Contacts of the helix formed by residues 1682 - 1687 (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 ALA1682 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1288G VAL* 3.4 19.4 - - + +
1289G ALA* 3.4 26.9 - - + +
1292G ASP* 3.2 20.6 + - - +
1615I PRO* 4.3 4.8 - - + +
1616I ASN* 5.2 0.2 - - - +
1681I ALA* 1.3 78.7 - - - +
1683I TYR* 1.3 62.5 + - - +
1684I SER 3.0 0.2 - - - -
1685I HIS* 3.0 25.5 + - - +
1686I THR* 3.6 9.4 + - - +
1760I CA2 3.2 9.5 + - - -
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Residues in contact with TYR1683 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1259G GLU* 3.5 45.4 + - - +
1260G GLY* 4.4 0.3 + - - -
1263G VAL* 5.2 0.2 - - - +
1289G ALA* 3.7 12.6 - - + +
2407H TRS 4.1 6.1 - - - -
1615I PRO* 3.4 31.8 - - + +
1657I ASN 2.8 22.0 + - - -
1658I HIS* 4.0 2.4 - - - -
1659I GLU* 3.5 32.5 + - + -
1662I LEU* 3.7 16.4 - - + -
1680I PRO* 3.1 9.2 + - + +
1681I ALA 3.0 1.0 + - - -
1682I ALA* 1.3 73.9 - - - +
1684I SER* 1.4 64.9 + - - +
1685I HIS 3.0 0.2 - - - -
1686I THR* 3.6 17.3 - - - -
1687I SER* 2.9 29.6 + - - +
1690I ILE* 3.9 18.8 - - + -
1722I VAL* 5.0 2.3 - - - +
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Residues in contact with SER1684 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1680I PRO* 3.2 22.7 - - - +
1681I ALA 2.4 24.5 + - - -
1683I TYR* 1.4 79.8 - - - +
1685I HIS* 1.3 68.9 + - - +
1686I THR 3.7 0.2 + - - -
1704I GLU* 4.0 1.1 - - - -
1706I HIS* 3.0 32.4 - - - -
1720I SER* 3.2 14.4 + - - -
1721I TYR* 2.8 31.9 + - - +
1722I VAL* 4.0 4.8 + - - -
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Residues in contact with HIS1685 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1288G VAL* 4.4 11.4 - - + -
1681I ALA 4.1 2.0 + - - -
1682I ALA* 3.0 22.8 + - - +
1684I SER* 1.3 89.7 - - - +
1686I THR* 1.3 67.3 + - + +
1706I HIS* 5.0 0.7 - + - -
1710I ILE* 4.5 11.2 - - + -
1716I PHE* 4.0 13.2 - + + +
1717I ARG* 3.1 42.1 + - + -
1719I HIS* 2.8 30.7 + - - +
1720I SER* 4.7 0.2 - - - +
1721I TYR* 3.4 17.0 - - - -
1760I CA2 2.8 32.1 + - - -
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Residues in contact with THR1686 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1286G THR 3.6 13.7 - - - +
1288G VAL* 3.6 33.4 + - + +
1289G ALA 5.8 0.3 + - - -
1321G TYR* 5.4 3.8 - - + +
1486H THR* 3.5 14.4 - - - +
2407H TRS 2.7 40.9 + - - -
1682I ALA 3.6 4.6 + - - +
1683I TYR* 3.2 19.0 + - - -
1685I HIS* 1.3 85.9 - - + +
1687I SER* 1.3 59.4 + - - +
1688I VAL 3.4 5.4 + - - -
1721I TYR* 3.9 8.8 - - - -
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Residues in contact with SER1687 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2407H TRS 3.6 7.0 - - - -
1659I GLU* 2.7 23.2 + - - -
1683I TYR* 2.9 28.5 + - - +
1685I HIS 3.9 0.6 - - - -
1686I THR* 1.3 74.3 + - - +
1688I VAL* 1.3 61.2 + - - +
1689I ALA 3.5 0.2 + - - -
1690I ILE* 2.9 35.3 + - - +
1691I LEU* 3.3 16.6 + - - +
1721I TYR* 3.9 11.3 - - - +
1722I VAL* 5.1 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
------------------------------------------------------------
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