Contacts of the strand formed by residues 1656 - 1664 (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 PHE1656 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0B ALA* 6.6 0.2 - - + -
1586B THR* 4.1 22.7 - - + -
1587B GLU* 5.9 1.3 - - - -
1588B ASP* 6.1 0.4 - - - -
1590B ALA* 6.2 2.7 - - + -
1592B PRO* 4.8 1.3 - - + -
1647B LEU* 3.2 6.3 - - - -
1648B SER* 2.8 41.9 + - - -
1650B GLU* 3.4 29.4 - - + -
1653B ARG* 3.5 44.4 - - - +
1654B GLU* 3.1 10.7 + - + +
1655B ASN* 1.3 75.9 - - - +
1657B PHE* 1.3 71.7 + - - +
1658B LEU* 3.5 21.9 + - + +
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Residues in contact with PHE1657 (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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0B ALA* 4.3 8.7 - - - +
1559B ILE* 3.8 19.7 - - + +
1645B SER* 3.8 26.2 - - - -
1646B VAL 3.8 8.5 - - - -
1647B LEU* 4.3 11.3 - - + +
1656B PHE* 1.3 80.5 - - - +
1658B LEU* 1.3 59.8 + - - +
1659B GLY* 3.2 44.2 - - - -
1660B GLY* 3.2 7.0 - - - -
1681B THR 3.7 10.3 - - - -
1682B ALA* 4.2 14.4 - - - -
1683B ALA* 4.3 6.7 - - - -
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Residues in contact with LEU1658 (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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0B ALA 3.7 9.7 - - - +
1559B ILE* 3.7 17.6 - - - +
1560B GLY 3.9 11.8 + - - +
1584B LEU* 4.2 14.6 - - + +
1585B VAL* 3.5 22.4 + - - +
1586B THR* 4.1 7.2 - - + -
1592B PRO* 4.0 10.3 - - + -
1594B PRO* 4.0 12.8 - - + -
1646B VAL* 2.7 30.5 + - + +
1647B LEU 3.7 22.9 - - - +
1648B SER* 3.8 14.6 - - - +
1656B PHE* 3.5 29.8 - - + -
1657B PHE* 1.3 75.2 - - - +
1659B GLY* 1.3 57.5 + - - +
1680B LEU* 4.6 1.0 - - - +
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Residues in contact with GLY1659 (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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1559B ILE* 3.8 9.6 - - - -
1646B VAL* 2.7 37.6 + - - +
1657B PHE* 3.2 22.6 - - - -
1658B LEU* 1.3 82.0 - - - +
1660B GLY* 1.3 55.4 + - - -
1680B LEU* 4.0 11.7 - - - -
1681B THR 3.6 6.3 - - - -
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Residues in contact with GLY1660 (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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1644B LEU 3.1 14.8 - - - -
1657B PHE* 3.2 10.6 - - - -
1659B GLY* 1.3 74.8 - - - -
1661B VAL* 1.3 64.6 + - - +
1680B LEU* 3.6 9.0 - - - +
1681B THR* 2.8 40.4 + - - +
1682B ALA 5.5 0.7 - - - -
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Residues in contact with VAL1661 (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* 4.5 7.2 - - + -
1565B LEU* 5.3 0.4 - - + -
1642B LEU 3.7 1.6 - - - +
1643B GLN* 5.7 0.2 - - - -
1644B LEU* 2.9 52.5 + - + +
1660B GLY* 1.3 76.3 - - - +
1662B THR* 1.3 67.9 + - - +
1663B LEU* 3.8 31.6 - - + +
1678B TYR* 4.2 22.4 - - + -
1679B GLN 3.9 17.0 - - - +
1680B LEU* 4.7 1.1 - - + -
1681B THR* 5.0 3.1 - - + +
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Residues in contact with THR1662 (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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1601B LEU* 6.5 0.2 - - + -
1641B GLU* 3.6 38.1 - - + +
1642B LEU 3.4 7.0 - - - +
1643B GLN* 4.1 18.5 + - + +
1661B VAL* 1.3 78.6 + - - +
1663B LEU* 1.3 68.8 + - - +
1664B PRO* 3.6 10.2 - - + +
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Residues in contact with LEU1663 (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* 4.1 19.3 - - + -
1567B ILE* 4.3 5.8 - - + -
1641B GLU* 4.0 1.8 - - - -
1642B LEU* 2.8 50.0 + - + +
1644B LEU* 6.2 0.9 - - + -
1661B VAL* 3.8 18.8 - - + -
1662B THR* 1.3 80.7 - - - +
1664B PRO* 1.3 67.2 - - + +
1665B LEU* 3.2 4.0 + - - +
1668B PHE* 4.3 18.2 - - + -
1678B TYR* 3.5 48.9 - - + +
1701B O4B 4.1 18.2 - - - +
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Residues in contact with PRO1664 (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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1640B ARG 3.9 7.9 - - - +
1641B GLU* 4.0 16.4 - - + +
1662B THR* 3.6 11.4 - - + +
1663B LEU* 1.3 83.9 - - + +
1665B LEU* 1.3 65.1 + - - +
1666B LYS* 3.1 21.1 + - + -
1667B ASP* 3.4 33.4 + - - +
1668B PHE* 3.8 6.8 - - - -
1701B O4B 5.2 2.8 - - - +
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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