Contacts of the helix formed by residues 348 - 359 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B GLY* 4.4 0.2 - - - -
311B ARG* 4.1 0.2 - - - -
336B PHE 2.7 29.2 + - - -
337B ALA 3.7 4.0 + - - -
338B PHE* 3.6 23.6 - - - -
345B THR* 2.7 22.0 + - - -
346B ARG 3.2 1.2 + - - -
347B GLU* 1.3 71.8 - - - +
349B SER* 1.3 64.7 + - - +
350B SER* 2.9 17.8 + - - -
351B ILE* 2.8 27.8 + - - +
352B TYR* 3.6 4.2 - - - -
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Residues in contact with SER 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL* 3.7 26.5 - - - -
271B GLY* 2.7 30.5 + - - -
273B GLY* 4.6 2.8 - - - -
311B ARG* 2.9 33.3 + - - +
338B PHE* 5.1 1.8 + - - +
347B GLU 3.4 3.2 + - - -
348B SER* 1.3 71.5 + - - +
350B SER* 1.3 61.1 + - - +
352B TYR* 3.0 4.7 + - - +
353B ILE* 2.9 26.6 + - - +
414B CYS* 5.3 1.3 - - - -
442B ARG* 5.4 4.6 - - - +
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Residues in contact with SER 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B ILE* 5.0 0.9 - - - -
335B GLY 2.9 21.7 + - - -
336B PHE* 3.4 29.7 - - - -
337B ALA 4.5 0.2 + - - -
348B SER* 2.9 16.9 + - - -
349B SER* 1.3 77.8 - - - +
351B ILE* 1.3 60.4 + - - -
353B ILE* 4.1 0.5 - - - +
354B SER* 2.8 32.4 + - - -
414B CYS* 3.0 27.9 + - - +
415B THR* 3.8 2.1 + - - -
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Residues in contact with ILE 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B PHE* 3.8 27.6 - - + -
345B THR 3.4 25.1 - - - +
346B ARG* 5.3 0.2 - - - -
347B GLU* 4.2 8.1 - - - +
348B SER* 2.8 20.5 + - - +
350B SER* 1.3 73.0 - - - +
352B TYR* 1.3 71.4 + - + +
354B SER* 3.5 2.8 + - - -
355B LYS* 3.1 41.7 + - - +
379B ASP* 3.7 41.7 - - + +
380B LEU* 4.0 2.6 - - + +
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Residues in contact with TYR 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B GLN* 4.5 5.7 + - - -
308B ASP* 6.0 1.1 - - - -
311B ARG* 3.3 45.1 - - + -
347B GLU* 2.7 34.9 + - - -
348B SER 3.6 15.9 - - - -
349B SER 3.0 5.8 + - - +
351B ILE* 1.3 85.5 - - + +
353B ILE* 1.3 68.4 + - - +
354B SER 3.1 0.7 - - - -
355B LYS* 3.0 19.6 + - + +
356B TYR* 3.0 38.5 + + + -
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Residues in contact with ILE 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B VAL* 3.7 28.3 - - + -
311B ARG* 3.6 31.9 - - + +
314B PHE* 3.8 8.5 - - + -
315B ALA* 4.2 9.0 - - + +
318B ILE* 4.4 9.0 - - + -
333B ILE* 5.2 2.2 - - + -
349B SER* 2.9 21.3 + - - +
350B SER 4.1 2.5 - - - +
352B TYR* 1.3 74.6 - - - +
354B SER* 1.3 64.2 + - - +
356B TYR* 3.3 7.3 + - + +
357B LEU* 3.1 40.1 + - + +
412B VAL* 4.4 19.3 - - + -
414B CYS* 4.4 11.9 - - - -
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Residues in contact with SER 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ILE* 4.2 15.9 - - - +
336B PHE* 3.8 11.8 - - - -
350B SER 2.8 22.6 + - - -
351B ILE 3.5 4.5 - - - -
353B ILE* 1.3 76.7 - - - +
355B LYS* 1.3 56.4 + - - +
357B LEU* 3.2 6.8 + - - -
358B MET* 2.8 33.0 + - - +
364B LEU* 3.6 24.4 - - - +
366B ILE* 4.4 1.2 - - - +
380B LEU* 3.9 18.6 - - - -
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Residues in contact with LYS 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B ILE* 3.1 27.0 + - + +
352B TYR* 3.0 14.6 + - + +
354B SER* 1.3 72.2 - - - +
356B TYR* 1.3 66.5 + - + +
358B MET* 3.3 14.2 + - + +
359B ASP* 3.0 31.8 + - - +
379B ASP 4.0 16.6 + - - -
380B LEU* 4.3 11.1 - - + +
381B SER* 4.0 29.1 - - - +
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Residues in contact with TYR 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ASP* 5.0 2.9 + - - +
311B ARG* 4.8 5.0 - - + +
312B ARG* 3.6 48.1 + - + +
315B ALA* 3.9 25.1 - - + -
319B ILE* 4.7 5.4 - - + +
352B TYR* 3.0 52.3 + + + -
353B ILE* 3.6 7.9 - - + +
355B LYS* 1.3 76.3 - - + +
357B LEU* 1.3 63.3 + - + +
359B ASP* 3.3 21.3 + - - +
360B GLU* 3.4 17.2 + - - +
98F MET* 4.1 19.5 - - + -
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Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B ALA* 4.7 2.9 - - + +
318B ILE* 4.0 31.4 - - + -
319B ILE* 4.0 22.4 - - + -
326B VAL* 5.3 4.3 - - + -
331B ILE* 4.4 17.5 - - + -
333B ILE* 4.1 22.0 - - + -
353B ILE* 3.1 33.3 + - + +
354B SER* 3.7 5.8 - - - +
356B TYR* 1.3 73.1 - - + +
358B MET* 1.3 64.0 + - - +
360B GLU* 3.3 10.9 + - - +
362B ALA* 3.1 28.1 + - + +
364B LEU* 4.2 16.6 - - + -
412B VAL* 4.7 0.2 - - + -
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Residues in contact with MET 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B SER 2.8 23.9 + - - +
355B LYS* 3.3 14.1 + - + +
357B LEU* 1.3 72.3 - - - +
359B ASP* 1.3 53.8 + - - +
360B GLU 2.9 4.9 - - - -
361B GLY* 2.7 25.6 + - - +
362B ALA 4.4 2.5 - - - +
364B LEU* 3.9 13.9 - - + -
380B LEU* 4.3 29.4 - - - +
390B GLN* 3.6 57.5 + - + +
391B VAL* 4.2 3.8 - - - +
394B LEU* 3.8 16.6 - - + +
395B VAL* 4.0 25.6 - - + -
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Residues in contact with ASP 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B LYS* 3.0 23.2 + - - +
356B TYR* 3.3 14.7 + - - +
358B MET* 1.3 75.3 - - - +
360B GLU* 1.3 58.1 + - + +
361B GLY 3.3 0.4 - - - -
390B GLN* 3.9 19.2 + - - +
96F TYR* 3.6 11.6 - - - +
97F GLY* 3.2 30.5 + - - +
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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