Contacts of the helix formed by residues 386 - 390 (chain A) in PDB entry 2DW1
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 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A ARG* 5.4 1.7 + - - +
307A MET* 4.2 20.0 - - + +
308A CYS* 3.7 9.9 - - + -
339A LEU* 6.1 0.4 - - + -
380A PHE* 3.6 27.8 - - + -
381A ILE* 3.6 30.7 - - + +
384A HIS 3.0 11.2 - - - +
385A ASN* 1.3 83.1 - - - +
387A GLU* 1.3 64.8 + - - +
388A CYS 2.8 6.0 + - - -
389A ILE* 2.9 37.2 + - + +
390A LEU* 4.3 2.6 + - - +
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Residues in contact with GLU 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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308A CYS* 4.3 2.5 - - + +
385A ASN* 2.6 40.7 + - - +
386A PRO* 1.3 70.4 - - - +
388A CYS* 1.3 58.7 + - - +
389A ILE 3.3 1.3 + - - -
390A LEU* 3.6 29.7 + - + +
391A ASN 5.0 0.2 + - - -
463A MET* 6.1 1.0 - - - +
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Residues in contact with CYS 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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284A HIS 5.9 0.2 - - - +
285A ASP* 3.1 38.0 - - - +
308A CYS* 2.0 52.5 - - + +
386A PRO 2.8 6.1 + - - -
387A GLU* 1.3 75.0 - - - +
389A ILE* 1.3 54.9 + - - -
390A LEU 3.3 2.7 - - - -
391A ASN* 3.2 4.8 - - - +
701A CA 2.3 31.6 - - - -
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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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198A ARG* 3.2 40.1 - - + +
199A PHE 2.8 49.1 + - - +
200A VAL* 4.3 7.4 - - + -
241A ILE* 5.3 1.1 - - + -
285A ASP* 4.3 2.9 - - + +
307A MET* 4.0 26.0 - - + -
308A CYS* 4.2 2.2 - - - -
339A LEU* 4.6 14.4 - - + -
381A ILE* 4.4 11.2 - - + -
386A PRO* 2.9 35.3 + - + +
388A CYS* 1.3 88.4 - - - +
390A LEU* 1.3 58.9 + - - +
391A ASN 3.7 1.1 - - - -
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Residues in contact with LEU 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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195A ASN* 6.1 0.3 - - - -
197A PHE 4.9 3.2 - - - +
198A ARG* 3.6 35.9 - - - +
199A PHE* 3.9 10.0 - - - -
385A ASN* 5.1 10.5 - - - +
386A PRO 4.9 1.6 - - - +
387A GLU* 3.7 32.3 - - + +
388A CYS 3.3 1.2 - - - -
389A ILE* 1.3 79.9 - - - +
391A ASN* 1.3 67.1 + - - +
392A GLU 3.6 1.6 + - - -
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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