Contacts of the helix formed by residues 386 - 390 (chain C) in PDB entry 3CB4
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 SER 386 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296C TYR* 6.1 0.2 - - - -
329C GLU* 5.6 2.2 - - - -
339C ARG* 4.1 25.7 + - - +
369C THR* 5.3 1.6 - - - -
384C VAL* 3.4 13.6 - - - +
385C ASP* 1.3 78.3 - - - +
387C PRO* 1.3 65.7 - - - +
388C SER* 3.6 16.3 + - - -
389C LYS* 2.8 46.7 + - - +
493C ASP 5.8 1.6 - - - -
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Residues in contact with PRO 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369C THR* 3.9 25.4 - - + +
385C ASP 4.0 0.2 - - - +
386C SER* 1.3 85.8 - - - +
388C SER* 1.3 56.9 + - - +
390C LEU* 2.9 19.3 + - + +
482C ARG* 3.1 23.1 + - - -
493C ASP 5.4 2.5 - - - +
496C ALA* 3.3 39.5 - - + +
497C LEU* 3.8 13.0 - - - +
498C ILE* 3.7 34.3 - - + +
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Residues in contact with SER 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C GLU* 5.3 2.1 + - - -
386C SER* 3.6 14.2 + - - -
387C PRO* 1.3 77.5 - - - +
389C LYS* 1.3 62.4 + - - +
390C LEU 3.4 3.7 + - - +
482C ARG* 3.9 21.5 + - - +
484C ASP* 5.7 0.4 - - - -
493C ASP* 3.6 50.2 + - - +
496C ALA* 4.4 4.7 - - - +
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Residues in contact with LYS 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C GLU* 4.2 17.0 + - - -
339C ARG* 5.0 9.2 - - - +
382C ILE* 5.5 2.3 - - - +
384C VAL* 4.2 11.1 - - + +
385C ASP* 5.8 3.4 - - + +
386C SER* 2.8 29.8 + - - +
388C SER* 1.3 79.7 + - - +
390C LEU* 1.3 65.9 + - - +
391C PRO* 3.5 5.9 - - - +
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Residues in contact with LEU 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C TYR* 5.3 0.2 - - + -
374C VAL* 3.6 31.4 - - + -
384C VAL* 4.0 11.6 - - + +
386C SER 3.6 2.8 + - - -
387C PRO* 2.9 19.0 + - + +
388C SER 4.2 3.8 - - - +
389C LYS* 1.3 78.5 - - - +
391C PRO* 1.3 78.7 - - + +
396C ILE* 4.0 16.4 - - + -
399C LEU* 4.2 20.0 - - + -
480C MET 5.6 0.2 - - - +
481C VAL 5.5 0.2 - - - -
482C ARG* 4.1 39.2 + - + +
498C ILE* 4.0 24.7 - - + -
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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