* 3.0 51.5 + + + -
353D ILE* 3.6 7.9 - - + +
355D LYS* 1.3 75.2 - - + +
357D LEU* 1.3 63.0 + - + +
359D ASP* 3.3 21.5 + - - +
360D GLU* 3.4 17.0 + - - +
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Residues in contact with LEU 357 (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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315D ALA* 4.8 3.4 - - + +
318D ILE* 4.0 32.5 - - + -
319D ILE* 4.1 21.3 - - + -
326D VAL* 5.2 5.2 - - + -
331D ILE* 4.4 19.1 - - + -
333D ILE* 4.1 22.0 - - + -
353D ILE* 3.1 36.0 + - + +
354D SER 3.6 5.8 - - - +
356D TYR* 1.3 75.6 - - + +
358D MET* 1.3 64.1 + - - +
360D GLU* 3.2 12.0 + - - +
361D GLY 3.3 0.3 + - - -
362D ALA* 3.1 27.4 + - + +
364D LEU* 4.1 15.5 - - + -
412D VAL* 4.7 0.4 - - + -
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Residues in contact with MET 358 (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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354D SER 2.8 18.2 + - - +
355D LYS* 3.3 20.8 + - + +
357D LEU* 1.3 73.3 - - - +
359D ASP* 1.3 57.8 + - - +
360D GLU 2.9 5.2 - - - -
361D GLY* 2.9 21.2 + - - +
362D ALA 4.5 2.7 - - - +
364D LEU* 3.9 13.9 - - + -
380D LEU* 4.2 31.9 - - + +
390D GLN* 3.6 54.4 + - + +
391D VAL* 4.3 3.6 - - + +
394D LEU* 3.8 16.5 - - + +
395D VAL* 4.2 24.9 - - + -
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Residues in contact with ASP 359 (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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96B TYR* 3.2 22.5 - - + +
97B GLY* 3.2 19.9 + - - +
355D LYS* 3.0 23.7 + - - +
356D TYR* 3.3 14.2 + - - +
358D MET* 1.3 73.4 - - - +
360D GLU* 1.3 58.4 + - + +
361D GLY 3.5 0.2 - - - -
390D GLN* 3.9 18.4 + - - +
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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