Contacts of the helix formed by residues 380 - 394 (chain E) in PDB entry 4P0S
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 PRO 380 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378E SER 4.5 2.0 - - - +
379E LEU* 1.4 101.5 - - + +
381E GLU* 1.3 64.7 + - - +
382E SER* 3.5 6.5 - - - +
383E THR* 3.2 41.2 - - + +
384E LEU* 3.5 8.3 + - - +
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Residues in contact with GLU 381 (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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375E HIS* 4.9 21.1 + - + -
379E LEU 4.1 0.2 + - - -
380E PRO* 1.3 67.6 - - - +
382E SER* 1.3 68.4 + - - +
383E THR 3.1 1.9 + - - -
384E LEU* 3.6 4.5 + - - +
385E LEU* 3.5 26.6 + - + +
434F ASP* 4.5 12.5 - - - +
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Residues in contact with SER 382 (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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380E PRO* 3.5 5.4 - - - +
381E GLU* 1.3 81.0 - - - +
383E THR* 1.3 65.9 + - - +
385E LEU* 3.8 9.0 + - - +
386E GLN* 3.1 29.9 + - - +
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Residues in contact with THR 383 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344E ILE* 6.1 1.3 - - + -
379E LEU* 4.2 16.4 - - + -
380E PRO* 3.2 30.2 + - + +
381E GLU 3.1 1.0 - - - -
382E SER* 1.3 81.3 + - - +
384E LEU* 1.3 79.1 + - + +
386E GLN* 3.0 9.6 + - - +
387E ALA* 3.0 18.9 + - + +
1Q G 4.4 18.2 - - + +
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Residues in contact with LEU 384 (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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337E LEU* 4.8 12.3 - - + +
340E LEU* 4.4 18.6 - - + -
341E CYS* 3.5 26.2 - - - -
344E ILE* 4.3 11.4 - - + -
377E LEU* 4.3 14.1 - - + -
379E LEU* 3.8 41.5 - - + +
380E PRO 3.5 5.9 + - - +
381E GLU* 3.6 4.7 + - - +
383E THR* 1.3 79.8 - - + +
385E LEU* 1.3 56.4 + - - +
387E ALA* 2.7 25.6 + - - +
388E VAL* 2.9 19.5 + - + +
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Residues in contact with LEU 385 (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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381E GLU* 3.5 23.2 + - + +
382E SER* 3.8 8.1 - - - +
383E THR 3.2 0.2 - - - -
384E LEU* 1.3 77.6 - - - +
386E GLN* 1.3 56.7 + - - +
388E VAL* 3.5 6.0 + - + +
389E THR* 2.5 38.5 + - - +
401E ARG* 4.1 27.6 - - - +
431F GLU* 6.5 0.4 - - - -
434F ASP* 3.2 46.2 - - + +
435F PHE* 4.5 9.4 - - + +
438F ALA* 4.5 1.8 - - + -
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Residues in contact with GLN 386 (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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382E SER 3.1 14.8 + - - +
383E THR* 3.0 15.0 + - - +
384E LEU 3.0 0.4 - - - -
385E LEU* 1.3 79.2 - - - +
387E ALA* 1.3 54.7 + - - +
389E THR* 3.3 3.1 + - - -
390E ASN* 3.0 52.2 + - - +
437F CYS* 4.4 4.0 - - - +
438F ALA* 2.9 46.3 + - - +
441F LYS* 2.9 52.6 + - + +
2Q A 4.0 9.2 - - - -
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Residues in contact with ALA 387 (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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340E LEU* 5.1 3.4 - - + -
344E ILE* 4.5 20.0 - - + -
349E PHE* 5.2 9.5 - - + -
383E THR* 3.0 9.0 + - + +
384E LEU* 2.7 26.1 + - + +
386E GLN* 1.3 66.5 - - - +
388E VAL* 1.3 59.3 + - + +
389E THR 3.0 1.3 - - - -
390E ASN* 3.2 7.6 + - - +
391E THR* 2.3 36.9 + - - +
1Q G 5.8 9.8 - - - +
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Residues in contact with VAL 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340E LEU* 5.3 10.8 - - + -
349E PHE* 6.1 0.4 - - - -
368E VAL* 5.2 13.2 - - + -
384E LEU* 2.9 16.1 + - + +
385E LEU* 4.1 6.7 - - + +
387E ALA* 1.3 76.1 - - + +
389E THR* 1.3 61.3 + - - +
391E THR* 3.1 9.8 + - - -
392E GLN* 2.9 26.6 + - - +
399E VAL* 3.5 34.4 - - + +
401E ARG* 4.0 28.3 - - + +
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Residues in contact with THR 389 (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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385E LEU* 2.5 27.3 + - - +
386E GLN 3.4 1.1 - - - -
387E ALA 3.0 0.2 - - - -
388E VAL* 1.3 78.8 - - - +
390E ASN* 1.3 60.5 + - - +
392E GLN* 2.7 22.4 + - - +
393E VAL* 3.1 12.8 + - - +
401E ARG* 4.4 1.0 + - - -
435F PHE* 3.8 29.8 - - + +
438F ALA* 3.3 18.0 - - + +
439F PHE* 3.2 41.3 - - + +
442F ALA* 4.6 1.1 - - + -
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Residues in contact with ASN 390 (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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386E GLN* 3.0 31.8 + - - +
387E ALA* 3.2 5.0 + - - +
389E THR* 1.3 75.4 - - - +
391E THR* 1.3 59.1 + - - +
394E ILE* 2.8 52.2 + - + +
395E ASP* 5.2 1.1 - - - -
442F ALA* 3.0 30.8 + - - +
1Q G 3.0 14.9 + - - +
2Q A 2.2 46.9 + - - +
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Residues in contact with THR 391 (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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349E PHE* 3.4 23.9 - - + -
353E LYS* 4.1 15.6 + - + -
366E TYR* 4.8 7.2 - - + -
387E ALA 2.3 23.3 + - - -
388E VAL* 3.1 14.4 - - - -
390E ASN* 1.3 81.5 - - - +
392E GLN* 1.3 59.9 + - - +
395E ASP* 3.6 13.7 + - - +
396E GLY 3.5 13.9 + - - -
397E PHE* 3.7 30.5 + - + +
399E VAL* 4.9 7.4 - - + -
1Q G 5.8 0.9 - - - -
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Residues in contact with GLN 392 (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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388E VAL* 2.9 10.9 + - - +
389E THR* 2.7 10.9 + - - +
391E THR* 1.3 79.2 - - - +
393E VAL* 1.3 65.8 + - + +
396E GLY* 3.4 19.9 - - - -
397E PHE 3.8 8.6 - - - +
399E VAL* 3.5 30.1 - - + +
401E ARG* 4.4 1.7 + - - -
360F SER* 4.4 4.5 - - - +
422F GLN* 3.8 40.6 + - + +
424F GLN* 3.2 15.7 + - - +
435F PHE* 2.9 41.7 - - + -
439F PHE* 4.3 5.6 - - + -
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Residues in contact with VAL 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389E THR 3.1 9.0 + - - +
392E GLN* 1.3 77.6 - - + +
394E ILE* 1.3 66.7 + - + +
396E GLY* 3.9 5.6 + - - -
311F THR* 4.6 12.1 - - + +
360F SER* 5.4 0.2 - - - +
439F PHE* 3.2 52.3 - - + -
442F ALA* 4.0 15.7 - - + -
443F VAL* 4.4 25.1 - - + +
446F ALA* 5.1 7.6 - - + +
450F LYS* 5.4 3.1 + - - -
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Residues in contact with ILE 394 (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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357E LYS* 5.2 4.5 + - - +
390E ASN* 2.8 52.0 + - + +
393E VAL* 1.3 73.0 - - - +
395E ASP* 1.3 76.5 + - - +
396E GLY* 3.0 2.0 + - - -
442F ALA* 4.1 24.7 - - + +
445F GLU* 4.5 9.6 - - + +
446F ALA* 4.5 16.2 - - + -
449F LYS* 4.2 34.5 - - + +
450F LYS* 3.8 25.4 - - + +
453F ASP* 6.2 0.2 - - - +
1Q G 4.9 2.9 - - - +
2Q A 4.3 5.4 - - - +
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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