Contacts of the strand formed by residues 2087 - 2095 (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 LYS2087 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2041r LEU 3.7 8.5 - - - +
2042r GLU* 4.6 2.0 - - + +
2084r LEU* 3.6 18.5 - - - +
2085r GLN 3.2 4.2 + - - +
2086r GLN* 1.3 80.7 - - - +
2088r ALA* 1.3 64.4 + - - +
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Residues in contact with ALA2088 (chain r).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2040r GLN* 3.8 2.9 - - - +
2041r LEU* 2.9 51.4 + - + +
2082r LEU* 6.1 4.3 - - + -
2084r LEU* 3.9 16.4 - - + -
2087r LYS* 1.3 77.3 - - - +
2089r LYS* 1.3 64.1 + - - +
2090r VAL* 4.3 3.6 - - + +
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Residues in contact with LYS2089 (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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2039r VAL 3.9 5.6 - - - +
2040r GLN* 4.6 4.7 - - + +
2088r ALA* 1.3 76.2 - - - +
2090r VAL* 1.3 59.9 + - - +
2091r LYS 4.3 0.6 + - - -
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Residues in contact with VAL2090 (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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2038r LEU* 4.9 0.2 - - - -
2039r VAL* 2.8 46.0 + - + +
2041r LEU 5.4 0.2 - - - +
2066r VAL* 5.4 12.1 - - + -
2080r LYS* 5.9 6.5 - - + -
2082r LEU* 5.8 8.7 - - + -
2088r ALA* 4.3 3.8 - - + -
2089r LYS* 1.3 73.3 - - - +
2091r LYS* 1.3 61.8 + - - +
2092r LEU 4.2 0.3 + - - -
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Residues in contact with LYS2091 (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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2036r VAL* 6.2 3.8 - - + -
2037r VAL 3.7 4.7 - - - +
2038r LEU* 4.0 21.1 - - + -
2089r LYS 4.3 0.8 + - - -
2090r VAL* 1.3 74.6 - - - +
2092r LEU* 1.3 62.3 + - - +
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Residues in contact with LEU2092 (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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2036r VAL* 3.8 1.4 - - - -
2037r VAL* 2.9 39.0 + - + +
2066r VAL 5.5 3.4 - - - +
2068r ILE* 6.1 2.5 - - + -
2078r SER* 4.8 15.7 - - - -
2079r ILE 4.9 5.8 - - - +
2080r LYS* 4.9 16.8 - - + -
2090r VAL 4.2 0.6 + - - -
2091r LYS* 1.3 75.6 - - - +
2093r ASP* 1.3 62.2 + - - +
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Residues in contact with ASP2093 (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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2034r PRO* 5.5 5.8 - - + -
2035r VAL 3.0 21.3 - - - +
2036r VAL* 4.0 9.2 - - + -
2078r SER* 4.0 12.3 - - - -
2092r LEU* 1.3 76.8 - - - +
2094r PHE* 1.3 65.0 + - - +
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Residues in contact with PHE2094 (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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2034r PRO* 3.4 7.3 - - - +
2035r VAL* 2.9 34.7 + - + +
2077r ILE* 3.9 26.2 - - + +
2078r SER* 4.4 4.9 - - - -
2093r ASP* 1.3 77.5 - - - +
2095r VAL* 1.3 64.0 + - - +
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Residues in contact with VAL2095 (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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2032r GLY* 4.4 16.6 - - - +
2033r GLY 3.7 4.3 - - - -
2034r PRO* 4.9 0.7 - - - -
2035r VAL* 5.3 0.9 - - - -
2094r PHE* 1.3 79.1 - - - +
2096r ALA* 1.3 65.1 + - - +
2097r PRO* 3.4 4.2 - - - +
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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