Contacts of the strand formed by residues 1675 - 1679 (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 GLY1675 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1609I ILE* 3.8 5.7 - - - -
1610I MET* 3.0 25.4 + - - +
1673I HIS* 3.4 4.3 - - - +
1674I CYS* 1.3 82.8 - - - +
1676I ILE* 1.3 68.0 + - - +
1700I LEU* 3.7 9.5 - - - +
1701I PRO* 3.3 14.6 - - - -
1745I ILE* 4.2 9.4 - - - -
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Residues in contact with ILE1676 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1609I ILE* 4.8 0.2 - - - -
1610I MET* 3.3 8.3 - - + +
1612I LEU* 4.2 15.3 - - + -
1666I ILE* 4.4 7.6 - - + -
1669I ALA* 3.8 23.8 - - + -
1675I GLY* 1.3 78.4 - - - +
1677I VAL* 1.3 75.5 + - - +
1678I ILE* 4.0 18.6 - - + -
1694I LEU* 3.9 23.8 - - + -
1697I CYS* 4.2 8.5 - - - -
1700I LEU* 3.5 24.7 - - + -
1701I PRO 3.0 5.9 + - - +
1702I VAL* 3.3 11.7 - - + -
1703I VAL 2.9 24.6 + - - -
1745I ILE* 3.9 5.1 - - - +
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Residues in contact with VAL1677 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1609I ILE* 4.1 12.3 - - + +
1610I MET 2.9 6.5 + - - +
1611I ILE* 3.2 14.8 - - + +
1612I LEU 2.8 25.6 + - - +
1676I ILE* 1.3 75.1 - - - +
1678I ILE* 1.3 61.8 + - - +
1679I ASN 4.3 0.4 + - - -
1703I VAL* 3.3 6.3 - - + +
1705I VAL* 3.8 26.5 - - + -
1738I TYR* 4.3 25.8 - - + +
1741I GLY* 3.6 30.7 - - - +
1742I VAL* 3.8 9.2 - - + +
1745I ILE* 4.0 8.7 - - + -
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Residues in contact with ILE1678 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1612I LEU* 3.3 24.0 - - + +
1662I LEU* 5.6 5.4 - - + -
1666I ILE* 4.3 15.7 - - + -
1676I ILE* 4.0 9.2 - - + -
1677I VAL* 1.3 74.1 - - - +
1679I ASN* 1.3 62.3 + - - +
1680I PRO* 3.2 26.5 - - + +
1690I ILE* 4.1 28.5 - - + -
1694I LEU* 4.4 4.9 - - + -
1702I VAL* 4.2 16.2 - - + -
1703I VAL 2.9 17.4 + - - +
1704I GLU* 3.3 2.3 - - - -
1705I VAL* 2.9 26.0 + - - -
1722I VAL* 4.2 21.8 - - + -
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Residues in contact with ASN1679 (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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1612I LEU 2.8 8.8 + - - -
1613I ASN* 3.4 4.9 + - - +
1614I GLY 2.8 30.0 + - - -
1617I LEU* 3.5 14.5 - - + +
1677I VAL 4.3 0.4 - - - -
1678I ILE* 1.3 71.1 - - - +
1680I PRO* 1.3 54.0 - - - +
1681I ALA* 3.0 7.4 + - - -
1705I VAL* 3.1 18.9 + - + +
1706I HIS* 4.0 0.2 + - - -
1707I ILE* 4.0 10.1 - - - +
1738I TYR* 3.0 38.6 + - + +
1760I CA2 2.8 41.7 + - - -
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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
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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