Contacts of the strand formed by residues 1651 - 1655 (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 VAL1651 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1608I PRO* 4.0 6.1 - - - +
1609I ILE* 3.3 14.1 - - + +
1611I ILE* 3.7 22.7 - - + -
1637I GLU* 4.8 1.6 - - + +
1640I CYS* 3.6 14.1 - - + +
1641I VAL* 3.7 33.5 - - + +
1644I ALA* 3.5 23.3 - - + -
1650I THR* 1.3 83.4 - - - +
1652I ASP* 1.3 60.9 + - - +
1653I PHE* 4.5 16.8 - - + -
1742I VAL* 4.9 0.4 - - + -
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Residues in contact with ASP1652 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1608I PRO* 4.2 6.1 - - + +
1609I ILE 2.9 6.9 + - - -
1610I MET* 3.5 6.4 - - - +
1611I ILE 2.9 23.1 + - - +
1651I VAL* 1.3 73.4 - - - +
1653I PHE* 1.3 62.2 + - - +
1654I ARG* 2.8 39.4 + - - +
1668I GLU* 4.5 0.3 - - - +
1673I HIS* 2.7 39.4 + - + +
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Residues in contact with PHE1653 (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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1611I ILE* 3.4 33.4 - - + -
1613I ASN* 3.4 20.2 - - - -
1633I LEU* 3.8 34.3 - - + -
1636I VAL* 4.0 7.4 - - + -
1637I GLU* 3.6 73.4 + - + +
1640I CYS* 3.9 17.3 - - + -
1651I VAL* 4.0 8.2 - - + -
1652I ASP* 1.3 73.6 + - - +
1654I ARG* 1.3 69.2 + - - +
1738I TYR* 4.9 0.2 - + - -
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Residues in contact with ARG1654 (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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1610I MET* 3.6 21.3 - - - +
1611I ILE 2.9 7.0 + - - +
1612I LEU* 4.1 5.2 - - + -
1613I ASN* 3.0 31.0 + - - -
1652I ASP* 2.8 36.3 + - - +
1653I PHE* 1.3 83.1 - - - +
1655I GLN* 1.3 60.5 + - - +
1665I TRP* 3.1 61.5 - - + +
1668I GLU* 2.9 41.4 + - - -
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Residues in contact with GLN1655 (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* 3.3 16.4 - - + +
1614I GLY 3.0 21.2 + - - +
1616I ASN 3.8 0.8 - - - +
1617I LEU* 4.4 0.2 - - + -
1618I ASN* 3.5 32.0 + - + +
1633I LEU* 3.7 31.4 - - + -
1653I PHE* 5.6 0.2 - - + -
1654I ARG* 1.3 75.7 - - - +
1656I SER* 1.3 78.6 + - - +
1657I ASN* 3.1 26.5 + - - +
1661I GLU* 5.0 0.2 - - - +
1665I TRP* 3.4 12.3 - - - -
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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
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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