Contacts of the helix formed by residues 1616 - 1620 (chain I) 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 ASN1616 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1263G VAL* 3.7 2.8 - - - +
1267G HIS* 2.9 28.0 + - - +
1289G ALA* 3.2 24.0 + - - +
1292G ASP* 3.2 18.9 + - + +
1293G ALA* 3.2 24.3 - - - +
1296G THR* 4.6 5.1 - - + +
1614I GLY 3.6 0.4 + - - -
1615I PRO* 1.3 85.6 + - - +
1617I LEU* 1.3 54.4 + - - +
1618I ASN* 3.1 13.9 - - - -
1619I LEU* 2.9 21.5 + - - +
1657I ASN* 3.0 12.7 + - - -
1760I CA2 3.5 31.7 - - + -
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Residues in contact with LEU1617 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1613I ASN* 3.9 16.6 - - + +
1614I GLY 3.4 21.0 + - - +
1615I PRO 3.1 4.6 + - - -
1616I ASN* 1.3 72.6 - - - +
1618I ASN* 1.3 65.3 + - - +
1619I LEU 3.0 3.2 + - - -
1620I LEU* 3.1 31.0 + - + +
1633I LEU* 3.7 16.6 - - + +
1655I GLN* 4.4 0.9 - - + -
1679I ASN* 3.5 55.2 - - + +
1681I ALA* 3.9 5.8 - - + -
1707I ILE* 4.3 16.4 - - + -
1738I TYR* 4.5 1.8 - - - +
1760I CA2 3.9 29.6 - - + +
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Residues in contact with ASN1618 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267G HIS* 3.3 40.5 + - - +
1616I ASN* 3.4 10.0 - - - -
1617I LEU* 1.3 77.8 - - - +
1619I LEU* 1.3 75.2 + - - +
1620I LEU 3.4 2.5 + - - +
1622I GLN* 4.2 5.9 - - - +
1633I LEU* 4.2 15.9 + - + +
1655I GLN* 3.5 30.9 + - + +
1657I ASN* 3.5 4.5 - - - +
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Residues in contact with LEU1619 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267G HIS* 3.7 27.1 - - + +
1270G ARG* 3.9 25.6 - - - +
1296G THR* 3.6 34.3 - - + +
1616I ASN 2.9 11.9 + - - +
1618I ASN* 1.3 95.2 - - - +
1620I LEU* 1.3 67.6 + - - +
1621I GLY 3.3 0.2 + - - -
1622I GLN* 3.1 41.3 + - + +
1623I ARG* 6.2 0.2 - - - -
1760I CA2 3.3 16.3 - - + -
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Residues in contact with LEU1620 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1617I LEU* 3.1 24.7 + - + +
1618I ASN 3.4 2.0 - - - +
1619I LEU* 1.3 78.3 - - - +
1621I GLY* 1.3 60.9 - - - +
1622I GLN* 3.6 5.9 + - - +
1628I TYR* 4.0 14.4 - - + +
1631I ASP 3.5 15.7 - - - +
1632I THR* 3.4 23.5 - - - +
1633I LEU* 4.0 14.2 + - + +
1636I VAL* 3.8 27.4 - - + -
1707I ILE* 3.7 29.6 - - + -
1735I VAL* 4.4 4.5 - - + -
1738I TYR* 5.7 0.2 - - - +
1760I CA2 3.6 32.6 - - + -
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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