Contacts of the helix formed by residues 369 - 383 (chain A) in PDB entry 2PFV
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 THR 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A PRO* 3.9 13.7 - - + -
367A GLY 3.6 4.7 - - - +
368A VAL* 1.3 73.7 - - - +
370A GLU* 1.3 65.0 + - - +
371A ALA* 3.6 10.6 + - - +
372A THR* 3.2 15.2 + - - -
373A VAL* 3.2 24.8 + - - +
442A LEU* 3.9 9.1 - - + +
445A LYS* 5.2 4.9 - - - +
475A PHE* 3.6 37.5 - - + -
479A ASN* 2.9 18.7 + - - +
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Residues in contact with GLU 370 (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 LYS* 4.6 20.7 + - + +
358A SER* 6.1 0.9 - - - +
359A ILE* 5.7 10.3 - - + -
369A THR* 1.3 73.7 - - - +
371A ALA* 1.3 58.2 + - - +
373A VAL* 3.0 14.1 + - - +
374A ASP* 2.8 42.8 + - - +
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Residues in contact with ALA 371 (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 ILE 5.2 0.4 - - - +
355A LYS* 3.8 42.1 + - + +
356A ALA* 3.8 10.8 - - - +
369A THR* 3.2 9.8 + - - +
370A GLU* 1.3 80.9 - - - +
372A THR* 1.3 53.9 + - - +
374A ASP* 3.8 2.7 - - - +
375A THR* 2.6 39.0 + - - +
438A LEU* 4.3 7.4 - - + -
442A LEU* 4.3 7.6 - - + -
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Residues in contact with THR 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A VAL* 4.3 1.3 - - + -
369A THR* 3.2 7.6 + - - -
370A GLU 3.2 0.6 - - - -
371A ALA* 1.3 74.9 - - - +
373A VAL* 1.3 67.2 + - - +
375A THR* 3.7 0.3 - - - -
376A MET* 2.9 26.6 + - + +
438A LEU* 3.8 13.3 - - + +
442A LEU* 3.7 8.1 - - - +
479A ASN* 2.6 53.1 + - - +
482A LEU* 3.6 23.3 - - + -
483A VAL* 4.1 16.4 - - + -
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Residues in contact with VAL 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A VAL* 3.9 16.8 - - + -
369A THR 3.2 14.8 + - - +
370A GLU* 3.0 16.7 + - - +
372A THR* 1.3 75.2 - - - +
374A ASP* 1.3 59.7 + - - +
376A MET* 3.9 2.6 - - - +
377A SER* 2.9 30.8 + - - -
482A LEU* 4.3 11.2 - - + -
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Residues in contact with ASP 374 (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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351A ARG* 2.8 46.9 + - - -
355A LYS* 3.9 23.4 + - - +
370A GLU* 2.8 28.8 + - - +
371A ALA* 3.8 5.8 - - - +
373A VAL* 1.3 79.1 - - - +
375A THR* 1.3 64.2 + - - +
377A SER* 2.6 25.8 + - - -
378A ARG* 2.9 10.3 + - - +
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Residues in contact with THR 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ARG* 6.1 0.9 - - - +
352A ILE* 3.7 47.5 - - + +
355A LYS* 5.4 1.4 - - - +
371A ALA* 2.6 26.6 + - - +
372A THR 3.7 4.3 - - - -
374A ASP* 1.3 81.2 + - - +
376A MET* 1.3 78.8 + - + +
378A ARG* 3.4 3.8 + - - +
379A LEU* 2.9 36.5 + - + +
434A CYS 4.8 0.9 - - - +
438A LEU* 4.2 13.7 - - + +
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Residues in contact with MET 376 (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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372A THR* 2.9 22.6 + - + +
373A VAL* 4.0 3.4 - - - +
375A THR* 1.3 109.5 - - + +
377A SER* 1.3 61.4 + - - +
379A LEU* 3.4 24.2 - - + +
380A ARG* 2.8 31.1 + - - +
435A ILE* 4.8 4.7 - - + -
438A LEU* 4.1 13.5 - - + -
482A LEU* 4.9 2.0 - - + -
483A VAL* 3.8 43.1 - - + +
486A ILE* 3.8 38.2 - - + +
487A VAL* 5.4 3.1 - - - -
492A LEU* 5.7 1.1 - - - -
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Residues in contact with SER 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A VAL* 2.9 18.0 + - - -
374A ASP* 2.6 28.5 + - - -
376A MET* 1.3 76.0 - - - +
378A ARG* 1.3 61.9 + - - +
380A ARG* 3.3 11.6 + - - +
381A LYS* 3.2 23.2 + - - +
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Residues in contact with ARG 378 (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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298A LEU 5.3 1.6 + - - -
299A GLU* 4.2 20.4 + - - +
302A GLY* 6.0 1.0 - - - -
303A PHE* 3.0 35.5 - - + -
344A LEU* 4.8 9.9 + - - +
347A ASP* 4.8 8.3 + - - -
348A ALA* 4.6 12.3 - - - +
351A ARG* 3.3 54.0 - - - +
374A ASP 2.9 12.9 + - - +
375A THR* 3.7 6.3 - - - +
377A SER* 1.3 79.4 + - - +
379A LEU* 1.3 61.5 + - + +
380A ARG 3.0 1.8 - - - -
381A LYS* 2.7 35.2 + - - +
382A PHE* 3.1 31.6 + - + -
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Residues in contact with LEU 379 (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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348A ALA* 5.3 3.1 - - + -
352A ILE* 5.0 2.5 - - + -
375A THR* 2.9 25.2 + - + +
376A MET* 3.4 35.4 - - + +
378A ARG* 1.3 84.8 - - + +
380A ARG* 1.3 61.1 + - - +
382A PHE* 3.5 15.2 + - + +
383A SER 3.2 15.9 + - - -
430A PHE* 5.3 4.3 - - + -
431A ILE* 4.4 17.0 - - + -
434A CYS* 4.1 33.9 - - + -
435A ILE* 4.4 11.9 - - + -
492A LEU* 3.5 26.0 - - + +
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Residues in contact with ARG 380 (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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376A MET 2.8 18.8 + - - +
377A SER* 3.3 11.0 - - - +
378A ARG 3.0 0.2 - - - -
379A LEU* 1.3 76.9 - - - +
381A LYS* 1.3 62.8 + - + +
383A SER* 2.5 25.8 + - - -
384A GLU* 3.1 21.6 + - + +
486A ILE* 4.7 16.6 - - + -
489A LYS 3.4 17.4 + - - -
490A SER* 2.7 39.8 + - - +
491A GLU 4.4 1.2 - - - +
492A LEU* 4.2 5.6 - - - +
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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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303A PHE* 3.4 26.7 - - + -
377A SER 3.4 14.6 - - - +
378A ARG* 2.7 13.2 + - - +
380A ARG* 1.3 75.5 - - + +
382A PHE* 1.3 56.8 + - - +
384A GLU* 2.6 48.3 + - - +
385A TYR* 3.7 7.4 - - + -
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Residues in contact with PHE 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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303A PHE* 3.3 31.6 - + - -
306A PHE* 4.7 3.6 - + - -
344A LEU* 3.9 30.7 - - + -
345A PHE* 4.1 33.2 - + - -
348A ALA* 4.1 13.0 - - + -
378A ARG* 3.1 48.7 + - + -
379A LEU* 3.8 12.6 - - + +
380A ARG 3.5 0.2 - - - -
381A LYS* 1.3 79.0 - - - +
383A SER* 1.3 57.9 - - - +
385A TYR 2.9 19.6 + - - -
386A LYS* 3.6 0.3 + - - -
389A CYS* 3.1 37.1 - - - -
427A LEU* 6.2 0.7 - - + -
430A PHE* 4.2 12.8 - + + -
431A ILE* 6.5 1.6 - - + -
492A LEU* 5.9 0.9 - - + -
495A MET* 5.0 4.0 - - + -
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Residues in contact with SER 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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379A LEU 3.2 3.3 + - - -
380A ARG* 2.5 24.8 + - - -
381A LYS 3.1 0.2 - - - -
382A PHE* 1.3 77.0 - - - +
384A GLU* 1.3 59.9 + - - +
385A TYR 3.2 0.8 + - - -
386A LYS* 4.0 7.1 + - - +
490A SER* 3.6 13.0 + - - -
491A GLU* 3.5 28.2 - - - +
492A LEU* 3.7 20.8 - - - +
495A MET* 3.5 29.8 - - - +
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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