Contacts of the helix formed by residues 372 - 390 (chain A) in PDB entry 3T2D
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 372 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A PRO* 4.1 6.5 - - + +
371A TYR* 1.4 82.4 - - + +
373A ALA* 1.3 60.1 + - - +
374A ASP* 3.3 3.7 + - + +
375A GLN* 3.4 14.3 + - + +
376A TYR* 2.9 25.5 + - - +
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A TYR 3.2 6.0 + - - +
372A PRO* 1.3 71.2 - - - +
374A ASP* 1.3 67.6 + - - +
376A TYR* 3.4 7.7 + - - +
377A GLU* 3.3 25.6 + - - +
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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
----------------------------------------------------------
372A PRO* 3.3 2.1 + - + +
373A ALA* 1.3 82.5 - - - +
375A GLN* 1.3 63.5 + - - +
377A GLU* 3.3 18.5 + - - +
378A LYS* 3.9 15.0 + - - +
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Residues in contact with GLN 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PRO* 3.4 19.4 + - + +
374A ASP* 1.3 78.6 - - - +
376A TYR* 1.4 64.8 + - - +
378A LYS* 3.1 49.2 + - - +
379A ASP* 3.2 39.6 + - - +
383A TYR* 5.4 1.6 - - - +
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Residues in contact with TYR 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A TYR* 3.9 29.6 - + + +
372A PRO 2.9 18.2 + - - +
373A ALA* 3.7 9.2 - - - +
374A ASP 3.3 0.2 - - - -
375A GLN* 1.4 75.9 - - - +
377A GLU* 1.3 67.5 + - - +
379A ASP 3.0 2.2 + - - +
380A ARG* 2.9 74.9 + - + +
383A TYR* 3.7 37.7 - + + -
384A ILE* 4.1 15.2 - - - +
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Residues in contact with GLU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ALA 3.3 13.7 + - - +
374A ASP* 3.6 11.0 - - - +
375A GLN 3.3 0.6 - - - -
376A TYR* 1.3 81.3 - - - +
378A LYS* 1.3 64.7 + - + +
380A ARG* 3.0 56.2 + - - +
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Residues in contact with LYS 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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374A ASP* 4.1 14.0 + - - +
375A GLN* 3.1 44.3 + - - +
377A GLU* 1.3 79.5 - - + +
379A ASP* 1.3 64.3 + - - +
380A ARG 3.5 0.6 + - - -
381A LYS* 4.8 13.9 + - - +
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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
----------------------------------------------------------
375A GLN* 3.2 39.1 + - - +
376A TYR 3.0 1.8 + - - -
378A LYS* 1.3 82.1 - - - +
380A ARG* 1.3 54.4 + - - +
381A LYS 3.3 3.4 - - - -
382A LYS* 3.0 34.3 + - - +
383A TYR* 2.8 69.4 + - + -
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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
----------------------------------------------------------
376A TYR* 2.9 51.5 + - + +
377A GLU* 3.0 51.0 + - - +
378A LYS 3.5 2.2 - - - -
379A ASP* 1.3 74.3 - - - +
381A LYS* 1.3 60.3 + - - +
383A TYR* 3.0 4.4 + - - +
384A ILE* 2.7 44.3 + - + +
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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
----------------------------------------------------------
378A LYS 4.8 10.8 + - - +
379A ASP 3.3 3.8 - - - +
380A ARG* 1.3 79.8 - - - +
382A LYS* 1.3 89.1 + - + +
384A ILE* 3.9 5.3 - - - +
385A GLU* 3.0 44.5 + - - +
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Residues in contact with LYS 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ASP* 3.0 40.3 + - - +
381A LYS* 1.3 95.3 - - + +
383A TYR* 1.3 74.5 + - + +
385A GLU* 3.3 10.3 + - - +
386A ALA* 2.9 29.4 + - + +
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Residues in contact with TYR 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A LYS* 5.7 0.6 - - - -
371A TYR* 3.4 49.6 - + + +
375A GLN* 5.4 1.9 - - - +
376A TYR* 3.7 34.8 - + + +
379A ASP* 2.8 53.2 + - + -
380A ARG* 3.5 5.2 - - - +
382A LYS* 1.3 91.9 + - + +
384A ILE* 1.3 61.2 + - + +
386A ALA* 3.1 9.7 + - + +
387A VAL* 2.9 33.2 + - + +
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Residues in contact with ILE 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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376A TYR* 4.1 14.6 - - - +
380A ARG* 2.7 37.0 + - + +
381A LYS* 4.0 4.7 - - - +
383A TYR* 1.3 73.6 - - + +
385A GLU* 1.4 62.4 + - + +
387A VAL* 3.2 11.8 + - + +
388A VAL* 2.9 40.5 + - + +
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Residues in contact with GLU 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* 3.0 37.8 + - + +
382A LYS* 3.8 8.3 - - - +
384A ILE* 1.4 73.8 - - + +
386A ALA* 1.3 57.2 + - - +
388A VAL* 3.6 7.0 - - - +
389A LYS* 2.8 64.0 + - - +
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Residues in contact with ALA 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LYS* 2.9 19.7 + - + +
383A TYR* 3.5 11.9 - - + +
385A GLU* 1.3 73.5 - - - +
387A VAL* 1.4 59.9 + - + +
389A LYS* 4.7 4.5 - - - +
390A GLY* 2.7 29.9 + - - +
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A TYR* 2.9 22.0 + - + +
384A ILE* 3.7 13.2 - - + +
386A ALA* 1.4 78.7 - - + +
388A VAL* 1.3 67.9 + - + +
390A GLY* 3.6 13.4 + - - -
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ILE* 2.9 35.9 + - + +
385A GLU* 3.6 7.0 - - - +
387A VAL* 1.3 82.1 - - + +
389A LYS* 1.3 65.9 + - + +
390A GLY 4.1 1.9 - - - -
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Residues in contact with LYS 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLU* 2.8 49.8 + - - +
386A ALA* 4.1 3.9 - - - +
388A VAL* 1.3 74.5 - - + +
390A GLY* 1.3 71.7 + - - +
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Residues in contact with GLY 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ALA 2.7 24.6 + - - -
387A VAL* 3.7 13.2 - - - -
388A VAL 4.1 2.5 - - - -
389A LYS* 1.3 84.4 - - - +
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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