Contacts of the strand formed by residues 1677 - 1684 (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 GLU1677 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1660B TYR* 2.4 42.8 + - - +
1661B GLN* 5.0 1.7 + - - -
1664B LYS* 3.9 28.0 - - - +
1675B MET* 3.4 8.2 - - - +
1676B ASN* 1.3 80.5 - - - +
1678B LYS* 1.3 74.9 + - - +
1742B ARG* 2.6 38.2 + - + +
1743B VAL 3.2 5.6 - - - +
1744B LEU* 4.3 2.0 - - + -
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Residues in contact with LYS1678 (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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1675B MET* 5.0 8.9 + - - +
1677B GLU* 1.3 80.9 + - - +
1679B GLN* 1.3 62.0 + - - +
1680B LEU* 3.9 17.8 + - + -
1741B VAL 3.5 1.0 - - - +
1742B ARG* 3.5 2.9 - - - -
1743B VAL* 2.7 34.4 + - - +
1745B THR* 3.4 24.5 - - + +
1748B TYR* 4.1 17.2 + - - -
1780B PRO* 5.7 1.3 - - - -
1783B PHE* 3.7 36.3 - - + -
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Residues in contact with GLN1679 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1635B LYS* 4.7 9.7 - - - -
1678B LYS* 1.3 76.1 - - - +
1680B LEU* 1.3 66.3 - - - +
1717B VAL 4.9 1.7 - - - +
1740B TYR* 3.2 55.6 + - + +
1741B VAL 3.2 9.0 - - - +
1742B ARG* 3.6 43.7 + - + +
1794B GLU* 4.2 10.3 + - - -
1795B TYR* 4.8 4.4 - - - -
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Residues in contact with LEU1680 (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* 4.0 17.9 - - + -
1679B GLN* 1.3 80.0 - - - +
1681B PHE* 1.3 65.6 + - - +
1715B PHE* 3.7 26.7 - - + +
1716B ALA 3.2 15.5 - - - +
1717B VAL* 4.0 15.9 - - + -
1740B TYR* 3.5 3.8 - - - -
1741B VAL* 2.7 42.4 + - - +
1743B VAL* 3.8 25.8 - - + -
1745B THR* 4.1 5.2 - - + -
1783B PHE* 3.8 39.5 - - + -
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Residues in contact with PHE1681 (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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1632B VAL 5.4 0.4 - - - -
1635B LYS* 3.5 34.1 - - + -
1636B PHE* 3.9 15.7 - - - -
1680B LEU* 1.3 74.4 - - - +
1682B HIS* 1.3 62.8 + - - +
1715B PHE* 3.3 9.4 - - - +
1716B ALA* 2.8 32.6 + - + +
1717B VAL 3.6 20.2 - - - -
1718B ASN* 3.7 1.8 - - - -
1719B ALA* 3.3 46.2 - - + -
1722B SER* 3.4 15.3 + - - +
1738B VAL* 3.8 14.1 - - + -
1739B TYR 3.2 12.1 - - - +
1740B TYR* 3.4 28.5 - + + -
1797B ILE* 4.4 9.0 - - + -
1901B 91J 4.3 0.2 - - - +
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Residues in contact with HIS1682 (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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1681B PHE* 1.3 76.0 - - - +
1683B GLY* 1.3 67.2 + - - +
1684B THR* 3.9 5.3 + - + -
1697B PHE* 3.3 23.8 - + + -
1701B TYR* 2.7 29.9 + + - -
1713B THR* 3.5 25.2 - - + +
1714B TYR 2.8 20.9 + - - -
1715B PHE* 3.9 14.3 - + + -
1722B SER* 4.0 1.6 - - - -
1738B VAL* 3.4 2.1 - - - +
1739B TYR* 2.9 37.5 + + + +
1741B VAL* 4.2 6.7 - - + -
1901B 91J 3.3 34.3 + + - -
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Residues in contact with GLY1683 (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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1682B HIS* 1.3 72.5 - - - +
1684B THR* 1.3 62.4 + - - -
1722B SER* 3.4 24.6 - - - -
1727B TYR* 3.6 6.0 - - - +
1728B SER* 4.0 2.2 - - - -
1737B HIS 3.5 9.6 - - - -
1738B VAL* 3.9 2.9 - - - -
1901B 91J 2.6 45.9 + - - -
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Residues in contact with THR1684 (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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1682B HIS* 4.2 2.7 - - + -
1683B GLY* 1.3 76.1 - - - -
1685B ASP* 1.3 84.9 + - - +
1688B SER* 3.3 13.5 - - - -
1689B VAL* 4.4 7.4 - - + -
1692B VAL* 4.9 1.6 - - + -
1701B TYR* 3.1 24.0 + - - +
1727B TYR 3.1 13.2 + - - -
1728B SER* 3.6 7.5 - - - -
1729B ARG 4.2 0.7 + - - +
1737B HIS* 3.1 25.3 + - + +
1739B TYR* 3.8 32.1 - - + -
1901B 91J 3.8 5.9 - - - -
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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