Contacts of the helix formed by residues 1721 - 1725 (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 TYR1721 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486H THR* 5.5 1.5 - - + +
1516H PHE* 4.0 28.8 - + + +
1684I SER 2.8 9.2 + - - +
1685I HIS 3.4 27.1 - - - -
1686I THR* 3.9 19.5 - - - -
1687I SER 3.9 16.4 - - - +
1688I VAL* 3.9 29.2 - - + +
1691I LEU* 3.4 23.2 - - + +
1719I HIS* 3.6 21.5 - + - -
1720I SER* 1.3 72.1 - - - +
1722I VAL* 1.3 63.3 + - + +
1724I GLN* 3.0 31.7 + - - +
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Residues in contact with VAL1722 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1678I ILE* 4.2 4.9 - - + -
1680I PRO* 3.9 24.5 - - + -
1683I TYR 5.0 2.7 - - - +
1684I SER* 4.0 7.6 + - - -
1687I SER 5.1 2.0 - - - +
1690I ILE* 3.9 25.1 - - + -
1691I LEU* 4.8 8.7 - - - +
1694I LEU* 3.7 22.4 - - + -
1704I GLU* 3.7 34.1 - - + +
1720I SER* 3.2 2.5 + - - +
1721I TYR* 1.3 77.6 - - + +
1723I SER* 1.3 62.0 + - - +
1724I GLN 3.0 0.2 - - - -
1725I ARG* 3.0 6.2 + - - +
1726I ALA* 3.0 23.0 + - + +
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Residues in contact with SER1723 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1704I GLU* 2.3 29.8 + - - -
1706I HIS* 5.2 0.2 + - - -
1720I SER* 3.1 23.5 + - - -
1721I TYR 3.1 1.0 + - - -
1722I VAL* 1.3 76.4 - - - +
1724I GLN* 1.3 60.2 + - - +
1725I ARG 3.1 1.0 + - - -
1726I ALA* 3.9 1.2 - - - +
1729I VAL* 3.7 20.9 - - - +
2420I GOL 4.3 1.7 + - - -
2109K ASN* 3.0 26.2 + - - -
2111K HIS* 4.0 26.2 + - - +
2112K GLN* 3.5 4.3 + - - +
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Residues in contact with GLN1724 (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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1514H GLU* 5.1 3.6 - - - +
1516H PHE* 3.4 27.7 - - - -
1691I LEU* 4.0 11.4 - - + +
1695I ASN* 5.2 0.7 - - - +
1719I HIS* 3.3 31.7 + - - -
1720I SER 4.1 5.2 - - - +
1721I TYR* 3.4 27.5 - - - +
1722I VAL 3.0 0.6 + - - -
1723I SER* 1.3 78.1 - - - +
1725I ARG* 1.3 57.0 + - - +
2420I GOL 5.4 3.0 - - - -
2111K HIS* 4.5 14.1 - - + +
2112K GLN* 3.1 22.5 + - - +
2118K HIS* 6.4 1.8 - - - -
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Residues in contact with ARG1725 (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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1691I LEU* 3.7 12.3 - - + +
1694I LEU* 3.4 39.2 + - + -
1695I ASN* 3.5 32.2 + - - +
1697I CYS 3.0 23.0 + - - -
1698I ASP* 4.9 0.6 - - - +
1699I GLY 4.4 4.4 - - - +
1700I LEU 2.9 24.4 + - - +
1702I VAL* 3.9 13.8 - - + +
1722I VAL 3.0 5.6 + - - +
1724I GLN* 1.3 79.5 - - - +
1726I ALA* 1.3 70.7 + - - +
1727I ASP* 3.1 26.9 + - - +
2112K GLN* 3.4 6.3 + - - +
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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
------------------------------------------------------------
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