Contacts of the helix formed by residues 81 - 96 (chain A) in PDB entry 2LCK
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 GLY 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A TYR 3.7 0.8 + - - -
80A ASN* 1.3 79.7 + - - +
82A LEU* 1.3 60.8 + - - +
83A VAL* 3.1 11.1 - - - +
84A ALA* 2.8 31.2 + - - +
85A GLY* 3.1 10.2 + - - -
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Residues in contact with LEU 82 (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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78A LEU 4.0 10.4 + - - +
79A TYR* 3.3 48.2 - - + +
80A ASN 3.2 2.6 + - - -
81A GLY* 1.3 78.7 - - - +
83A VAL* 1.3 79.2 + - + +
85A GLY* 3.3 6.2 + - - +
86A LEU* 3.3 34.4 - - + +
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Residues in contact with VAL 83 (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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79A TYR 5.6 1.3 - - - +
81A GLY* 4.3 11.9 - - - +
82A LEU* 1.3 94.6 - - + +
84A ALA* 1.3 65.4 + - + +
86A LEU* 3.8 7.2 + - - +
87A GLN* 3.6 17.8 + - - +
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Residues in contact with ALA 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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81A GLY* 2.8 21.0 + - - +
83A VAL* 1.3 83.1 - - + +
85A GLY* 1.3 63.1 + - - +
86A LEU 3.3 0.2 - - - -
87A GLN* 3.5 18.2 + - - +
88A ARG 3.5 6.4 + - - -
141A LYS* 4.3 16.3 + - - +
144A PHE* 6.2 4.5 - - + -
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Residues in contact with GLY 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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28A ASP* 5.5 0.5 - - - +
32A PHE* 6.2 5.2 - - - -
81A GLY 3.1 10.6 + - - -
82A LEU* 3.3 4.3 + - - -
84A ALA* 1.3 76.3 - - - +
86A LEU* 1.3 61.1 + - - +
88A ARG* 2.9 37.3 + - - +
89A GLN* 3.4 4.0 + - - +
141A LYS* 5.8 0.7 - - - -
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.3 30.7 + - + +
83A VAL* 4.0 9.4 - - - +
84A ALA 3.3 0.6 - - - -
85A GLY* 1.3 74.9 - - - +
87A GLN* 1.3 53.8 + - - +
88A ARG 3.0 2.0 - - - -
89A GLN* 2.7 20.1 + - + +
90A MET* 2.6 37.8 + - + +
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Residues in contact with GLN 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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83A VAL 3.6 10.5 + - - +
84A ALA* 3.5 15.2 + - - +
85A GLY 3.2 0.4 - - - -
86A LEU* 1.3 75.7 - - - +
88A ARG* 1.3 67.2 + - - +
90A MET* 3.1 28.8 + - + +
91A SER* 3.2 14.4 + - - -
141A LYS* 5.9 0.7 - - - -
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Residues in contact with ARG 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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28A ASP* 3.3 39.4 + - - +
32A PHE* 4.3 25.0 - - - -
84A ALA 3.5 6.1 + - - +
85A GLY* 2.9 23.5 + - - +
87A GLN* 1.3 82.3 - - - +
89A GLN* 1.3 63.6 + - - +
91A SER* 3.4 10.2 + - - -
92A PHE* 3.8 9.2 + - - +
137A THR* 5.8 4.7 - - + -
141A LYS* 3.8 42.8 - - + +
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Residues in contact with GLN 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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21A GLY 4.4 0.3 - - - +
24A ALA* 3.2 28.8 + - + +
25A CYS* 2.7 44.8 + - - +
28A ASP* 2.6 34.2 + - - +
85A GLY 3.4 2.6 + - - +
86A LEU* 2.7 26.5 + - - +
88A ARG* 1.3 81.0 - - - +
90A MET* 1.3 61.3 + - - +
91A SER 3.4 0.5 + - - -
92A PHE* 3.4 13.5 + - + +
93A ALA* 3.8 11.4 + - - +
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Residues in contact with MET 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 LEU* 2.6 18.1 + - + +
87A GLN* 3.1 27.3 + - + +
89A GLN* 1.3 74.8 - - - +
91A SER* 1.3 59.8 + - - +
93A ALA* 3.9 3.6 + - - +
94A SER* 2.8 30.1 + - - +
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Residues in contact with SER 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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87A GLN* 3.2 9.0 + - - -
88A ARG* 4.0 7.4 - - - -
89A GLN 3.3 0.4 - - - -
90A MET* 1.3 78.2 - - - +
92A PHE* 1.3 66.7 + - - +
94A SER* 3.2 7.2 + - - -
95A VAL* 3.0 27.8 + - - +
137A THR* 5.7 10.2 - - - +
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Residues in contact with PHE 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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24A ALA* 4.9 16.4 - - + -
88A ARG 3.8 7.7 + - - +
89A GLN* 3.4 12.2 + - + +
90A MET 3.4 1.0 - - - -
91A SER* 1.3 77.2 - - - +
93A ALA* 1.3 62.0 + - + +
95A VAL* 2.9 28.1 - - + +
96A ARG* 3.2 41.6 - - + +
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Residues in contact with ALA 93 (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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17A PHE* 3.5 35.3 - - + -
21A GLY* 5.9 7.4 - - - -
24A ALA* 5.9 5.2 - - + -
89A GLN 3.8 8.6 + - - +
90A MET* 4.4 5.2 - - - +
91A SER 3.3 0.4 - - - -
92A PHE* 1.3 83.3 - - + +
94A SER* 1.3 63.0 + - - +
96A ARG* 3.2 25.5 + - - +
97A ILE 3.6 2.1 + - - -
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Residues in contact with SER 94 (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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17A PHE* 5.4 1.1 - - - -
90A MET* 2.8 24.7 + - - +
91A SER* 3.2 13.1 + - - -
93A ALA* 1.3 79.0 - - - +
95A VAL* 1.3 52.2 + - - +
97A ILE* 2.6 40.9 - - - +
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Residues in contact with VAL 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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91A SER* 3.0 16.5 + - - +
92A PHE* 2.9 37.5 - - + +
94A SER* 1.3 72.2 - - - +
96A ARG* 1.3 61.7 + - + +
97A ILE* 2.8 8.6 + - - -
98A GLY* 3.0 2.3 + - - -
99A LEU* 2.8 56.9 + - + +
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Residues in contact with ARG 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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16A LYS 5.4 0.4 + - - -
17A PHE* 4.4 24.5 + - - +
20A ALA* 3.6 30.3 - - - +
92A PHE* 3.2 47.3 - - + +
93A ALA* 3.2 26.2 + - - +
94A SER 3.2 1.4 - - - -
95A VAL* 1.3 79.1 - - + +
97A ILE* 1.3 56.8 + - - +
98A GLY 3.1 4.7 - - - -
99A LEU* 5.2 1.1 - - + -
100A TYR* 3.4 60.4 - - + +
101A ASP* 4.5 0.5 - - - +
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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