Contacts of the helix formed by residues 84 - 91 (chain e) 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 LYS 84 (chain e).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B VAL* 3.0 14.6 - - + +
117B ASP* 1.6 69.7 + - + +
118B PHE 4.5 0.2 - - - +
77e LEU 4.5 12.3 - - - +
78e LYS* 5.3 1.8 - - - -
79e ASN 5.8 0.9 - - - +
82e MET 3.9 3.4 + - - +
83e LEU* 1.3 73.6 - - - +
85e SER* 1.3 50.7 + - - +
86e MET 3.4 1.8 - - - +
87e LYS* 4.6 4.3 - - + -
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Residues in contact with SER 85 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B THR 5.4 0.2 - - - -
113B VAL* 2.4 18.3 + - - -
114B TYR 2.4 15.9 - - - -
115B GLU* 0.9 133.2 - - - +
116B MET 1.4 39.9 + - - -
83e LEU* 3.6 6.2 - - - +
84e LYS* 1.3 70.8 - - - +
86e MET* 1.3 26.7 - - - +
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Residues in contact with MET 86 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU* 1.5 15.0 - - + +
116B MET* 3.9 6.6 - - - +
83e LEU 5.4 0.8 + - - +
84e LYS* 3.4 0.6 - - - +
85e SER* 1.3 69.0 - - - +
87e LYS* 1.3 63.5 + - - +
88e ASN 3.5 0.2 - - - -
89e LYS* 4.3 2.9 - - - +
90e ASN* 4.2 6.8 + - - +
94f ARG 2.9 8.5 - - - +
95f VAL* 4.0 27.0 - - - +
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Residues in contact with LYS 87 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASP* 3.0 19.0 - - + +
84e LYS* 4.0 5.1 - - + +
85e SER 3.4 0.4 - - - -
86e MET* 1.3 77.5 - - - +
88e ASN* 1.3 62.9 + - - +
89e LYS 3.6 0.2 + - - -
90e ASN* 3.7 13.2 + - - +
91e GLN* 4.0 5.2 + - - +
94f ARG* 2.7 39.3 + - + +
95f VAL* 5.5 0.2 - - - -
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Residues in contact with ASN 88 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B MET* 1.0 145.1 - - - +
117B ASP* 1.6 62.3 - - - +
118B PHE 2.5 3.8 - - - +
119B LEU* 3.3 9.0 - - - +
120B ALA* 4.2 7.0 - - + +
87e LYS* 1.3 65.0 - - - +
89e LYS* 1.3 62.6 + - - +
91e GLN* 3.0 25.8 + - - +
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Residues in contact with LYS 89 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B MET* 0.7 150.4 - - + +
119B LEU* 5.4 2.5 - - - -
85e SER 4.2 0.7 - - - +
86e MET* 4.3 5.6 - - - +
88e ASN* 1.3 57.3 - - - +
90e ASN* 1.3 61.4 + - - +
91e GLN 3.1 8.1 + - - -
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Residues in contact with ASN 90 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B MET* 3.0 0.6 - - - +
86e MET 4.2 8.1 + - - +
87e LYS 3.7 11.1 + - - +
88e ASN 3.2 0.8 + - - -
89e LYS* 1.3 76.4 - - - +
91e GLN* 1.3 59.5 + - - +
93f ALA 4.1 19.7 - - - +
94f ARG* 4.6 3.8 - - - +
95f VAL 6.2 0.7 - - - -
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Residues in contact with GLN 91 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ALA* 6.1 5.2 - - + -
87e LYS 4.0 4.8 + - - +
88e ASN* 3.0 17.9 + - - +
89e LYS 3.5 9.4 - - - -
90e ASN* 1.3 82.7 - - - +
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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