Contacts of the strand formed by residues 1562 - 1570 (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 ALA1562 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1561A GLY* 1.3 75.8 - - - +
1563A VAL* 1.3 60.8 + - - +
1581A ILE* 3.2 4.9 - - - +
1582A LYS* 3.0 35.5 + - + +
1583A ASP* 6.1 0.4 - - - +
1677A TRP* 3.7 23.4 - - + -
1678A TYR 3.2 14.8 - - - +
1679A GLN* 4.5 2.2 - - - -
1680A LEU* 3.9 6.5 - - - +
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Residues in contact with VAL1563 (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* 1.3 74.8 - - - +
1564A LYS* 1.3 64.3 + - - +
1565A LEU* 3.8 28.7 + - + -
1578A VAL* 4.4 9.0 - - + -
1580A HIS 3.5 4.5 - - - +
1581A ILE* 3.6 26.5 - - + -
1596A VAL* 5.3 0.4 - - + -
1644A LEU* 4.5 10.1 - - + -
1661A VAL* 4.4 8.7 - - + -
1676A LYS 3.7 1.0 - - - +
1677A TRP* 3.4 4.1 - - - -
1678A TYR* 2.8 52.0 + - + +
1680A LEU* 3.8 25.5 - - + +
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Residues in contact with LYS1564 (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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1563A VAL* 1.3 72.6 - - - +
1565A LEU* 1.3 64.4 + - - +
1579A MET* 2.8 63.2 + - + +
1580A HIS* 2.8 34.5 + - - +
1675A VAL* 3.7 20.1 - - + +
1676A LYS* 3.5 11.7 - - - +
1677A TRP* 3.6 45.7 - - + +
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Residues in contact with LEU1565 (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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1563A VAL* 3.8 16.6 - - + -
1564A LYS* 1.3 81.9 - - - +
1566A SER* 1.3 61.0 + - - +
1567A ILE* 4.1 16.6 - - + +
1576A ILE* 4.4 9.0 - - + -
1577A MET 3.2 11.7 - - - +
1578A VAL* 3.9 15.0 - - + -
1579A MET* 4.5 4.3 - - - -
1642A LEU* 4.8 2.5 - - + -
1644A LEU* 3.8 33.4 - - + -
1661A VAL* 5.3 0.9 - - + -
1663A LEU* 3.9 26.7 - - + -
1674A THR 3.5 1.7 - - - +
1675A VAL* 3.4 3.5 - - - +
1676A LYS 3.0 31.0 + - - +
1678A TYR* 3.9 21.4 - - + -
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Residues in contact with SER1566 (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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1565A LEU* 1.3 73.2 - - - +
1567A ILE* 1.3 62.0 + - - +
1568A SER* 5.0 1.0 + - - -
1575A PHE 3.4 3.8 - - - +
1576A ILE* 3.5 1.7 - - - -
1577A MET* 2.7 52.1 + - - +
1579A MET* 4.4 10.2 - - - -
1673A GLU* 2.5 34.8 + - - +
1674A THR 3.3 4.0 - - - -
1675A VAL* 3.7 12.8 - - - -
1570B ARG* 4.7 3.5 + - - -
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Residues in contact with ILE1567 (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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1565A LEU* 4.4 27.8 - - + +
1566A SER* 1.3 79.2 + - - +
1568A SER* 1.3 64.4 + - - +
1574A LEU* 4.0 13.2 - - + -
1575A PHE 3.4 2.0 - - - -
1576A ILE* 3.7 30.7 - - + -
1642A LEU* 4.4 9.4 - - + -
1663A LEU* 4.4 3.6 - - + -
1665A LEU* 4.6 8.1 - - + -
1668A PHE* 3.6 44.3 - - + -
1670A LEU* 4.7 5.9 - - + +
1672A LYS 3.7 1.9 - - - +
1673A GLU* 3.5 0.9 - - - -
1674A THR* 2.8 38.7 + - - +
1678A TYR* 4.4 3.4 - - - +
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Residues in contact with SER1568 (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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1566A SER* 5.1 0.9 + - - -
1567A ILE* 1.3 77.1 - - - +
1569A TYR* 1.3 61.2 + - - +
1570A ARG* 4.4 11.0 - - - +
1574A LEU* 3.4 8.8 - - - +
1575A PHE* 2.8 49.3 + - - +
1670A LEU* 5.0 2.7 - - - -
1672A LYS 3.8 6.7 - - - -
1673A GLU* 4.0 25.5 - - - +
1570B ARG* 3.9 15.3 + - - -
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Residues in contact with TYR1569 (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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1568A SER* 1.3 78.1 - - - +
1570A ARG* 1.3 76.9 + - - +
1571A ASN 5.2 0.4 - - - -
1572A GLY* 3.2 35.9 - - - -
1573A THR 3.3 19.7 - - - -
1574A LEU* 3.8 4.5 - - + -
1632A TYR* 2.6 31.8 + - + -
1633A SER* 3.6 8.1 - - - -
1634A LYS* 3.5 40.1 + - + -
1637A LEU* 3.7 27.6 - - + -
1670A LEU* 3.5 36.3 + - + +
1671A SER* 5.3 1.0 - - - -
1672A LYS 4.5 0.8 + - - -
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Residues in contact with ARG1570 (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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1568A SER* 4.6 9.0 - - - +
1569A TYR* 1.3 92.6 + - - +
1571A ASN* 1.3 81.4 + - - +
1572A GLY 3.2 2.9 - - - -
1573A THR* 3.0 23.2 + - - +
1575A PHE* 3.7 19.0 - - + -
1671A SER* 4.5 15.6 + - - +
1672A LYS 6.4 1.3 - - - -
1570B ARG* 6.2 2.0 - - - +
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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