Contacts of the strand formed by residues 1562 - 1570 (chain B) 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 ALA1562 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1561B GLY* 1.3 74.6 - - - +
1563B VAL* 1.3 61.0 + - - +
1581B ILE* 3.2 7.3 - - - +
1582B LYS* 2.9 38.9 + - - +
1677B TRP* 3.5 21.6 - - + -
1678B TYR 3.2 17.5 - - - +
1679B GLN* 4.6 2.7 - - + -
1680B LEU* 4.2 4.1 - - - +
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Residues in contact with VAL1563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1562B ALA* 1.3 73.9 - - - +
1564B LYS* 1.3 64.7 + - - +
1565B LEU* 3.8 28.3 - - + -
1578B VAL* 4.4 9.9 - - + -
1580B HIS 3.6 4.9 - - - +
1581B ILE* 3.8 25.4 - - + -
1596B VAL* 5.2 0.4 - - + -
1644B LEU* 4.4 15.9 - - + -
1661B VAL* 4.5 4.3 - - + -
1677B TRP* 3.4 3.7 - - - -
1678B TYR* 2.8 52.1 + - + +
1680B LEU* 4.0 20.9 - - + -
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Residues in contact with LYS1564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1563B VAL* 1.3 73.3 - - - +
1565B LEU* 1.3 65.9 + - - +
1579B MET* 3.0 54.1 + - + +
1580B HIS* 2.9 41.4 + - + +
1675B VAL* 3.6 24.7 - - + +
1676B LYS* 3.5 12.6 - - - +
1677B TRP* 3.6 34.5 - - + +
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Residues in contact with LEU1565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1563B VAL* 3.8 19.9 + - + -
1564B LYS* 1.3 81.9 - - - +
1566B SER* 1.3 60.7 + - - +
1567B ILE* 4.1 16.6 - - + -
1576B ILE* 4.4 9.4 - - + -
1577B MET 3.4 11.0 - - - +
1578B VAL* 3.8 22.4 - - + -
1579B MET* 4.4 4.0 - - - -
1642B LEU* 4.7 2.5 - - + -
1644B LEU* 3.8 22.9 - - + -
1661B VAL* 5.3 0.7 - - + -
1663B LEU* 4.1 17.3 - - + -
1674B THR 3.5 2.5 - - - +
1675B VAL* 3.3 3.8 - - - +
1676B LYS 3.0 30.2 + - - +
1678B TYR* 3.9 29.8 + - + -
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Residues in contact with SER1566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1565B LEU* 1.3 72.4 - - - +
1567B ILE* 1.3 59.6 + - - +
1568B SER* 5.2 1.8 + - - -
1575B PHE 3.4 3.3 - - - +
1576B ILE* 3.6 1.2 - - - -
1577B MET* 2.8 55.5 + - - +
1579B MET* 4.1 12.5 - - - -
1673B GLU* 2.5 35.4 + - - +
1674B THR 3.4 4.5 - - - -
1675B VAL* 3.7 11.2 - - - -
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Residues in contact with ILE1567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1565B LEU* 4.3 15.9 - - + -
1566B SER* 1.3 79.4 + - - +
1568B SER* 1.3 63.5 + - - +
1574B LEU* 4.2 11.7 - - + -
1575B PHE 3.5 2.5 - - - -
1576B ILE* 3.8 34.1 - - + -
1642B LEU* 4.4 4.5 - - + -
1663B LEU* 4.3 13.7 - - + -
1665B LEU* 4.8 5.8 - - + -
1668B PHE* 3.6 46.6 - - + -
1670B LEU* 4.9 5.4 - - + -
1672B LYS 3.7 2.4 - - - +
1673B GLU* 3.5 1.1 - - - -
1674B THR* 2.9 41.4 + - - +
1678B TYR* 4.3 7.0 - - - +
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Residues in contact with SER1568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1566B SER* 5.2 1.6 + - - -
1567B ILE* 1.3 77.3 - - - +
1569B TYR* 1.3 62.3 + - - +
1570B ARG* 4.3 2.4 - - - +
1574B LEU* 3.5 8.4 - - - +
1575B PHE* 2.8 48.7 + - - +
1670B LEU* 5.2 3.4 - - - -
1672B LYS 3.9 15.5 - - - -
1673B GLU* 4.0 18.7 - - - +
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Residues in contact with TYR1569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1568B SER* 1.3 77.3 - - - +
1570B ARG* 1.3 65.4 + - - +
1571B ASN 5.2 0.2 - - - -
1572B GLY* 3.2 37.4 - - - -
1573B THR 3.2 16.2 - - - -
1574B LEU* 3.8 3.4 - - + -
1632B TYR* 2.7 29.8 + - + -
1633B SER* 3.8 7.1 - - - -
1634B LYS* 3.5 40.6 + - + -
1637B LEU* 3.6 29.8 - - + -
1670B LEU* 3.4 35.9 + - + +
1671B SER* 5.2 1.4 - - - -
1672B LYS 4.7 0.2 + - - -
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Residues in contact with ARG1570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1566A SER* 5.1 2.0 + - - -
1568A SER* 3.9 19.2 + - - -
1570A ARG* 6.2 1.8 - - - +
1575A PHE* 4.9 3.8 - - - +
1577A MET* 5.8 2.6 - - - +
1626A MET* 4.1 16.8 - - - +
1673A GLU* 3.0 37.0 + - - -
1568B SER* 5.5 2.9 - - - +
1569B TYR* 1.3 78.1 - - - +
1571B ASN* 1.3 85.5 + - - +
1572B GLY 3.1 2.5 - - - -
1573B THR* 2.9 23.2 + - - +
1575B PHE* 3.5 36.2 - - + -
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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
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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