Contacts of the helix formed by residues 348 - 359 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273E GLY* 4.6 0.2 - - - -
311E ARG* 4.0 0.2 - - - -
336E PHE 2.8 28.1 + - - -
337E ALA 3.7 4.5 + - - -
338E PHE* 3.7 23.0 - - - -
345E THR* 2.8 22.4 + - - -
346E ARG 3.3 0.8 - - - -
347E GLU* 1.3 72.3 - - - +
349E SER* 1.3 64.3 + - - +
350E SER* 2.7 19.8 + - - -
351E ILE* 2.9 26.7 + - - +
352E TYR* 3.5 4.7 - - - -
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Residues in contact with SER 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E VAL* 3.8 26.0 - - - -
271E GLY* 2.7 30.1 + - - -
273E GLY* 4.7 2.8 - - - +
311E ARG* 2.9 34.0 + - - +
338E PHE* 5.1 2.4 + - - +
347E GLU 3.4 3.4 + - - -
348E SER* 1.3 72.0 + - - +
350E SER* 1.3 62.8 + - - +
352E TYR* 3.1 3.4 + - - +
353E ILE* 2.9 27.0 + - - +
414E CYS* 5.4 1.1 - - - -
442E ARG* 5.6 3.8 - - - +
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Residues in contact with SER 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333E ILE* 5.1 1.1 - - - -
335E GLY 2.8 22.7 + - - -
336E PHE* 3.3 30.1 - - - -
337E ALA 4.4 0.2 + - - -
348E SER* 2.7 17.2 + - - -
349E SER* 1.3 78.3 - - - +
351E ILE* 1.3 60.2 + - - -
353E ILE* 3.9 0.9 - - - +
354E SER* 2.8 30.5 + - - -
414E CYS* 3.1 25.9 + - - +
415E THR* 3.8 2.1 + - - -
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Residues in contact with ILE 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E PHE* 3.7 28.3 - - + -
345E THR 3.4 25.6 - - - +
346E ARG* 5.2 0.4 - - - -
347E GLU* 4.2 7.4 - - - +
348E SER* 2.9 16.7 + - - +
350E SER* 1.3 76.0 - - - +
352E TYR* 1.3 71.5 + - + +
354E SER* 3.4 3.3 + - - -
355E LYS* 3.0 41.4 + - - +
379E ASP* 3.7 40.6 - - + +
380E LEU* 4.0 4.4 - - + +
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Residues in contact with TYR 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E GLN* 4.5 5.5 + - - -
308E ASP* 5.9 1.3 - - - -
311E ARG* 3.4 42.8 - - - -
347E GLU* 2.8 34.2 + - - -
348E SER 3.5 16.4 - - - -
349E SER 3.1 4.9 + - - +
351E ILE* 1.3 85.7 - - + +
353E ILE* 1.3 68.2 + - - +
354E SER 3.0 1.1 - - - -
355E LYS* 2.9 22.1 + - + +
356E TYR* 3.0 37.1 + + + -
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Residues in contact with ILE 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E VAL* 3.7 29.2 - - + -
311E ARG* 3.5 31.9 - - + +
314E PHE* 3.7 8.5 - - + -
315E ALA* 4.2 8.7 - - + +
318E ILE* 4.5 8.1 - - + -
333E ILE* 5.2 2.7 - - + -
349E SER* 2.9 24.2 + - - +
350E SER 4.0 2.5 - - - +
352E TYR* 1.3 72.4 - - - +
354E SER* 1.3 64.3 + - - +
356E TYR* 3.2 7.1 + - + +
357E LEU* 3.2 37.8 + - + +
412E VAL* 4.4 20.0 - - + -
414E CYS* 4.4 12.8 - - - -
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Residues in contact with SER 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333E ILE* 4.3 16.5 - - - +
336E PHE* 3.8 12.6 - - - -
350E SER 2.8 23.4 + - - -
351E ILE 3.4 4.9 - - - -
353E ILE* 1.3 77.5 - - - +
355E LYS* 1.3 57.8 + - - +
357E LEU* 3.1 8.1 + - - +
358E MET* 2.9 31.1 + - - +
364E LEU* 3.7 21.8 - - - +
366E ILE* 4.5 1.4 - - - +
380E LEU* 3.8 19.3 - - - -
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Residues in contact with LYS 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351E ILE* 3.0 24.3 + - - +
352E TYR* 2.9 15.5 + - + +
354E SER* 1.3 72.7 - - - +
356E TYR* 1.3 68.2 + - + +
358E MET* 3.2 14.5 + - + +
359E ASP* 3.0 31.8 + - - +
379E ASP 4.0 15.7 + - - -
380E LEU* 4.3 11.8 - - + +
381E SER* 4.0 29.7 - - - +
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Residues in contact with TYR 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A MET* 4.7 9.6 - - + -
308E ASP* 4.9 3.5 + - - +
311E ARG* 4.8 5.1 - - + +
312E ARG* 3.7 47.9 + - + +
315E ALA* 3.9 26.0 - - + -
319E ILE* 4.7 5.0 - - + +
352E TYR* 3.0 51.6 + + + -
353E ILE* 3.6 9.6 - - + +
355E LYS* 1.3 78.5 - - + +
357E LEU* 1.3 62.8 + - - +
359E ASP* 3.3 18.9 + - - +
360E GLU* 3.4 17.4 + - - +
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Residues in contact with LEU 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315E ALA* 4.9 2.2 - - + +
318E ILE* 4.0 31.9 - - + -
319E ILE* 4.1 20.9 - - + -
326E VAL* 5.3 4.3 - - + -
331E ILE* 4.4 18.6 - - + -
333E ILE* 4.1 22.2 - - + -
353E ILE* 3.2 29.1 + - + +
354E SER* 3.1 8.3 + - - +
356E TYR* 1.3 72.5 - - + +
358E MET* 1.3 65.3 + - - +
360E GLU* 3.2 14.2 + - - +
361E GLY 3.3 0.2 + - - -
362E ALA* 3.2 25.5 + - + +
364E LEU* 4.1 15.9 - - + -
412E VAL* 4.8 0.7 - - + -
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Residues in contact with MET 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354E SER 2.9 17.5 + - - +
355E LYS* 3.5 18.6 - - + +
357E LEU* 1.3 73.5 - - - +
359E ASP* 1.3 57.6 + - - +
360E GLU 2.9 4.9 - - - -
361E GLY* 2.8 20.7 + - - +
362E ALA 4.5 2.7 - - - +
364E LEU* 3.8 15.0 - - + -
380E LEU* 4.3 29.8 - - - +
390E GLN* 3.6 58.5 + - + +
391E VAL* 4.3 4.0 - - - +
394E LEU* 3.8 18.1 - - + +
395E VAL* 4.1 24.0 - - + -
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Residues in contact with ASP 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A TYR* 3.0 15.0 - - - +
97A GLY* 3.0 24.8 + - - +
355E LYS* 3.0 22.6 + - - +
356E TYR* 3.3 15.5 + - - +
358E MET* 1.3 74.6 - - - +
360E GLU* 1.3 57.7 + - - +
361E GLY 3.4 0.2 - - - -
390E 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