Contacts of the helix formed by residues 387 - 401 (chain A) in PDB entry 3V4O
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 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354A ARG* 3.7 26.7 - - - +
385A ASP 5.3 0.2 - - - +
386A LEU* 1.3 74.1 - - - +
388A GLU* 1.3 66.2 + - - +
389A TYR* 3.6 8.9 + - - +
390A GLU* 2.8 41.8 + - - +
391A MET* 2.8 20.6 + - - +
427A PRO* 3.6 2.0 - - - -
428A VAL* 3.8 8.0 - - + +
429A ASP* 3.4 24.9 - - + +
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Residues in contact with GLU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A THR* 1.3 72.2 - - - +
389A TYR* 1.3 64.6 + - - +
391A MET* 3.2 4.5 + - - +
392A ARG* 2.5 72.0 + - - +
427A PRO* 3.2 21.8 - - + +
429A ASP* 2.9 19.8 + - - +
437A GLU 3.4 7.9 - - - +
438A ASN* 3.8 26.0 - - - +
440A LEU* 4.3 2.7 - - + -
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Residues in contact with TYR 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A THR* 3.2 7.7 + - - +
388A GLU* 1.3 81.7 - - - +
390A GLU* 1.3 65.9 + - + +
392A ARG* 3.4 6.6 + - + +
393A ASN* 3.0 59.9 + - - -
429A ASP* 5.0 0.8 + - - +
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Residues in contact with GLU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A LEU* 5.5 0.2 - - - +
385A ASP 3.6 5.5 - - - +
386A LEU* 3.4 29.4 - - + +
387A THR* 2.8 45.1 + - - +
389A TYR* 1.3 87.0 - - + +
391A MET* 1.3 56.5 + - - +
393A ASN* 3.4 8.3 + - - +
394A ALA* 2.9 30.7 + - - +
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Residues in contact with MET 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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348A ILE* 4.3 15.9 - - + -
350A ASN* 3.6 21.8 - - - -
386A LEU* 3.4 24.9 - - + -
387A THR 2.8 16.1 + - - +
388A GLU 3.5 6.7 - - - +
390A GLU* 1.3 74.4 - - - +
392A ARG* 1.3 65.0 + - - +
394A ALA* 3.3 2.0 + - - +
395A VAL* 2.9 29.6 + - - +
412A TYR* 4.1 12.3 - - + -
425A MET* 3.8 37.7 - - + -
427A PRO* 3.8 25.1 - - - -
440A LEU* 3.9 19.5 - - + -
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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 GLU* 2.5 57.9 + - - +
389A TYR* 3.9 6.1 - - + +
391A MET* 1.3 75.2 - - - +
393A ASN* 1.3 64.9 + - - +
395A VAL* 3.3 6.1 + - - +
396A ASP* 3.0 32.2 + - - +
437A GLU* 3.3 13.5 + - - +
439A CYS 3.2 23.1 + - - -
440A LEU* 4.0 26.9 - - + +
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Residues in contact with ASN 393 (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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389A TYR* 3.0 63.5 + - - +
390A GLU* 3.7 7.3 - - - +
391A MET 3.3 0.2 - - - -
392A ARG* 1.3 78.2 - - - +
394A ALA* 1.3 62.1 + - - +
396A ASP* 3.2 12.9 + - - +
397A GLU* 3.0 33.7 + - + +
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Residues in contact with ALA 394 (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 LEU* 3.8 18.4 - - + +
348A ILE* 4.5 1.3 - - + -
381A VAL* 6.2 0.7 - - - -
383A LEU* 3.7 28.9 - - + -
386A LEU* 4.2 7.9 - - + -
390A GLU 2.9 21.6 + - - +
391A MET* 3.6 4.0 - - - +
393A ASN* 1.3 72.3 - - - +
395A VAL* 1.3 63.9 + - - +
397A GLU* 3.3 8.6 + - - +
398A PHE* 3.0 22.3 + - - +
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Residues in contact with VAL 395 (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 LEU* 3.9 20.6 - - + -
348A ILE* 4.9 6.5 - - + -
391A MET 2.9 18.4 + - - +
392A ARG* 4.0 7.0 - - - +
393A ASN 3.3 0.2 - - - -
394A ALA* 1.3 77.4 - - - +
396A ASP* 1.3 61.0 + - - +
398A PHE* 3.2 4.3 + - + +
399A LEU* 2.8 48.3 + - + +
410A LEU* 5.3 2.7 - - + -
425A MET* 5.5 1.6 - - + -
440A LEU* 3.8 20.2 - - + -
445A ILE* 4.0 33.0 - - + -
448A LEU* 5.8 2.2 - - + -
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Residues in contact with ASP 396 (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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392A ARG* 3.0 25.8 + - - +
393A ASN* 3.5 14.2 - - - +
395A VAL* 1.3 77.3 - - - +
397A GLU* 1.3 70.3 + - - +
399A LEU* 3.4 17.5 + - - +
400A LEU* 3.1 27.1 + - + +
448A LEU* 5.8 1.4 - - - +
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Residues in contact with GLU 397 (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 VAL* 6.4 3.4 - - + -
393A ASN* 3.0 26.7 + - + +
394A ALA* 3.7 7.9 - - - +
396A ASP* 1.3 82.1 - - - +
398A PHE* 1.3 63.0 + - - +
400A LEU* 3.3 29.3 + - - +
401A LEU* 3.4 18.4 + - + +
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Residues in contact with PHE 398 (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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344A VAL* 3.7 31.2 - - + -
345A ALA 4.1 1.3 - - - -
346A LEU* 3.7 33.4 - - + -
381A VAL* 6.5 1.1 - - + -
394A ALA 3.0 13.8 + - - +
395A VAL* 3.4 13.9 - - + +
397A GLU* 1.3 76.7 - - - +
399A LEU* 1.3 69.9 + - + +
401A LEU* 3.0 21.6 + - - +
402A LEU* 3.5 23.4 - - + +
408A GLY* 4.2 0.7 - - - -
409A LEU 3.6 37.0 - - - -
410A LEU* 4.8 10.8 - - + -
445A ILE* 4.9 4.3 - - + -
449A MET* 4.0 31.9 - - + -
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Residues in contact with LEU 399 (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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395A VAL* 2.8 45.7 + - + +
396A ASP* 3.5 16.2 - - - +
398A PHE* 1.3 77.8 - - + +
400A LEU* 1.3 61.9 + - - +
402A LEU* 3.0 23.3 + - + +
445A ILE* 4.5 4.7 - - + +
448A LEU* 3.9 40.6 - - + +
449A MET* 3.8 32.3 - - + +
452A LYS* 3.1 25.4 + - + -
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Residues in contact with LEU 400 (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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396A ASP 3.1 15.8 + - - +
397A GLU* 3.5 26.9 - - - +
398A PHE 3.2 0.2 - - - -
399A LEU* 1.3 75.4 - - - +
401A LEU* 1.3 62.9 + - + +
402A LEU 3.2 5.4 + - - +
452A LYS* 4.1 11.4 + - - +
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Residues in contact with LEU 401 (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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342A ASP* 5.1 2.3 - - - +
344A VAL* 3.8 37.3 - - + +
379A LYS* 5.8 13.5 - - + +
381A VAL* 5.0 15.9 - - + -
397A GLU* 3.6 15.3 - - + +
398A PHE* 3.0 14.5 + - + +
400A LEU* 1.3 79.6 - - + +
402A LEU* 1.3 62.7 + - - +
403A ASP* 4.0 1.6 + - - +
406A VAL* 4.3 5.7 - - - +
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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