Contacts of the helix formed by residues 379 - 394 (chain A) in PDB entry 3PEI
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 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A ALA* 3.2 6.8 - - - +
378A ASN* 1.3 91.6 - - - +
380A ASP* 1.3 64.8 + - - +
381A LYS* 3.4 2.9 + - - +
382A LEU* 3.3 14.6 + - - +
383A ALA* 3.0 22.9 + - - +
399A ARG* 4.4 1.1 - - - +
443A GLU* 2.7 43.3 + - - -
444A TRP 4.4 0.7 - - - -
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Residues in contact with ASP 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A SER* 1.3 69.4 - - - +
381A LYS* 1.3 68.1 + - - +
383A ALA* 3.7 0.5 - - - +
384A ASN* 2.9 35.9 + - - +
399A ARG* 2.8 32.8 + - - +
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Residues in contact with LYS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A LYS* 6.0 2.8 - - - +
379A SER* 3.3 1.6 + - - +
380A ASP* 1.3 79.3 - - - +
382A LEU* 1.3 62.7 + - - +
384A ASN* 3.3 7.2 + - - +
385A SER* 3.1 25.8 + - - +
443A GLU* 3.8 21.3 + - - +
502A EDO 4.0 24.0 + - - +
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Residues in contact with LEU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A ALA* 3.9 8.7 - - + -
354A VAL 4.1 4.0 - - - +
355A ILE* 4.7 4.0 - - + -
377A ALA* 5.3 0.2 - - + -
379A SER* 3.3 17.0 + - - +
381A LYS* 1.3 78.2 - - - +
383A ALA* 1.3 66.1 + - - +
385A SER* 3.1 4.5 + - - -
386A LEU* 3.0 28.9 + - + +
443A GLU* 3.7 8.5 - - - +
444A TRP* 3.4 18.8 - - - +
445A ALA* 3.4 40.2 - - + +
473A TYR* 3.5 31.0 - - + +
502A EDO 3.5 22.8 - - - +
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Residues in contact with ALA 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A MSE 3.3 32.9 - - + +
377A ALA* 3.9 6.2 - - + +
379A SER 3.0 13.9 + - - +
380A ASP 3.7 2.7 - - - +
382A LEU* 1.3 76.9 - - - +
384A ASN* 1.3 57.0 + - - +
386A LEU* 3.3 2.1 + - - -
387A GLU* 2.8 30.8 + - - +
399A ARG* 3.4 34.5 - - - +
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Residues in contact with ASN 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380A ASP* 2.9 27.6 + - - +
381A LYS* 3.7 6.3 - - - +
383A ALA* 1.3 79.0 - - - +
385A SER* 1.3 56.4 + - - +
387A GLU* 3.2 20.4 + - - +
388A GLN* 2.9 40.6 + - - +
399A ARG* 5.5 1.7 + - - -
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Residues in contact with SER 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A LYS* 3.1 11.0 + - - +
382A LEU 3.1 5.6 + - - -
384A ASN* 1.3 73.2 - - - +
386A LEU* 1.3 66.3 + - - +
388A GLN* 3.3 11.5 + - - +
389A ALA* 3.0 23.7 + - - +
473A TYR* 3.7 19.2 - - - -
476A SER* 6.1 1.1 - - - -
477A GLN* 4.2 6.6 + - - -
480A GLU* 5.7 0.7 + - - -
502A EDO 2.9 27.1 + - - -
510A EDO 4.6 2.3 - - - +
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A ILE* 4.4 19.5 - - + -
375A MSE 4.3 10.1 - - + -
382A LEU* 3.0 23.0 + - + +
383A ALA 3.7 7.2 - - - +
385A SER* 1.3 75.5 - - - +
387A GLU* 1.3 58.2 + - - +
389A ALA* 3.4 3.1 + - - +
390A ALA* 2.9 29.3 + - - +
397A ILE* 3.5 16.4 - - + +
445A ALA* 3.5 32.1 - - + -
447A LEU* 5.0 8.5 - - + -
469A LEU* 3.7 19.6 - - + +
470A LEU* 4.9 4.5 - - + -
473A TYR* 4.0 30.5 - - + -
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Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A MSE 3.9 4.9 - - - -
383A ALA* 2.8 21.2 + - - +
384A ASN* 3.2 26.6 - - - +
385A SER 3.2 0.2 - - - -
386A LEU* 1.3 77.5 - - - +
388A GLN* 1.3 57.5 + - + +
390A ALA* 3.4 3.8 + - - +
391A ASN* 3.0 37.6 + - - +
397A ILE* 3.9 21.3 - - + +
399A ARG* 3.6 29.7 + - - +
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Residues in contact with GLN 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A ASN* 2.9 27.4 + - + +
385A SER* 3.7 9.2 - - - +
386A LEU 3.3 0.2 - - - -
387A GLU* 1.3 74.8 - - + +
389A ALA* 1.3 60.0 + - - +
391A ASN* 3.2 11.0 + - - +
392A ALA* 2.9 30.0 + - - +
476A SER* 5.7 1.0 + - - -
510A EDO 3.8 21.7 - - + +
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Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A SER 3.0 17.1 + - - +
386A LEU* 3.7 2.2 - - - +
388A GLN* 1.3 74.6 - - - +
390A ALA* 1.3 57.4 + - - +
392A ALA* 3.3 1.2 + - - +
393A SER* 2.8 34.8 + - - -
469A LEU* 3.7 18.8 - - + +
472A HIS* 4.1 1.6 - - + +
473A TYR* 3.7 35.7 - - + +
510A EDO 3.5 14.6 + - - +
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Residues in contact with ALA 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A LEU 2.9 17.9 + - - +
387A GLU 3.6 4.9 - - - +
388A GLN 3.2 0.2 - - - -
389A ALA* 1.3 74.1 - - - +
391A ASN* 1.3 60.8 + - - +
393A SER* 4.0 0.9 - - - -
394A ASN* 2.9 30.5 + - - -
395A ASP 3.5 19.9 + - - +
396A LEU* 4.5 5.8 - - + +
397A ILE* 3.7 27.6 - - + +
469A LEU* 3.4 9.8 - - + +
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Residues in contact with ASN 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A GLU* 3.0 24.1 + - - +
388A GLN* 3.2 11.1 + - - +
390A ALA* 1.3 80.7 - - - +
392A ALA* 1.3 65.1 + - - +
394A ASN* 3.5 17.0 + - - +
396A LEU* 5.8 4.1 - - - +
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Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLN* 3.2 35.1 + - - +
388A GLN 2.9 10.7 + - - +
389A ALA 3.7 2.5 - - - +
391A ASN* 1.3 80.3 - - - +
393A SER* 1.3 61.2 + - - +
394A ASN* 3.5 5.0 + - - -
472A HIS* 4.0 7.6 - - - +
510A EDO 3.3 34.8 - - + +
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Residues in contact with SER 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLN* 4.1 2.5 - - - +
115A ASP* 4.0 11.6 - - - +
118A ARG* 5.1 0.9 + - - -
389A ALA 2.8 22.6 + - - -
390A ALA* 3.8 0.7 + - - -
392A ALA* 1.3 73.9 - - - +
394A ASN* 1.3 69.1 + - - +
395A ASP* 3.1 24.0 + - - +
468A PRO* 4.0 7.8 - - - +
469A LEU* 3.8 5.5 - - - -
472A HIS* 3.2 39.0 - - - -
501A FMT 3.1 12.1 - - - +
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Residues in contact with ASN 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ALA* 3.5 32.9 + - - +
75A SER* 3.7 33.4 + - - +
111A GLN* 5.2 1.6 - - - +
115A ASP* 4.0 14.5 + - - -
390A ALA 2.9 12.4 + - - +
391A ASN* 3.8 9.6 + - - +
392A ALA 3.3 10.1 + - - -
393A SER* 1.3 81.4 + - - +
395A ASP* 1.3 59.1 + - - +
396A LEU* 3.4 13.9 + - - +
465A ARG* 6.0 0.2 - - - -
501A FMT 3.4 9.6 - - - +
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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