Contacts of the strand formed by residues 1674 - 1679 (chain A) in PDB entry 6BTY
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 THR1674 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1565A LEU 3.5 2.4 - - - +
1566A SER* 3.3 1.0 - - - -
1567A ILE* 2.8 43.8 + - - +
1668A PHE* 3.9 30.0 - - + -
1669A ASN* 4.3 17.5 + - - +
1672A LYS* 3.9 2.1 + - - +
1673A GLU* 1.3 73.2 - - - +
1675A VAL* 1.3 61.4 + - - +
1676A LYS* 3.9 28.0 + - + -
1678A TYR* 5.3 0.7 + - - -
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Residues in contact with VAL1675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1564A LYS* 3.7 28.9 - - - +
1565A LEU 3.4 8.1 - - - +
1566A SER* 3.7 20.0 - - - +
1579A MET* 4.2 10.1 - - + -
1673A GLU* 3.9 18.9 + - + +
1674A THR* 1.3 78.1 - - - +
1676A LYS* 1.3 66.4 + - - +
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Residues in contact with LYS1676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1564A LYS* 4.3 3.8 - - - +
1565A LEU 3.0 30.1 + - - +
1668A PHE* 6.1 0.4 - - - -
1674A THR* 3.9 17.3 - - + -
1675A VAL* 1.3 79.8 - - - +
1677A TRP* 1.3 72.1 + - - +
1678A TYR* 3.2 52.2 + - + +
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Residues in contact with TRP1677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1562A ALA* 3.7 33.0 - - + -
1563A VAL 3.4 7.4 - - - -
1564A LYS* 3.6 47.4 - - + +
1580A HIS* 3.3 44.6 - + - -
1582A LYS* 3.8 25.1 - - + -
1676A LYS* 1.3 86.1 - - - +
1678A TYR* 1.3 64.3 - - - +
1679A GLN 4.3 0.3 + - - -
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Residues in contact with TYR1678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1562A ALA* 3.2 5.0 - - - -
1563A VAL* 2.8 53.6 + - + +
1565A LEU* 3.9 30.5 - - + -
1567A ILE* 4.4 2.0 - - + +
1661A VAL* 4.4 14.6 - - + -
1663A LEU* 3.7 34.8 - - + -
1668A PHE* 3.2 28.9 - + - -
1674A THR* 4.2 2.1 + - - +
1676A LYS* 3.2 62.8 + - + +
1677A TRP* 1.3 72.7 - - - +
1679A GLN* 1.3 64.0 + - - +
1680A LEU 3.5 0.2 + - - -
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Residues in contact with GLN1679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1561A GLY 3.6 11.5 - - - +
1562A ALA* 4.4 3.4 - - + +
1661A VAL* 3.8 19.6 - - - +
1677A TRP 4.3 0.4 + - - -
1678A TYR* 1.3 73.9 - - - +
1680A LEU* 1.3 74.1 + - - +
1681A THR* 4.0 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