Contacts of the helix formed by residues 380 - 392 (chain A) in PDB entry 3V42
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 ASP 380 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A PRO* 4.4 12.1 - - - +
378A SER* 2.9 10.1 + - - +
379A ARG* 1.3 78.5 - - + +
381A VAL* 1.3 64.2 + - - +
382A ASP* 3.2 12.5 + - - +
383A LEU* 3.2 35.1 + - + +
384A VAL* 3.3 17.9 + - - +
405A TYR* 4.7 1.1 - - - -
463A TYR* 2.7 33.6 + - + +
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ARG 3.6 5.3 + - - -
380A ASP* 1.3 74.3 + - - +
382A ASP* 1.3 76.4 + - - +
384A VAL* 3.5 3.6 + - - +
385A GLN* 3.1 27.0 + - + +
404A PRO 5.6 0.2 - - - +
405A TYR* 3.9 44.6 - - + -
397B VAL* 4.3 19.3 - - + -
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Residues in contact with ASP 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A PRO 5.8 0.2 - - - +
345A VAL* 4.2 14.2 - - + +
380A ASP* 3.2 8.7 + - - +
381A VAL* 1.3 91.3 - - - +
383A LEU* 1.3 64.3 + - - +
385A GLN* 3.7 7.7 - - - +
386A SER* 3.0 23.2 + - - -
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A PRO 3.6 22.8 + - - +
345A VAL* 4.1 2.7 - - - -
346A PHE* 3.6 28.7 - - + -
376A TRP* 5.1 2.2 - - + -
378A SER* 4.3 10.1 - - - +
380A ASP* 3.2 25.5 + - + +
382A ASP* 1.3 76.9 - - - +
384A VAL* 1.3 63.1 + - - +
386A SER* 2.6 22.1 + - - -
387A ALA* 3.0 8.0 + - - +
441A VAL* 4.2 31.4 - - + -
460A LEU* 4.1 16.6 - - + -
463A TYR* 4.2 15.5 - - + -
465A PHE* 4.3 8.7 - - + -
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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
----------------------------------------------------------
376A TRP* 4.1 25.1 - - + +
378A SER* 3.6 27.6 - - - +
380A ASP 3.3 12.7 + - - +
381A VAL 3.7 7.4 - - - +
382A ASP 3.3 0.2 - - - -
383A LEU* 1.3 75.5 - - + +
385A GLN* 1.3 65.3 + - - +
387A ALA* 3.1 16.3 + - - +
388A PHE* 3.2 37.6 + - + -
404A PRO 3.8 15.0 - - - +
405A TYR* 4.5 9.6 - - + -
419A GLY* 4.1 8.3 - - - -
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Residues in contact with GLN 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A VAL* 3.1 19.8 + - + +
382A ASP* 3.8 9.0 - - - +
384A VAL* 1.3 77.9 - - - +
386A SER* 1.3 63.6 + - - +
388A PHE* 3.3 9.1 + - - +
389A GLU* 3.0 50.4 + - + +
402A ILE* 5.9 0.5 - - - +
404A PRO* 3.9 15.0 + - + +
392B ARG* 3.7 30.0 + - - +
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Residues in contact with SER 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A VAL* 3.6 21.7 - - - +
346A PHE* 2.9 30.3 + - - -
382A ASP 3.0 13.7 + - - -
383A LEU 2.6 19.1 + - - -
385A GLN* 1.3 78.2 - - - +
387A ALA* 1.3 60.7 + - - +
389A GLU* 3.4 9.4 + - - +
390A VAL* 3.1 27.4 + - - +
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Residues in contact with ALA 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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346A PHE* 3.9 3.6 - - + -
352A MET* 3.6 10.7 - - + +
376A TRP* 3.8 48.9 - - + +
383A LEU 3.0 10.7 + - - +
384A VAL 3.1 10.3 + - - +
386A SER* 1.3 76.9 + - - +
388A PHE* 1.3 59.4 + - + +
390A VAL* 3.3 4.2 + - - +
391A LEU* 2.9 31.8 + - - +
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Residues in contact with PHE 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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374A VAL* 4.0 8.7 - - + -
376A TRP* 3.9 25.6 - + - -
384A VAL* 3.2 35.0 + - + -
385A GLN* 3.8 9.4 - - - +
387A ALA* 1.3 76.5 - - + +
389A GLU* 1.3 67.9 + - - +
391A LEU* 4.4 8.1 - - + +
392A ARG* 3.1 31.5 + - - +
402A ILE* 4.2 16.4 - - + -
404A PRO* 4.2 11.4 - - + -
417A PHE* 3.6 37.1 - + + -
418A LEU 3.5 28.3 - - - -
419A GLY* 3.8 11.7 - - - -
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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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385A GLN* 3.0 45.6 + - + +
386A SER* 3.6 9.2 - - - +
388A PHE* 1.3 79.0 - - - +
390A VAL* 1.3 62.9 + - + +
392A ARG* 3.4 41.7 + - - +
393A THR* 3.7 11.1 - - - +
389B GLU* 5.6 1.9 - - - +
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Residues in contact with VAL 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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346A PHE* 4.0 24.9 - - + +
347A LYS 4.5 1.6 - - - -
348A SER* 3.8 27.6 - - - +
349A LEU* 3.7 25.2 - - + +
352A MET* 3.6 20.2 - - + -
386A SER 3.1 16.8 + - - +
387A ALA 3.5 2.9 - - - +
389A GLU* 1.3 77.0 - - + +
391A LEU* 1.3 60.9 + - - +
393A THR* 2.7 29.7 + - - -
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Residues in contact with LEU 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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349A LEU* 4.9 3.6 - - + -
352A MET* 3.7 21.5 - - - -
361A PHE* 5.0 2.5 - - + -
364A LEU* 3.9 23.3 - - + -
368A VAL* 3.9 18.7 - - + +
374A VAL* 4.2 10.5 - - + -
376A TRP* 3.7 28.9 - - + +
387A ALA 2.9 24.0 + - - +
388A PHE* 4.2 9.0 - - + +
390A VAL* 1.3 75.1 - - - +
392A ARG* 1.3 62.7 + - - +
393A THR 3.1 1.2 + - - -
394A MET* 3.2 42.7 + - + +
417A PHE* 4.3 13.2 - - + -
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Residues in contact with ARG 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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388A PHE* 3.1 22.9 + - - +
389A GLU* 3.4 40.8 + - - +
391A LEU* 1.3 76.6 - - - +
393A THR* 1.3 60.1 + - + +
394A MET 2.9 6.2 + - - -
395A LEU* 3.0 24.1 + - - +
397A VAL* 4.6 10.3 - - - +
400A VAL* 4.1 20.6 - - + +
402A ILE* 3.8 23.0 - - - +
417A PHE* 4.0 18.3 - - + -
508A LYS* 4.3 0.2 + - - -
385B GLN* 3.0 38.8 + - - +
402B ILE* 6.4 0.2 - - - +
404B PRO* 3.5 18.1 - - - +
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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