Contacts of the helix formed by residues 94 - 103 (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 ASN 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A VAL* 2.9 34.4 + - - +
91A PHE 3.3 3.3 + - - +
93A GLU* 1.3 79.3 - - - +
95A LYS* 1.3 64.2 + - - +
96A GLU* 3.3 17.8 + - - +
97A ILE* 3.7 33.5 - - + +
98A GLN* 3.1 25.2 + - - +
157A THR* 3.8 24.2 + - - -
161A LEU* 5.8 1.0 - - - +
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Residues in contact with LYS 95 (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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93A GLU 3.3 8.7 + - - +
94A ASN* 1.3 70.7 - - - +
96A GLU* 1.3 64.0 + - + +
98A GLN* 3.1 14.8 + - - +
99A LYS* 2.8 37.0 + - - +
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Residues in contact with GLU 96 (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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94A ASN* 3.9 18.7 + - - -
95A LYS* 1.3 95.6 + - + +
97A ILE* 1.3 62.8 + - + +
99A LYS* 3.5 6.2 + - - +
100A LEU* 3.4 21.0 + - - +
161A LEU* 3.4 44.4 - - + +
164A MET* 4.6 0.9 - - - +
165A LYS* 5.0 5.3 + - - +
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Residues in contact with ILE 97 (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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91A PHE* 3.4 50.7 - - + +
94A ASN* 3.4 39.9 + - + +
95A LYS 3.2 0.6 - - - -
96A GLU* 1.3 80.8 - - + +
98A GLN* 1.3 63.0 + - - +
101A ALA* 3.1 24.7 + - - +
157A THR* 4.4 12.8 - - + +
160A LEU* 4.5 17.0 - - + -
161A LEU* 5.0 11.4 - - + +
164A MET* 3.2 30.8 - - + +
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Residues in contact with GLN 98 (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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91A PHE* 3.9 15.5 - - + +
92A ALA* 3.0 34.4 + - - +
93A GLU 4.0 1.6 - - - -
94A ASN 3.1 25.2 + - - +
95A LYS* 3.1 13.8 + - - +
97A ILE* 1.3 78.1 - - + +
99A LYS* 1.3 53.1 + - - +
101A ALA* 3.6 5.5 - - - +
102A GLU* 2.8 42.5 + - - +
106A LEU* 6.3 0.2 - - - -
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Residues in contact with LYS 99 (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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95A LYS 2.8 18.3 + - - +
96A GLU* 3.7 7.9 - - - +
98A GLN* 1.3 75.7 - - - +
100A LEU* 1.3 60.1 + - - +
102A GLU* 3.0 44.9 + - - +
103A GLN* 3.6 9.1 + - - +
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Residues in contact with LEU 100 (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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73A MET* 3.9 14.4 - - + -
96A GLU 3.4 8.1 + - - +
98A GLN 3.4 0.4 - - - -
99A LYS* 1.3 79.7 - - - +
101A ALA* 1.3 62.9 + - - +
103A GLN* 3.2 11.7 + - - +
104A PHE* 3.0 47.1 - - + -
164A MET* 3.5 40.6 - - + +
165A LYS* 3.8 35.4 - - + +
168A LEU* 4.0 22.9 - - + -
171A LEU* 5.4 7.4 - - + -
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Residues in contact with ALA 101 (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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52A LEU 4.7 0.5 + - - -
73A MET* 6.4 1.8 - - + -
75A ILE* 5.7 1.6 - - + -
91A PHE* 5.4 4.9 - - + -
97A ILE* 3.1 21.6 + - + +
98A GLN* 3.2 5.8 + - - +
100A LEU* 1.3 79.1 - - - +
102A GLU* 1.3 54.1 + - - +
104A PHE* 2.7 35.1 + - - +
105A VAL 5.5 1.1 - - - +
106A LEU* 3.8 37.6 - - + +
164A MET* 3.8 13.2 - - + +
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Residues in contact with GLU 102 (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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51A GLN* 4.0 24.0 - - + +
52A LEU* 4.0 20.9 - - + -
70A LYS* 5.2 0.2 + - - -
98A GLN* 2.8 18.6 + - - +
99A LYS* 3.0 56.6 + - + +
101A ALA* 1.3 73.3 - - - +
103A GLN* 1.3 59.3 + - + +
104A PHE 3.3 1.7 + - - -
106A LEU* 5.2 0.4 - - - +
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Residues in contact with GLN 103 (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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50A ASP* 5.1 0.2 - - - +
70A LYS* 3.2 23.7 + - - +
99A LYS* 4.0 10.3 - - - +
100A LEU* 3.2 11.6 + - - +
101A ALA 3.1 0.6 - - - -
102A GLU* 1.3 80.8 - - + +
104A PHE* 1.3 69.4 + - + +
171A LEU* 3.6 39.1 - - + +
172A LYS* 5.3 4.4 - - - +
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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