Contacts of the helix formed by residues 81 - 92 (chain B) in PDB entry 2LNS
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 CYS 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78B LEU* 3.2 16.1 - - + +
79B ASP 3.0 4.8 - - - +
80B GLU* 1.3 81.8 - - - +
82B PRO* 1.3 57.0 - - - +
83B HIS* 2.4 40.1 + - + +
84B SER* 2.9 19.9 + - - -
85B GLN 4.1 0.3 + - - -
124B TYR* 5.0 5.6 - - - -
125B VAL* 4.5 16.2 - - + -
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Residues in contact with PRO 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ASP 4.3 0.9 - - - +
80B GLU 3.3 10.8 - - - +
81B CYS* 1.3 81.4 - - + +
83B HIS* 1.3 68.3 + - + +
84B SER 3.3 0.2 - - - -
85B GLN* 3.1 31.4 + - + +
86B ALA* 3.3 5.5 + - - +
89B LYS* 4.7 1.6 + - - -
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Residues in contact with HIS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B CYS* 2.4 32.8 + - + +
82B PRO* 1.3 74.3 - - + +
84B SER* 1.3 53.1 + - - +
86B ALA* 2.7 35.8 + - - +
87B LEU* 3.7 2.3 + - - +
124B TYR* 2.7 36.5 + + + -
125B VAL* 4.7 9.6 - - + -
126B PRO* 5.2 7.9 - - + -
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B HIS* 4.4 13.4 + - - +
78B LEU* 2.8 33.6 + - - -
79B ASP* 3.2 11.7 + - - -
81B CYS* 2.9 11.9 + - - +
83B HIS* 1.3 72.4 - - - +
85B GLN* 1.3 55.6 + - - +
86B ALA 2.7 11.8 + - - -
87B LEU* 2.9 18.6 + - - +
88B LYS* 3.0 14.0 + - - +
125B VAL* 5.5 6.8 - - - +
126B PRO* 6.0 2.2 - - - +
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Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ASP* 2.4 53.3 + - - +
82B PRO* 3.1 25.5 + - + +
84B SER* 1.3 76.4 - - - +
86B ALA* 1.3 52.8 + - - +
88B LYS* 3.4 26.1 + - - +
89B LYS* 2.6 43.7 + - - +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PRO 3.3 6.0 + - - +
83B HIS* 2.7 20.6 + - - +
84B SER 2.7 5.1 + - - -
85B GLN* 1.3 70.6 - - - +
87B LEU* 1.3 65.1 + - - +
89B LYS* 2.9 38.3 + - + +
90B VAL* 4.0 2.6 + - - +
152B TYR 5.6 4.5 - - - +
154B PRO* 4.9 25.2 - - + +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ILE* 5.5 6.3 - - + -
83B HIS 3.7 1.7 + - - +
84B SER* 2.9 12.2 + - - +
86B ALA* 1.3 76.8 - - - +
88B LYS* 1.3 59.7 + - - +
89B LYS 2.8 6.4 + - - -
90B VAL* 3.4 17.9 + - + +
91B PHE* 2.8 31.5 + - + +
97B ILE* 4.6 4.3 - - + -
126B PRO* 6.3 2.2 - - + -
128B ILE* 4.8 16.6 - - + -
152B TYR* 6.0 8.5 - - + -
153B GLU 5.2 9.2 - - - +
154B PRO* 5.5 3.4 - - - -
157B THR* 4.5 7.4 - - + +
160B LEU* 3.9 31.9 - - + -
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Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ASP* 4.6 11.7 - - - +
84B SER* 3.0 17.8 + - - +
85B GLN* 3.4 30.9 + - - +
87B LEU* 1.3 76.0 - - - +
89B LYS* 1.3 64.3 + - - +
91B PHE* 3.5 23.8 - - + +
92B ALA* 3.8 6.8 + - - +
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PRO 4.7 1.4 + - - -
85B GLN* 2.6 48.6 + - - +
86B ALA* 2.9 21.4 + - + +
87B LEU 2.8 1.6 + - - -
88B LYS* 1.3 78.6 - - - +
90B VAL* 1.3 70.6 + - + +
91B PHE 3.0 0.4 - - - -
92B ALA* 3.2 14.7 + - - +
93B GLU* 4.3 1.2 + - - +
154B PRO* 5.9 4.7 - - + -
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 3.6 15.0 - - + +
89B LYS* 1.3 84.5 - - + +
91B PHE* 1.3 56.9 + - - +
93B GLU* 2.8 13.4 + - - +
94B ASN* 2.7 55.0 + - - +
154B PRO* 3.0 35.2 - - + +
155B ALA* 5.0 3.4 - - + -
157B THR* 3.5 17.3 - - + -
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Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 2.8 27.5 + - + +
88B LYS* 3.5 21.3 - - + +
89B LYS 3.0 0.2 - - - -
90B VAL* 1.3 78.3 - - - +
92B ALA* 1.3 65.8 + - + +
93B GLU 3.4 0.2 + - - -
94B ASN 3.6 7.3 + - - +
97B ILE* 3.3 49.1 - - + -
98B GLN* 3.3 36.4 + - + -
101B ALA* 4.5 15.7 - - + -
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LYS 3.8 4.7 + - - +
89B LYS 3.2 12.1 + - - +
90B VAL 3.0 0.8 + - - -
91B PHE* 1.3 85.4 - - + +
93B GLU* 1.3 56.9 + - - +
95B LYS* 5.2 1.4 - - - +
98B GLN* 3.2 20.0 + - - +
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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