Contacts of the strand formed by residues 1700 - 1707 (chain r) 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 GLY1700 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1521r VAL* 5.9 1.3 - - - -
1522r PRO 2.9 10.7 + - - -
1523r LEU* 3.3 7.8 - - - +
1524r GLU* 2.9 25.9 + - - +
1659r HIS* 3.7 11.0 - - - -
1691r ALA* 4.5 15.5 - - - -
1692r ASN* 5.8 1.6 - - - -
1693r ARG 6.2 0.2 - - - -
1699r GLU* 1.3 78.6 - - - +
1701r ARG* 1.3 61.2 + - - +
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Residues in contact with ARG1701 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1524r GLU* 3.5 13.5 - - + +
1553r HIS* 4.5 21.1 - - + +
1554r SER* 5.8 0.9 - - - -
1659r HIS 2.9 12.8 + - - +
1660r LEU* 3.2 13.5 - - + -
1661r VAL 2.8 24.4 + - - -
1691r ALA* 3.6 6.1 - - - +
1700r GLY* 1.3 75.3 - - - +
1702r CYS* 1.3 63.4 + - - +
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Residues in contact with CYS1702 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1523r LEU* 6.6 0.2 - - + -
1524r GLU 2.9 11.2 + - - +
1525r LEU* 4.8 7.0 - - + -
1526r HIS* 2.9 29.5 + - - +
1660r LEU* 5.9 0.2 - - - -
1661r VAL* 3.1 16.6 - - + +
1688r VAL* 5.0 21.5 - - + +
1691r ALA* 5.3 0.9 - - + -
1701r ARG* 1.3 77.7 - - - +
1703r VAL* 1.3 61.4 + - - +
1704r ILE* 4.2 0.7 - - + -
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Residues in contact with VAL1703 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1526r HIS* 3.4 11.7 - - + -
1528r GLN* 6.1 3.6 - - + -
1549r ALA* 4.6 21.3 - - + -
1661r VAL 2.9 8.7 + - - +
1662r ILE* 3.2 9.6 - - + +
1663r ILE 2.8 26.3 + - - +
1702r CYS* 1.3 74.1 - - - +
1704r ILE* 1.3 60.7 + - - +
1705r MET* 3.9 0.6 + - + -
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Residues in contact with ILE1704 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1526r HIS 2.9 15.1 + - - +
1527r ILE* 3.6 8.1 - - + +
1528r GLN* 2.9 25.5 + - - +
1663r ILE* 3.7 15.3 - - + -
1702r CYS* 4.2 0.9 - - + -
1703r VAL* 1.3 73.4 - - - +
1705r MET* 1.3 60.9 + - - +
1706r CYS* 3.6 6.4 + - + +
1714r PHE* 6.0 5.4 - - + -
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Residues in contact with MET1705 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1528r GLN* 3.5 18.4 - - + +
1530r PHE* 6.2 0.2 - - - -
1542r MET* 4.6 20.2 - - + -
1545r PRO* 6.3 2.0 - - + -
1663r ILE 2.8 16.6 + - - +
1664r MET* 4.6 3.1 - - - -
1665r ASP* 2.7 35.9 + - - +
1666r THR 3.9 1.7 + - - -
1703r VAL* 3.9 2.1 + - + -
1704r ILE* 1.3 72.3 - - - +
1706r CYS* 1.3 57.8 + - - +
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Residues in contact with CYS1706 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1528r GLN 2.9 9.8 + - - +
1529r GLY* 3.6 0.7 - - - -
1530r PHE* 2.9 29.1 + - - +
1665r ASP* 4.7 2.5 - - - +
1666r THR* 4.6 20.9 - - - +
1704r ILE* 3.6 7.5 + - + +
1705r MET* 1.3 75.5 - - - +
1707r GLN* 1.3 68.5 + - - +
1710r LYS* 4.5 18.6 - - + +
1711r LYS* 5.3 2.2 - - - +
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Residues in contact with GLN1707 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1529r GLY* 4.6 0.2 - - - -
1530r PHE* 3.5 9.8 + - - +
1532r ILE 5.0 9.0 - - - +
1533r SER* 5.9 3.4 - - - -
1665r ASP* 5.9 0.2 - - - +
1706r CYS* 1.3 81.8 - - - +
1708r GLY* 1.3 68.4 + - - +
1709r SER* 3.3 9.0 - - - +
1710r LYS* 3.2 19.2 + - + +
1711r LYS* 3.3 10.9 + - - +
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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