Contacts of the helix formed by residues 374 - 392 (chain A) in PDB entry 4D2Y
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 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A ARG* 2.9 40.6 + - - +
372A PHE 4.8 0.4 - - - -
373A GLY* 1.3 79.9 - - - +
375A LYS* 1.3 58.5 + - - +
376A ALA* 3.5 7.8 + - - +
377A HIS* 2.9 20.7 + - - +
378A MET* 2.8 32.1 + - - +
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Residues in contact with LYS 375 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A SER* 1.3 71.8 - - - +
376A ALA* 1.3 53.2 + - - +
378A MET* 3.1 6.8 + - + +
379A ASP* 2.6 69.6 + - - +
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Residues in contact with ALA 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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366A TYR* 3.6 15.6 + - + +
371A ARG* 5.4 7.4 - - - +
374A SER* 3.3 8.4 + - - +
375A LYS* 1.3 79.5 - - - +
377A HIS* 1.3 55.7 + - - +
379A ASP* 3.8 8.6 - - - +
380A ARG* 2.9 31.2 + - - +
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Residues in contact with HIS 377 (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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362A LEU 3.9 1.2 + - - -
363A ASP* 2.8 39.1 + - - -
366A TYR* 3.6 32.6 - + + -
371A ARG 3.5 7.0 - - - +
372A PHE* 3.8 27.1 - + - -
373A GLY 3.2 20.1 + - - -
374A SER* 2.9 25.0 + - - +
376A ALA* 1.3 75.9 - - - +
378A MET* 1.3 75.8 + - + +
380A ARG* 3.2 2.9 + - - +
381A LEU* 2.9 36.5 + - + +
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Residues in contact with MET 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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372A PHE* 5.9 2.5 - - + -
373A GLY* 3.7 28.7 - - - +
374A SER 2.8 21.3 + - - +
375A LYS* 3.7 6.5 - - + +
377A HIS* 1.3 95.1 - - + +
379A ASP* 1.3 59.8 + - - +
381A LEU* 3.4 17.5 + - + +
382A GLU* 2.8 30.0 + - - +
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Residues in contact with ASP 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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375A LYS* 2.6 64.1 + - - +
376A ALA* 3.8 8.0 + - - +
378A MET* 1.3 75.4 - - - +
380A ARG* 1.3 52.2 + - - +
382A GLU* 3.1 8.6 + - - +
383A GLU* 2.7 36.2 + - - +
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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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362A LEU* 4.3 10.2 - - + +
366A TYR* 3.3 31.0 - - + +
376A ALA 2.9 19.0 + - - +
377A HIS 3.6 3.4 - - - +
379A ASP* 1.3 73.7 - - - +
381A LEU* 1.3 60.0 + - - +
383A GLU* 2.6 43.4 + - - +
384A VAL* 2.8 57.6 + - - +
387A GLU* 4.7 4.6 + - - -
394A TYR* 4.6 2.4 - - - -
395A GLN 3.0 25.5 + - - -
396A LEU* 4.0 0.4 - - - +
397A LYS* 3.5 25.4 - - - +
400A GLU* 2.8 37.0 + - - +
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Residues in contact with LEU 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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355A PHE* 3.6 19.2 - - + -
359A LYS* 4.0 36.3 - - + -
362A LEU* 3.7 39.0 - - + -
363A ASP* 4.0 16.8 - - - +
377A HIS* 2.9 23.8 + - + +
378A MET* 3.5 19.1 - - + +
380A ARG* 1.3 75.8 - - - +
382A GLU* 1.3 58.8 + - - +
384A VAL* 3.9 0.2 - - - +
385A ASN* 2.9 31.6 + - - +
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Residues in contact with GLU 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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378A MET 2.8 15.0 + - - +
379A ASP* 3.3 13.2 - - - +
381A LEU* 1.3 77.1 - - - +
383A GLU* 1.3 58.8 + - - +
385A ASN* 3.2 10.3 + - - +
386A LYS* 2.9 64.9 + - + +
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Residues in contact with GLU 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 ASP 2.7 19.5 + - - +
380A ARG* 2.6 39.5 + - - +
382A GLU* 1.3 74.5 - - - +
384A VAL* 1.3 61.8 + - - +
386A LYS* 3.4 8.7 + - - +
387A GLU* 3.0 31.2 + - + +
397A LYS* 3.9 16.4 + - - -
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Residues in contact with VAL 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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355A PHE* 4.5 2.2 - - + -
358A ALA* 3.9 14.8 - - + -
362A LEU* 3.8 15.0 - - + -
380A ARG* 2.8 58.7 + - - +
381A LEU 3.9 3.4 - - - +
383A GLU* 1.3 73.1 - - - +
385A ASN* 1.3 58.2 + - - +
387A GLU* 3.1 8.1 + - - +
388A ILE* 2.9 41.7 + - + +
394A TYR* 3.7 31.6 - - + -
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Residues in contact with ASN 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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355A PHE* 3.1 48.5 - - + +
381A LEU 2.9 19.4 + - - +
382A GLU* 3.2 12.6 + - - +
384A VAL* 1.3 76.9 - - - +
386A LYS* 1.3 58.3 + - + +
388A ILE* 3.5 2.5 + - - +
389A GLU* 3.0 45.6 + - - +
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Residues in contact with LYS 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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382A GLU* 2.9 45.6 + - + +
383A GLU* 3.7 7.6 - - - +
385A ASN* 1.3 76.5 - - + +
387A GLU* 1.3 53.4 + - - +
389A GLU* 3.4 5.8 + - - +
390A SER* 2.7 37.6 + - - -
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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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380A ARG* 4.7 8.0 + - - -
383A GLU* 3.0 28.6 + - - +
384A VAL* 3.4 7.1 - - - +
386A LYS* 1.3 78.4 - - - +
388A ILE* 1.3 52.5 + - - +
390A SER* 4.2 4.9 - - - -
391A THR* 2.3 56.5 + - + +
393A THR 3.7 3.8 - - - +
394A TYR* 3.2 13.4 - - + +
395A GLN* 2.9 36.9 + - - +
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Residues in contact with ILE 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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351A LYS* 3.5 36.3 + - + +
354A LEU* 3.9 22.7 - - + -
355A PHE* 3.7 42.4 - - + +
358A ALA* 4.2 2.0 - - + -
384A VAL* 2.9 20.3 + - + +
385A ASN* 3.7 4.9 - - - +
387A GLU* 1.3 72.7 - - - +
389A GLU* 1.3 65.6 + - + +
390A SER 3.1 1.1 - - - -
392A SER* 2.7 32.0 + - - +
393A THR 3.5 10.8 - - - +
394A TYR* 3.9 24.0 - - + -
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Residues in contact with GLU 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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351A LYS* 2.4 32.9 + - - +
385A ASN* 3.0 35.0 + - - +
386A LYS* 3.7 6.7 - - - +
388A ILE* 1.3 80.1 - - + +
390A SER* 1.3 57.2 + - - +
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Residues in contact with SER 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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351A LYS* 4.1 3.6 + - - -
386A LYS 2.7 23.8 + - - -
387A GLU* 3.7 5.8 - - - -
389A GLU* 1.3 78.5 - - - +
391A THR* 1.3 69.4 + - - +
392A SER 3.7 0.4 + - - -
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Residues in contact with THR 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* 2.3 44.1 + - + +
390A SER* 1.3 83.3 - - - +
392A SER* 1.3 69.4 + - - +
393A THR* 2.8 32.7 + - - +
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Residues in contact with SER 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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350A THR 5.5 1.6 - - - -
351A LYS* 3.5 35.5 + - - +
354A LEU* 3.8 12.4 - - - +
388A ILE* 2.7 26.6 + - - -
390A SER 3.7 1.2 - - - -
391A THR* 1.3 80.7 + - - +
393A THR* 1.3 59.1 + - - +
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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