Contacts of the helix formed by residues 95 - 108 (chain L) 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 GLN 95 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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890A ALA* 5.1 5.6 - - + -
93L ALA* 3.1 8.8 + - + +
94L ALA* 1.3 77.9 - - - +
96L CYS* 1.3 62.3 + - - +
97L LEU 3.2 1.6 - - - -
98L GLU* 3.3 11.5 + - + +
99L HIS* 3.1 23.9 + - - +
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Residues in contact with CYS 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L LYS 5.8 4.0 - - - +
60L LYS* 5.8 7.4 - - - +
91L ARG* 5.3 9.9 - - + +
93L ALA* 4.2 19.8 - - + +
94L ALA 4.4 0.4 - - - +
95L GLN* 1.3 76.5 - - - +
97L LEU* 1.3 59.4 + - - +
99L HIS* 3.4 8.2 + - - +
100L TYR* 3.0 28.1 + - - +
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Residues in contact with LEU 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L LEU* 6.4 1.6 - - + -
82L TRP* 5.1 15.5 - - + +
86L ALA* 6.1 3.6 - - + -
89L ILE* 6.4 2.0 - - + -
91L ARG* 5.5 10.3 - - + +
94L ALA* 5.0 13.2 - - - +
95L GLN 3.2 1.4 - - - +
96L CYS* 1.3 78.8 - - - +
98L GLU* 1.3 57.9 + - - +
100L TYR* 3.4 7.0 + - - +
101L GLU* 2.9 29.7 + - - +
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Residues in contact with GLU 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890A ALA* 5.7 4.7 - - + -
82L TRP* 5.5 8.1 - - + +
94L ALA 4.9 3.5 + - - +
95L GLN* 3.3 18.1 + - - +
96L CYS 3.3 0.2 - - - -
97L LEU* 1.3 76.9 - - - +
99L HIS* 1.3 59.6 + - - +
101L GLU* 3.3 6.0 + - - +
102L PHE* 3.0 31.2 + - - +
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Residues in contact with HIS 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95L GLN 3.1 14.2 + - - +
96L CYS* 3.7 11.0 - - - +
98L GLU* 1.3 77.4 - - - +
100L TYR* 1.3 56.7 + - - +
102L PHE* 3.6 2.8 + - - +
103L LEU* 2.9 32.8 + - - +
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Residues in contact with TYR 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L GLU* 6.4 1.3 - - + -
96L CYS 3.0 18.1 + - - +
97L LEU* 3.7 7.0 - - - +
99L HIS* 1.3 74.6 - - - +
101L GLU* 1.3 58.4 + - - +
103L LEU* 3.9 4.0 - - - +
104L LEU* 2.9 33.3 + - - +
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Residues in contact with GLU 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L ALA* 5.9 7.4 - - + -
97L LEU 2.9 18.3 + - - +
98L GLU* 3.6 7.6 - - - +
100L TYR* 1.3 76.4 - - - +
102L PHE* 1.3 57.1 + - - +
104L LEU* 3.8 2.8 - - - +
105L ASP* 3.0 29.9 + - - +
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Residues in contact with PHE 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98L GLU 3.0 15.0 + - - +
99L HIS* 4.4 3.1 - - - +
101L GLU* 1.3 75.9 - - - +
103L LEU* 1.3 58.2 + - - +
105L ASP* 3.7 5.4 - - - +
106L LYS* 2.9 28.9 + - - +
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Residues in contact with LEU 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L HIS 2.9 22.1 + - - +
100L TYR* 3.9 5.2 - - - +
102L PHE* 1.3 77.7 - - - +
104L LEU* 1.3 57.8 + - - +
106L LYS* 3.3 7.2 + - - +
107L ALA* 2.9 27.7 + - - +
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Residues in contact with LEU 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100L TYR 2.9 18.3 + - - +
101L GLU* 4.2 2.5 - - - +
103L LEU* 1.3 75.7 - - - +
105L ASP* 1.3 59.5 + - - +
107L ALA* 3.8 7.8 - - - +
108L ALA* 3.2 25.6 + - - +
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Residues in contact with ASP 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L GLU 3.0 20.0 + - - +
102L PHE* 4.0 5.8 - - - +
104L LEU* 1.3 77.0 - - - +
106L LYS* 1.3 62.1 + - - +
108L ALA* 4.1 5.5 - - - +
109L GLN* 3.5 21.8 + - - +
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Residues in contact with LYS 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102L PHE 2.9 19.0 + - - +
103L LEU* 3.7 7.2 - - - +
105L ASP* 1.3 75.9 - - - +
107L ALA* 1.3 59.6 + - - +
109L GLN* 4.8 2.5 - - - -
110L ARG* 2.9 30.1 + - - +
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Residues in contact with ALA 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103L LEU 2.9 16.4 + - - +
104L LEU* 3.7 8.7 + - - +
106L LYS* 1.3 78.6 - - - +
108L ALA* 1.3 58.5 + - - +
109L GLN 3.6 0.5 + - - -
110L ARG* 4.4 11.0 - - - +
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Residues in contact with ALA 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104L LEU 3.2 19.2 + - - +
105L ASP* 4.1 7.2 - - - +
106L LYS 3.3 0.2 - - - -
107L ALA* 1.3 75.9 - - - +
109L GLN* 1.3 58.6 + - - +
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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