Contacts of the helix formed by residues 420 - 426 (chain B) in PDB entry 6CNC
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 LEU 420 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B TYR 4.9 3.4 - - - +
417B ASP* 3.4 23.3 + - - +
418B ALA* 5.7 1.1 - - - +
419B LEU* 1.3 73.4 - - - +
421B SER* 1.3 66.4 + - - +
422B ILE* 3.1 4.8 + - - +
423B ASN* 3.7 10.7 + - - +
424B VAL* 3.9 0.9 - - - +
148R SER* 3.3 23.3 - - - +
149R ARG* 3.3 60.3 + - + +
150R LEU* 5.2 2.5 - - - +
411S TYR* 5.6 5.4 - - - +
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Residues in contact with SER 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B PHE* 4.8 5.8 - - - -
402B SER* 4.5 18.4 + - - -
406B VAL* 5.6 5.9 - - - +
418B ALA* 3.7 14.8 + - - -
419B LEU 2.6 5.3 + - - -
420B LEU* 1.3 81.7 - - - +
422B ILE* 1.3 58.1 + - - -
423B ASN 3.3 0.2 - - - -
424B VAL* 2.9 20.7 + - - +
425B HIS* 2.8 27.9 + - - +
149R ARG 4.7 4.7 + - - -
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Residues in contact with ILE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 5.7 3.4 - - + -
133B ILE* 6.5 0.7 - - + -
147B VAL* 3.5 31.6 - - + -
148B GLU 3.5 14.8 - - - +
149B ILE* 4.6 10.8 - - + -
395B PHE* 4.3 16.0 - - + -
399B PHE* 3.3 32.3 - - + -
419B LEU* 2.6 34.1 + - + +
420B LEU* 4.7 0.4 - - - -
421B SER* 1.3 72.3 - - - +
423B ASN* 1.3 78.3 + - - +
425B HIS* 2.8 23.4 + - - +
426B SER* 2.8 17.0 + - - -
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Residues in contact with ASN 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B VAL* 4.8 5.1 - - - +
148B GLU* 3.6 21.2 + - - +
420B LEU* 3.7 10.9 + - - +
421B SER 3.3 0.2 - - - -
422B ILE* 1.3 92.9 - - - +
424B VAL* 1.3 64.0 + - - +
426B SER* 2.8 25.3 + - - +
92R TYR* 3.2 10.7 - - - -
93R ALA* 4.4 6.1 - - - +
95R HIS* 5.9 3.6 - - + -
149R ARG* 3.7 22.8 - - - +
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Residues in contact with VAL 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B SER* 3.0 26.7 - - - +
423B ASN* 1.3 77.0 - - - +
425B HIS* 1.3 51.8 + - + +
89R ALA* 3.6 35.7 - - + +
90R VAL* 4.2 4.7 - - + +
92R TYR* 2.2 28.8 + - - -
93R ALA* 3.7 23.1 - - + +
149R ARG* 3.7 28.9 - - + +
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Residues in contact with HIS 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 3.7 20.5 + + + -
398B ASP* 3.2 28.6 + - + +
399B PHE* 3.2 53.5 - - + +
402B SER* 4.3 14.2 - - - +
421B SER 2.8 15.3 + - - +
422B ILE* 2.8 10.4 + - - +
424B VAL* 1.3 76.5 - - + +
426B SER* 1.3 60.6 + - - +
428B ASN* 3.1 24.0 + - - -
92R TYR* 3.4 2.7 - - - -
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Residues in contact with SER 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ILE* 3.2 26.6 - - - -
150B GLY* 5.0 1.8 - - - -
395B PHE* 4.0 11.4 - - - -
422B ILE 2.8 11.6 + - - -
423B ASN* 2.8 25.9 + - - -
424B VAL 3.4 0.4 - - - -
425B HIS* 1.3 78.1 - - - +
427B ASN* 1.3 78.4 + - - +
428B ASN* 2.8 11.1 + - - -
92R TYR* 2.8 14.3 + - - -
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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