Contacts of the helix formed by residues 386 - 394 (chain A) in PDB entry 4JVA
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 CYS 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A PHE* 3.1 33.2 - - + +
275A LEU* 3.9 19.3 - - - -
277A SER* 3.8 9.9 - - - -
278A LEU* 4.4 9.6 - - - -
379A PHE* 6.3 0.4 - - + -
383A LEU* 2.6 37.3 + - + +
385A PRO* 1.3 73.3 - - - +
387A MET* 1.3 57.1 + - - +
388A GLU 2.9 12.8 + - - -
389A ILE* 3.2 9.0 + - + +
390A MET* 3.1 23.5 + - + +
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Residues in contact with MET 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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354A VAL* 5.4 17.4 - - + +
379A PHE* 6.3 3.8 - - + -
383A LEU 3.4 3.7 + - - +
384A GLY* 3.2 16.6 + - - +
386A CYS* 1.3 77.1 - - - +
388A GLU* 1.3 52.7 + - - +
390A MET* 3.8 6.7 - - - +
391A LYS* 2.6 37.9 + - - +
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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
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384A GLY 4.7 1.2 + - - -
385A PRO 5.1 4.7 - - - +
386A CYS 2.9 2.5 + - - -
387A MET* 1.3 75.2 - - - +
389A ILE* 1.3 56.1 + - - +
390A MET 2.7 14.0 + - - -
391A LYS* 3.0 4.9 + - - +
392A ARG* 2.9 26.8 + - - +
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Residues in contact with ILE 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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274A PHE* 5.8 12.1 - - + +
277A SER* 5.6 4.3 - - - +
347A TYR* 4.9 0.6 + - - -
385A PRO 5.6 0.4 + - - +
386A CYS* 3.2 10.1 + - - +
388A GLU* 1.3 77.8 - - - +
390A MET* 1.3 57.2 + - - +
392A ARG* 4.2 5.0 - - - +
393A ASN* 3.2 26.9 + - - +
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Residues in contact with MET 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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347A TYR* 3.8 24.4 + - + +
350A GLU* 5.3 9.6 - - + -
354A VAL* 5.8 5.6 - - + -
379A PHE* 6.5 0.7 - - + -
386A CYS* 3.1 17.6 + - + +
387A MET* 3.8 7.6 - - - +
388A GLU 2.7 1.6 + - - -
389A ILE* 1.3 76.2 - - - +
391A LYS* 1.3 54.9 + - - +
392A ARG 2.9 1.9 + - - -
393A ASN* 3.0 2.2 + - - -
394A ILE* 2.5 40.6 + - + +
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Residues in contact with LYS 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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354A VAL* 5.6 11.2 - - + +
387A MET* 2.6 25.0 + - + +
388A GLU* 3.7 5.2 - - - +
390A MET* 1.3 72.0 - - - +
392A ARG* 1.3 62.5 + - - +
394A ILE* 3.4 17.6 - - - +
395A ALA* 3.7 5.2 + - - +
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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 GLU 2.9 16.9 + - - +
389A ILE* 4.2 5.8 - - - +
390A MET 2.9 0.2 + - - -
391A LYS* 1.3 73.3 - - - +
393A ASN* 1.3 52.8 + - - +
394A ILE 2.8 3.8 + - - -
395A ALA* 2.7 37.5 + - - +
396A THR* 4.2 0.7 + - - -
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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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347A TYR* 4.9 7.9 - - - +
389A ILE 3.2 18.2 + - - +
390A MET* 3.0 5.8 + - - +
392A ARG* 1.3 76.9 - - - +
394A ILE* 1.3 57.2 + - - +
395A ALA 3.2 1.8 - - - -
396A THR* 3.4 26.7 + - - +
397A TYR* 3.9 9.5 - - - -
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Residues in contact with ILE 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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350A GLU* 5.5 3.4 - - - +
351A LEU* 4.8 17.7 - - + +
390A MET 2.5 20.7 + - - +
391A LYS* 3.4 16.4 - - - +
392A ARG 2.8 0.6 + - - -
393A ASN* 1.3 71.3 - - - +
395A ALA* 1.3 63.3 + - - +
396A THR 3.0 2.2 - - - -
397A TYR* 3.2 34.0 - - + +
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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