Contacts of the strand formed by residues 1660 - 1667 (chain A) in PDB entry 6FF7
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 TYR1660 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1629A ILE 4.9 0.2 - - - -
1630A LEU* 3.6 1.4 - - - -
1631A LEU* 2.9 44.5 + - + +
1658A GLN 5.5 0.4 - - - +
1659A LYS* 1.3 78.7 - - - +
1661A TRP* 1.3 64.4 + - - +
1662A ILE* 4.0 1.0 + - - +
1697A SER* 5.4 0.9 - - - -
1699A THR* 5.8 1.6 - - - -
1700A GLY* 5.0 8.5 - - - +
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Residues in contact with TRP1661 (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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1627A ALA* 3.7 27.4 - - + -
1629A ILE 3.5 6.7 - - - +
1630A LEU* 4.4 4.5 - - + +
1659A LYS 4.4 0.2 - - - -
1660A TYR* 1.3 74.8 - - - +
1662A ILE* 1.3 61.3 + - - +
1695A TYR* 5.9 1.8 - - + -
1696A PRO* 5.0 16.6 - - + -
1697A SER* 5.3 10.2 - - - +
1700A GLY* 3.3 29.8 - - - +
1701A VAL 3.3 7.2 + - - +
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Residues in contact with ILE1662 (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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1628A ASP* 3.3 6.0 + - - +
1629A ILE* 2.9 40.5 + - + +
1660A TYR 4.0 1.5 + - - +
1661A TRP* 1.3 75.1 - - - +
1663A ASP* 1.3 60.0 + - - +
1701A VAL* 3.8 9.4 - - + +
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Residues in contact with ASP1663 (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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1626A CYS 3.8 23.3 - - - +
1627A ALA* 4.2 3.1 - - - -
1628A ASP* 3.8 12.1 - - + +
1661A TRP 4.3 0.2 - - - -
1662A ILE* 1.3 74.4 - - - +
1664A ILE* 1.3 62.5 + - - +
1701A VAL 3.6 9.0 + - - +
1702A LEU* 3.8 7.4 - - + +
1703A ILE* 2.9 29.7 + - - +
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Residues in contact with ILE1664 (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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1586A HIS* 6.1 1.6 - - - +
1589A ILE* 5.8 7.9 - - + -
1590A VAL* 6.2 5.4 - - + +
1628A ASP* 4.5 7.3 - - + +
1663A ASP* 1.3 77.4 - - - +
1665A GLN* 1.3 63.4 - - - +
1703A ILE* 3.3 13.9 - - + +
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Residues in contact with GLN1665 (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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1619A SER 5.9 0.9 - - - -
1664A ILE* 1.3 76.7 - - - +
1666A LEU* 1.3 63.3 + - - +
1683A LYS* 6.4 1.6 - - + -
1702A LEU* 6.5 0.4 - - + -
1703A ILE 2.7 15.6 + - - +
1704A ALA* 4.1 13.5 - - + -
1705A ILE* 3.3 25.4 + - - +
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Residues in contact with LEU1666 (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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1559A GLY* 6.0 1.4 - - - -
1619A SER 5.0 12.8 + - - +
1665A GLN* 1.3 77.7 - - - +
1667A ARG* 1.3 64.8 + - - +
1705A ILE 3.9 6.3 - - - -
1707A LEU* 6.0 3.6 - - + -
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Residues in contact with ARG1667 (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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1559A GLY* 4.8 9.4 - - - +
1666A LEU* 1.3 78.2 - - - +
1668A TRP* 1.3 65.2 + - - +
1669A GLY 5.3 0.4 - - - +
1705A ILE 3.8 10.0 + - - +
1706A ASP* 5.2 4.7 - - + -
1707A LEU* 3.4 27.9 + - - +
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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