Contacts of the strand formed by residues 1701 - 1706 (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 VAL1701 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1661A TRP 3.3 9.1 + - - +
1662A ILE* 3.8 5.6 - - + +
1663A ASP* 3.6 21.1 + - - +
1700A GLY* 1.3 75.2 - - - -
1702A LEU* 1.3 60.5 + - - +
1703A ILE* 4.1 1.3 - - + +
1714A ALA* 5.1 8.7 - - + -
1715A TYR 4.6 0.7 - - - -
1716A GLY* 3.8 22.7 - - - +
1717A ASN 4.6 9.7 + - - +
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Residues in contact with LEU1702 (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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1663A ASP* 3.8 8.5 - - + +
1680A ALA* 4.3 9.7 - - + +
1683A LYS* 5.7 2.0 - - + -
1684A PHE* 4.1 21.8 - - + +
1700A GLY 3.8 1.7 + - - +
1701A VAL* 1.3 71.4 - - - +
1703A ILE* 1.3 61.2 + - - +
1704A ALA* 4.0 0.6 + - - -
1714A ALA* 3.3 2.9 - - - -
1715A TYR* 2.9 37.1 + - - +
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Residues in contact with ILE1703 (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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1663A ASP 2.9 14.8 + - - +
1664A ILE* 3.3 10.3 - - + -
1665A GLN* 2.7 35.4 + - - +
1701A VAL* 4.1 1.7 - - + -
1702A LEU* 1.3 72.5 - - - +
1704A ALA* 1.3 55.7 + - - +
1713A SER 3.7 8.3 - - - +
1714A ALA* 3.9 9.4 - - + -
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Residues in contact with ALA1704 (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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1665A GLN* 4.0 15.5 - - + +
1676A ILE* 4.4 12.5 - - + +
1679A TYR* 5.2 2.2 - - + -
1680A ALA* 3.7 31.0 - - + +
1683A LYS* 6.4 0.7 - - + -
1702A LEU 4.0 1.6 + - - -
1703A ILE* 1.3 74.2 - - - +
1705A ILE* 1.3 62.0 + - - +
1712A HIS* 5.5 0.2 - - - -
1713A SER* 2.9 34.9 + - - +
1714A ALA* 4.4 0.2 - - - +
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Residues in contact with ILE1705 (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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1665A GLN 3.3 20.0 + - - +
1666A LEU* 3.9 2.1 - - - -
1667A ARG* 3.8 17.3 + - - +
1676A ILE* 5.5 0.9 - - - -
1703A ILE 4.2 0.2 - - - -
1704A ALA* 1.3 75.5 - - - +
1706A ASP* 1.3 61.0 - - - +
1707A LEU* 3.8 1.9 + - - +
1711A LEU 3.4 11.4 - - - +
1712A HIS* 4.5 9.9 - - + -
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Residues in contact with ASP1706 (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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1667A ARG* 4.9 8.5 - - + -
1669A GLY 5.9 1.8 - - - +
1674A HIS* 6.1 6.7 - - + -
1676A ILE* 4.7 16.2 - - + -
1705A ILE* 1.3 71.6 - - - +
1707A LEU* 1.3 53.6 - - - +
1708A ALA 3.7 6.5 - - - +
1709A TYR 3.1 12.6 - - - +
1710A ASN* 2.6 36.7 - - - +
1711A LEU* 2.8 16.4 + - + +
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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