Contacts of the helix formed by residues 358 - 374 (chain A) in PDB entry 3DCT
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 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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356A GLY 3.7 0.8 + - - -
357A ILE* 1.3 75.2 - - - +
359A ASP* 1.3 62.6 + - - +
360A GLU* 3.7 18.3 + - - +
361A TYR* 2.9 31.7 + - - +
362A ILE* 3.1 10.0 + - - +
450A MET* 3.3 29.3 - - - +
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Residues in contact with ASP 359 (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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357A ILE 3.5 4.2 + - - +
358A SER* 1.3 69.1 + - - +
360A GLU* 1.3 70.5 + - + +
361A TYR 2.9 7.0 + - - -
362A ILE* 4.3 14.0 - - - +
363A THR* 3.1 35.8 + - - +
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Residues in contact with GLU 360 (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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358A SER* 3.1 15.0 - - - +
359A ASP* 1.3 83.5 - - + +
361A TYR* 1.3 74.5 + - + +
363A THR* 5.5 0.4 - - - -
364A PRO* 3.1 22.6 - - - +
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Residues in contact with TYR 361 (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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357A ILE* 4.0 10.5 - - + -
358A SER* 2.9 15.1 + - - +
360A GLU* 1.3 95.6 - - + +
362A ILE* 1.3 63.5 + - - +
363A THR 3.4 1.6 - - - -
364A PRO* 3.2 7.5 - - + +
365A MET* 3.2 30.3 + - + +
443A PHE* 4.9 2.8 - - - -
446A HIS* 3.5 42.3 - - + -
449A GLU* 2.9 37.1 + - + +
450A MET* 3.6 39.0 - - + -
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Residues in contact with ILE 362 (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* 3.5 42.6 - - + +
353A ARG* 3.4 39.3 - - - +
357A ILE* 4.0 24.7 - - + +
358A SER 3.1 14.1 + - - +
359A ASP* 3.3 14.8 + - - +
361A TYR* 1.3 73.3 - - - +
363A THR* 1.3 67.6 + - - +
365A MET* 3.2 5.5 + - - +
366A PHE* 2.9 35.4 + - + -
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Residues in contact with THR 363 (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 ARG* 5.8 1.3 - - - +
359A ASP* 3.1 20.9 + - - +
360A GLU* 4.9 0.9 - - - -
362A ILE* 1.3 81.7 - - - +
364A PRO* 1.3 65.7 - - + +
366A PHE* 3.3 3.2 + - - +
367A SER* 2.9 33.3 + - - -
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Residues in contact with PRO 364 (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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360A GLU 3.1 26.0 - - - +
361A TYR* 3.2 9.6 - - + +
363A THR* 1.3 99.8 - - + +
365A MET* 1.3 60.8 + - - +
367A SER* 3.8 7.4 - - - -
368A PHE* 3.0 24.6 + - - +
443A PHE* 3.3 22.5 - - + -
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Residues in contact with MET 365 (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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1A 064 3.8 31.9 - - + -
329A PHE* 3.7 22.0 - - + -
352A ILE* 3.9 23.3 - - - -
357A ILE* 4.4 21.3 - - + -
361A TYR* 3.2 21.3 + - + +
362A ILE* 3.3 7.2 - - + +
363A THR 3.2 0.2 - - - -
364A PRO* 1.3 79.4 - - - +
366A PHE* 1.3 65.8 + - + +
368A PHE* 3.3 6.2 - - - +
369A TYR* 3.1 45.5 + - + -
443A PHE* 3.8 11.6 - - + -
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Residues in contact with PHE 366 (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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336A PHE* 4.4 7.2 - + - -
349A GLU* 3.2 39.7 - - + -
352A ILE* 4.0 23.6 - - + -
353A ARG* 3.7 25.8 - - - +
362A ILE* 2.9 59.6 + - + +
363A THR* 4.1 2.5 - - - +
365A MET* 1.3 78.3 - - + +
367A SER* 1.3 61.1 + - - +
368A PHE 3.1 1.3 - - - -
369A TYR* 3.1 28.3 + + + +
370A LYS* 2.8 30.5 + - - +
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Residues in contact with SER 367 (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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363A THR* 2.9 21.3 + - - -
364A PRO* 3.8 9.2 - - - -
366A PHE* 1.3 75.8 - - - +
368A PHE* 1.3 62.1 + - - +
370A LYS* 3.3 7.0 + - - +
371A SER* 3.0 25.8 + - - -
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Residues in contact with PHE 368 (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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329A PHE* 3.7 44.2 - + - -
330A LEU* 5.1 1.6 - - + -
333A ALA* 4.0 9.6 - - + -
364A PRO 3.0 19.8 + - - +
365A MET 3.3 4.0 - - - +
366A PHE 3.1 0.2 - - - -
367A SER* 1.3 77.6 - - - +
369A TYR* 1.3 70.7 + + - +
371A SER* 3.6 4.0 + - - -
372A ILE* 3.0 51.3 + - + +
436A ARG* 4.4 6.3 - - + -
439A GLU* 3.6 31.0 - - + -
440A LEU* 3.5 30.7 - - + -
443A PHE* 3.7 19.7 - + + -
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Residues in contact with TYR 369 (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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1A 064 3.7 19.8 - - - -
329A PHE* 3.7 5.8 - + - -
332A SER* 2.6 25.1 + - - -
333A ALA* 3.4 41.7 - - + -
336A PHE* 3.5 28.4 - + + -
337A ASN* 3.1 27.1 + - - +
352A ILE* 5.0 2.7 - - + +
365A MET* 3.1 34.6 + - + -
366A PHE* 3.1 36.5 + + + +
368A PHE* 1.3 89.7 - + - +
370A LYS* 1.3 61.2 + - - +
372A ILE* 3.1 3.5 - - - +
373A GLY 3.1 6.9 + - - -
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Residues in contact with LYS 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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366A PHE 2.8 15.1 + - - +
367A SER* 3.6 7.9 - - - +
368A PHE 3.2 0.2 - - - -
369A TYR* 1.3 74.6 - - - +
371A SER* 1.3 65.3 + - - +
373A GLY* 3.0 9.9 + - - -
374A GLU* 3.0 28.4 + - + +
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Residues in contact with SER 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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367A SER* 3.0 12.3 + - - -
368A PHE* 3.6 8.5 + - - -
370A LYS* 1.3 78.3 - - - +
372A ILE* 1.3 65.4 + - - +
374A GLU* 3.3 30.0 + - - +
375A LEU* 3.8 2.8 + - - +
436A ARG* 3.2 27.2 + - - -
439A GLU* 4.3 9.2 + - - -
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Residues in contact with ILE 372 (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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330A LEU* 4.1 19.7 - - + -
333A ALA* 3.9 10.8 - - + -
337A ASN* 3.4 12.8 - - - +
368A PHE* 3.0 41.2 + - + +
369A TYR* 3.1 13.0 - - - +
371A SER* 1.3 78.2 + - - +
373A GLY* 1.3 70.9 + - - +
375A LEU* 2.9 17.3 + - - +
376A LYS 4.1 1.2 + - - -
377A MET* 3.1 37.0 + - + +
382A TYR* 4.4 10.3 + - + +
436A ARG* 3.6 24.5 - - + +
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Residues in contact with GLY 373 (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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337A ASN* 3.1 34.4 - - - +
369A TYR 3.1 0.8 + - - -
370A LYS 3.0 8.2 + - - -
372A ILE* 1.3 83.6 - - - +
374A GLU* 1.3 57.6 + - - +
375A LEU 2.9 7.0 + - - -
376A LYS* 3.1 14.4 + - - +
377A MET 5.0 0.2 + - - -
382A TYR* 5.0 0.7 - - - -
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Residues in contact with GLU 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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370A LYS* 3.0 21.7 + - - +
371A SER* 3.4 21.4 - - - +
372A ILE 3.1 0.2 - - - -
373A GLY* 1.3 75.3 - - - +
375A LEU* 1.3 61.0 + - - +
376A LYS* 3.4 1.5 - - - +
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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