Contacts of the helix formed by residues 83 - 92 (chain A) in PDB entry 2LNT
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 HIS 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A LEU 4.8 1.8 - - - -
79A ASP* 4.4 21.5 - - - +
81A CYS 3.0 10.4 + - - -
82A PRO* 1.3 72.6 - - + +
84A SER* 1.3 53.7 + - - +
85A GLN* 2.7 45.6 + - + +
86A ALA* 2.8 24.0 + - + +
87A LEU 3.9 0.3 + - - -
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Residues in contact with SER 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A HIS* 2.6 47.9 + - - +
78A LEU* 4.0 16.5 + - - -
82A PRO 3.1 6.5 + - - -
83A HIS* 1.3 69.1 - - - +
85A GLN* 1.3 50.9 + - - +
86A ALA 3.1 0.4 - - - -
87A LEU* 3.1 21.7 + - - +
88A LYS* 2.6 35.9 + - - +
110A VAL* 5.4 2.9 - - - -
152A TYR* 6.3 1.3 - - - -
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A HIS* 2.7 35.9 + - + +
84A SER* 1.3 75.5 - - - +
86A ALA* 1.3 62.1 + - + +
88A LYS* 3.4 16.8 - - + +
89A LYS* 3.0 48.1 + - - +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PRO* 5.6 4.5 - - + -
83A HIS* 2.8 13.2 + - + +
85A GLN* 1.3 84.1 - - + +
87A LEU* 1.3 61.6 + - - +
89A LYS* 3.5 22.8 + - - +
90A VAL* 3.7 7.6 + - - +
154A PRO* 4.6 13.3 - - + +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 6.4 0.7 - - + -
77A HIS* 5.1 6.3 - - + +
83A HIS 3.9 0.4 + - - -
84A SER* 3.1 25.4 + - - +
86A ALA* 1.3 77.7 - - - +
88A LYS* 1.3 59.2 - - - +
90A VAL* 3.0 9.0 - - + +
91A PHE* 2.8 38.7 + - + +
127A ARG* 4.9 15.9 - - + +
152A TYR* 3.3 36.3 - - + +
153A GLU 4.2 2.2 - - - +
154A PRO* 4.0 27.0 - - + +
156A ASP* 6.3 0.2 - - + -
157A THR* 4.0 16.2 - - + -
160A LEU* 4.9 11.7 - - + -
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Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A HIS* 5.5 11.6 - - + -
84A SER* 2.6 20.3 + - - +
85A GLN* 3.4 17.0 - - + +
86A ALA 3.3 0.2 - - - -
87A LEU* 1.3 75.0 - - - +
89A LYS* 1.3 54.0 + - + +
91A PHE* 3.4 9.9 - - + +
92A ALA* 2.8 41.1 + - + +
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Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLN* 3.0 36.9 + - - +
86A ALA* 3.5 14.1 - - - +
87A LEU 3.2 0.2 - - - -
88A LYS* 1.3 76.9 - - - +
90A VAL* 1.3 57.1 + - - +
92A ALA* 3.4 5.0 + - - +
93A GLU* 3.1 29.4 + - - +
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA 3.7 4.4 + - - +
87A LEU* 3.0 28.9 - - + +
89A LYS* 1.3 76.9 - - - +
91A PHE* 1.3 60.1 + - - +
93A GLU* 3.1 14.4 + - - +
94A ASN* 2.9 49.8 + - - +
154A PRO* 4.3 12.8 - - + -
157A THR* 3.5 35.4 - - + +
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Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 3.9 40.4 - - + -
77A HIS* 6.2 3.6 - + - -
87A LEU* 2.8 27.6 + - + +
88A LYS* 3.2 12.3 + - + +
90A VAL* 1.3 79.9 - - + +
92A ALA* 1.3 63.1 + - + +
93A GLU 3.2 0.9 + - - -
94A ASN* 3.3 23.3 + - - +
97A ILE* 3.4 41.7 - - + +
98A GLN* 3.9 11.7 - - + +
101A ALA* 5.4 6.1 - - + -
106A LEU* 5.2 11.9 - - + -
127A ARG 5.7 1.1 - - - -
128A ILE* 5.4 4.0 - - + -
157A THR* 5.8 0.9 - - - -
160A LEU* 5.2 11.7 - - + -
164A MET* 5.6 0.7 - - + -
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A LYS* 2.8 22.3 + - + +
89A LYS* 3.9 5.4 - - - +
91A PHE* 1.3 79.8 - - + +
93A GLU* 1.3 58.2 + - - +
94A ASN 3.5 0.2 - - - -
98A GLN* 3.0 28.7 + - - +
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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