Contacts of the strand formed by residues 1702 - 1706 (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 VAL1702 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1676I ILE* 3.3 22.9 - - + +
1678I ILE* 4.2 14.6 - - + -
1694I LEU* 4.1 31.9 - - + -
1697I CYS* 5.1 2.0 - - + -
1700I LEU* 3.6 14.6 - - + +
1701I PRO* 1.3 79.2 - - - +
1703I VAL* 1.3 65.7 + - - +
1725I ARG* 3.9 18.4 - - - +
1726I ALA* 3.6 18.1 - - + +
1727I ASP* 2.8 42.0 + - - +
1728I GLY 3.4 1.2 + - - -
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Residues in contact with VAL1703 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1676I ILE 2.9 9.3 + - - +
1677I VAL* 3.3 5.6 - - - +
1678I ILE* 2.9 24.9 + - - +
1702I VAL* 1.3 82.3 - - - +
1704I GLU* 1.3 73.5 + - - +
1705I VAL* 4.0 5.1 + - + -
1727I ASP* 5.6 1.1 - - + -
1728I GLY* 3.4 17.0 - - - +
1730I VAL* 4.4 11.0 - - + -
1741I GLY* 3.9 24.0 - - - +
1744I ARG* 3.9 28.3 - - + -
1745I ILE* 3.9 18.4 - - + -
1748I LEU* 5.8 1.1 - - + -
2133K CYS* 5.1 2.0 - - - -
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Residues in contact with GLU1704 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1678I ILE* 3.3 12.6 - - - +
1680I PRO* 4.1 3.9 - - + +
1684I SER* 4.0 1.6 - - - -
1703I VAL* 1.3 76.4 - - - +
1705I VAL* 1.4 57.8 + - - +
1706I HIS* 2.7 31.7 + - + +
1720I SER* 2.6 22.4 + - - -
1722I VAL* 3.4 20.0 - - + +
1723I SER* 2.3 40.3 + - - -
1726I ALA* 3.8 13.0 - - + +
1728I GLY 2.8 9.6 + - - +
1729I VAL* 3.3 9.6 - - + +
1730I VAL 2.8 30.2 + - - -
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Residues in contact with VAL1705 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1677I VAL* 3.8 27.1 - - + -
1678I ILE 2.9 9.8 + - - +
1679I ASN* 3.1 31.1 - - + +
1680I PRO* 4.1 0.3 - - - +
1703I VAL* 4.2 10.5 - - + -
1704I GLU* 1.4 78.0 - - - +
1706I HIS* 1.3 77.1 + - - +
1707I ILE 4.5 0.2 - - - +
1730I VAL* 3.3 7.6 - - + +
1734I GLY 4.9 1.3 - - - +
1737I GLY* 3.6 26.2 - - - +
1738I TYR* 3.8 37.2 - - + +
1741I GLY* 4.7 0.2 - - - -
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Residues in contact with HIS1706 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1680I PRO* 4.0 9.4 - - + -
1684I SER* 3.0 33.8 - - - -
1685I HIS* 5.0 1.3 - + - -
1704I GLU* 2.7 31.6 + - + +
1705I VAL* 1.3 78.1 + - - +
1707I ILE* 1.3 66.6 + - - +
1708I SER 3.5 14.1 - - - +
1710I ILE* 3.9 30.4 - - + +
1720I SER* 4.5 0.6 + - - -
1729I VAL* 4.5 7.4 - - + -
1730I VAL* 2.9 13.9 + - - +
1731I ALA* 3.3 8.3 - - + -
1732I GLY 3.1 18.4 + - - -
1733I CYS 4.3 2.1 + - - -
1734I GLY 4.8 0.5 - - - +
1737I GLY* 5.8 0.3 - - - -
1760I CA2 3.0 33.2 + - + +
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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
------------------------------------------------------------
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