Contacts of the strand formed by residues 1736 - 1744 (chain B) in PDB entry 5V7W
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 LYS1736 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1643B PHE* 3.9 16.4 - - + -
1723B ALA 2.9 25.7 + - - -
1725B ASP* 2.6 30.5 + - - +
1728B SER* 2.6 34.9 + - - +
1729B ARG 4.5 1.3 - - - -
1730B PRO* 3.8 15.9 - - + -
1734B GLY 3.9 6.5 - - - +
1735B ARG* 1.3 74.3 - - - +
1737B HIS* 1.3 66.4 + - - +
1798B THR* 3.4 6.9 - - - +
1799B PHE* 2.7 69.7 + - + +
1800B ARG* 4.7 1.3 - - - -
1801B LYS* 4.4 10.3 - - + -
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Residues in contact with HIS1737 (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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1690A PRO* 5.8 5.5 - - + +
1684B THR* 3.1 36.9 + - + +
1686B ALA* 3.7 31.7 + - + +
1689B VAL* 4.3 20.6 - - + -
1728B SER* 3.2 11.4 - - - -
1729B ARG 4.8 2.0 + - - -
1731B ASP* 4.0 10.0 + - - -
1735B ARG* 3.5 27.0 + - + +
1736B LYS* 1.3 75.7 - - - +
1738B VAL* 1.3 62.6 + - - +
1796B LEU* 4.0 21.3 - - + -
1797B ILE 3.4 3.4 - - - -
1798B THR* 3.9 28.0 - - - +
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Residues in contact with VAL1738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1636B PHE* 5.0 7.4 - - + -
1681B PHE* 3.8 28.3 - - + -
1682B HIS 3.4 8.7 - - - +
1683B GLY* 3.9 2.9 - - - -
1719B ALA 5.1 2.2 - - - +
1722B SER* 3.6 30.7 - - - +
1723B ALA* 4.4 1.3 - - + +
1728B SER* 3.8 1.8 - - - -
1737B HIS* 1.3 80.5 - - - +
1739B TYR* 1.3 74.3 + - - +
1796B LEU* 4.0 2.7 - - - -
1797B ILE* 2.8 41.8 + - + +
1799B PHE* 3.6 27.3 - - + -
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Residues in contact with TYR1739 (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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1651B ILE* 4.2 4.5 - - + -
1680B LEU 3.7 0.3 - - - +
1681B PHE* 3.2 6.9 - - - -
1682B HIS* 2.9 39.4 + + - +
1684B THR* 3.8 24.5 - - + -
1689B VAL* 3.1 26.1 + - + +
1692B VAL* 3.6 20.6 - - + +
1693B ASN* 2.7 28.5 + - - -
1697B PHE* 4.5 6.7 - + + -
1738B VAL* 1.3 77.8 - - - +
1740B TYR* 1.3 59.7 + - - +
1741B VAL* 3.6 18.6 + - + -
1793B PRO* 3.6 25.1 - - + -
1795B TYR 3.1 17.9 - - - -
1796B LEU* 3.7 29.4 - - + -
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Residues in contact with TYR1740 (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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1631B THR* 5.1 2.5 - - + -
1632B VAL* 3.9 32.5 - - + -
1635B LYS* 3.3 42.4 - - + +
1679B GLN* 3.2 61.3 + - + +
1680B LEU 3.5 9.4 - - - -
1681B PHE* 3.4 26.2 - + + -
1738B VAL 4.0 0.8 + - - -
1739B TYR* 1.3 72.3 - - - +
1741B VAL* 1.3 59.6 + - - +
1794B GLU* 3.7 7.7 + - - +
1795B TYR* 2.8 51.9 + + + +
1797B ILE* 4.6 3.1 - - + -
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Residues in contact with VAL1741 (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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1678B LYS 3.5 0.2 - - - +
1679B GLN* 3.2 6.8 - - - -
1680B LEU 2.7 42.6 + - - +
1682B HIS* 4.2 3.4 - - + -
1697B PHE* 3.6 27.8 - - + -
1715B PHE* 4.0 9.6 - - + -
1739B TYR* 3.6 28.7 - - + +
1740B TYR* 1.3 71.7 - - - +
1742B ARG* 1.3 65.1 + - - +
1743B VAL* 3.6 10.2 + - + +
1791B ALA* 3.7 19.1 - - + -
1792B TYR 3.3 24.2 - - - +
1793B PRO* 4.5 1.6 - - + -
1794B GLU 4.5 0.2 - - - +
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Residues in contact with ARG1742 (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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1657B TRP* 4.3 22.3 - - - -
1660B TYR* 3.3 22.1 - - + +
1677B GLU* 2.6 42.6 + - - +
1678B LYS 3.5 5.8 - - - -
1679B GLN* 3.6 34.9 + - + +
1740B TYR 4.3 0.2 + - - -
1741B VAL* 1.3 70.6 - - - +
1743B VAL* 1.3 59.1 + - - +
1791B ALA* 3.2 3.1 - - - -
1792B TYR* 2.9 41.1 + - + +
1794B GLU* 2.8 37.9 + - + +
1795B TYR* 6.1 0.2 - - - -
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Residues in contact with VAL1743 (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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1660B TYR* 3.7 4.4 + - - -
1677B GLU* 3.2 2.4 - - - -
1678B LYS 2.7 38.5 + - - +
1680B LEU* 3.8 32.5 - - + -
1715B PHE* 4.0 24.5 - - + -
1741B VAL* 3.8 23.3 - - + +
1742B ARG* 1.3 78.2 - - - +
1744B LEU* 1.3 69.6 + - - +
1745B THR* 3.1 10.6 + - + +
1772B THR* 4.9 2.2 - - + -
1783B PHE* 5.7 0.9 - - + -
1785B ALA* 4.5 10.5 - - + -
1790B GLN* 3.7 8.7 - - + +
1791B ALA* 3.9 9.4 - - + -
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Residues in contact with LEU1744 (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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1660B TYR* 3.8 30.3 - - + +
1663B LYS* 3.7 31.0 - - + +
1664B LYS* 3.7 45.8 - - + +
1667B MET* 3.4 16.9 - - + +
1676B ASN* 3.3 15.3 - - + -
1677B GLU* 4.3 10.8 - - + -
1743B VAL* 1.3 71.1 - - - +
1745B THR* 1.3 63.6 + - - +
1746B GLY 3.4 0.9 - - - -
1772B THR* 3.6 0.5 - - - +
1789B TYR 4.4 0.2 - - - +
1790B GLN* 2.9 48.1 + - + +
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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