Contacts of the helix formed by residues 2216 - 2220 (chain L) in PDB entry 2BT4
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 ASN2216 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1863J VAL* 3.6 2.6 - - - +
1867J HIS* 2.7 30.2 + - - +
1889J ALA* 3.3 13.7 + - - +
1892J ASP* 3.1 32.1 + - + +
1893J ALA* 3.2 20.9 - - - +
1896J THR* 4.8 4.1 - - + +
2214L GLY 3.6 0.2 + - - -
2215L PRO* 1.3 85.7 + - - +
2217L LEU* 1.3 61.1 + - - +
2218L ASN* 3.1 11.7 - - - -
2219L LEU* 3.0 15.9 + - - +
2257L ASN* 2.8 13.3 + - - -
2360L CA2 3.2 31.0 - - + -
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Residues in contact with LEU2217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2213L ASN* 3.9 12.3 - - + +
2214L GLY 3.5 32.6 + - - +
2215L PRO 3.1 9.7 + - - +
2216L ASN* 1.3 77.6 - - - +
2218L ASN* 1.3 60.1 + - - +
2219L LEU 3.0 1.1 - - - -
2220L LEU* 3.1 26.3 + - + +
2233L LEU* 3.7 19.3 - - + +
2255L GLN* 4.3 6.5 - - + -
2279L ASN* 3.6 39.5 - - - +
2281L ALA* 4.1 3.8 - - + -
2307L ILE* 4.3 16.4 - - + -
2338L TYR* 4.8 0.9 - - - +
2360L CA2 3.7 29.2 - - + +
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Residues in contact with ASN2218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1867J HIS* 3.2 35.0 + - - +
2216L ASN* 3.2 15.8 - - - -
2217L LEU* 1.3 71.8 - - - +
2219L LEU* 1.3 74.9 + - - +
2220L LEU 3.4 2.7 + - - +
2222L GLN* 4.3 4.2 - - - +
2233L LEU* 4.2 16.9 + - + +
2255L GLN* 3.5 23.5 + - - +
2257L ASN* 3.6 11.5 - - - +
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Residues in contact with LEU2219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1867J HIS* 3.6 29.8 - - + +
1870J ARG* 4.0 20.2 - - - +
1896J THR* 3.5 31.4 - - + +
2216L ASN 3.0 10.4 + - - +
2217L LEU 3.0 1.6 - - - -
2218L ASN* 1.3 95.2 - - - +
2220L LEU* 1.3 66.4 + - - +
2221L GLY 3.2 0.2 + - - -
2222L GLN* 3.0 44.9 + - + +
2223L ARG* 6.1 0.2 - - + -
2360L CA2 3.3 17.5 - - + -
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Residues in contact with LEU2220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2217L LEU* 3.1 20.2 + - + +
2218L ASN 3.4 2.7 - - - +
2219L LEU* 1.3 79.6 - - - +
2221L GLY* 1.3 62.2 + - - +
2222L GLN* 3.5 4.0 + - - +
2228L TYR* 3.8 29.6 - - + +
2231L ASP 3.4 13.7 - - - +
2232L THR* 3.4 21.7 - - - +
2233L LEU* 4.0 15.1 + - + +
2236L VAL* 3.7 30.1 - - + -
2307L ILE* 3.7 32.1 - - + -
2335L VAL* 4.3 4.9 - - + -
2360L CA2 3.8 20.2 - - + -
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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