Contacts of the helix formed by residues 82 - 100 (chain A) in PDB entry 1LKO
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 ASP 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A GLN* 4.7 3.1 - - - +
37A ASP* 4.0 9.0 - - - +
81A ALA* 1.3 84.2 - - - +
83A THR* 1.3 60.0 + - - +
84A HIS* 3.4 14.0 + - - +
85A ALA* 3.1 35.9 + - - +
86A ASN* 2.9 24.1 + - - -
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Residues in contact with THR 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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30A PHE 4.9 0.6 + - - -
33A GLN* 3.9 0.9 - - - +
34A ALA* 3.2 26.3 + - + -
37A ASP* 2.6 26.6 + - - +
39A PHE* 4.0 19.5 - - + -
42A ILE* 4.0 15.3 - - + -
46A PHE* 4.6 3.6 - - + -
81A ALA 3.8 0.2 + - - -
82A ASP* 1.3 69.8 - - - +
84A HIS* 1.3 67.4 + - - +
86A ASN* 3.1 9.3 + - - +
87A LEU* 2.8 41.4 + - + +
142A ILE* 3.8 9.6 - - + -
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Residues in contact with HIS 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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39A PHE* 5.8 0.4 - - - -
82A ASP* 3.4 10.8 + - - +
83A THR* 1.3 76.5 - - - +
85A ALA* 1.3 67.8 + - + +
87A LEU* 3.1 6.5 + - - +
88A ILE* 3.0 43.7 + - + +
139A ALA* 3.2 43.1 + - + +
142A ILE* 4.1 28.9 - - + +
143A LYS* 4.0 25.8 + - + +
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Residues in contact with ALA 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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81A ALA* 3.8 14.4 - - + -
82A ASP* 3.1 31.3 + - - +
84A HIS* 1.3 81.7 - - + +
86A ASN* 1.3 58.4 + - - +
88A ILE* 3.3 6.0 + - - +
89A ALA* 2.9 29.8 + - - +
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Residues in contact with ASN 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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30A PHE* 3.5 45.9 + - + +
33A GLN* 3.7 16.6 - - - +
46A PHE* 4.2 4.5 - - + -
79A ILE 4.1 2.3 - - - +
80A ILE* 4.1 0.8 - - - +
81A ALA* 2.8 44.9 + - - +
82A ASP 2.9 16.6 + - - +
83A THR* 3.6 8.9 - - - +
85A ALA* 1.3 76.4 - - - +
87A LEU* 1.3 58.1 + - - +
89A ALA* 3.9 5.3 - - - +
90A SER* 2.8 35.7 + - - -
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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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42A ILE* 4.1 11.0 - - + -
45A ILE* 6.3 0.2 - - + -
46A PHE* 3.5 28.9 - - + -
83A THR* 2.8 24.5 + - + +
84A HIS* 3.5 5.6 - - - +
86A ASN* 1.3 75.5 - - - +
88A ILE* 1.3 59.4 + - - +
90A SER* 3.7 2.7 - - - -
91A ALA* 2.9 30.5 + - - +
135A PHE* 3.6 41.1 - - + +
138A PHE* 4.0 10.5 - - + -
139A ALA* 3.7 21.8 - - + +
142A ILE* 3.7 27.4 - - + -
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Residues in contact with ILE 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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84A HIS* 3.0 39.9 + - + +
85A ALA* 3.3 8.7 + - - +
87A LEU* 1.3 77.0 - - - +
89A ALA* 1.3 63.2 + - - +
91A ALA* 3.3 5.3 + - - +
92A ALA* 3.0 22.7 + - + +
136A LEU* 4.6 15.3 - - + -
139A ALA* 3.7 21.8 - - + -
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Residues in contact with ALA 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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30A PHE* 5.2 9.0 - - + -
79A ILE 6.0 0.9 - - - +
85A ALA 2.9 16.2 + - - +
86A ASN* 3.9 6.5 - - - +
88A ILE* 1.3 79.1 - - - +
90A SER* 1.3 62.6 + - - +
92A ALA* 3.2 8.8 + - - +
93A GLY* 3.1 18.0 + - - -
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Residues in contact with SER 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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27A TYR* 3.3 26.5 + - - -
30A PHE* 3.2 26.0 - - - -
46A PHE* 3.5 7.4 - - - -
86A ASN 2.8 21.0 + - - -
87A LEU 3.7 4.0 - - - -
89A ALA* 1.3 77.8 - - - +
91A ALA* 1.3 61.6 + - - +
93A GLY* 3.1 3.1 + - - -
94A GLU* 3.0 25.3 + - - +
135A PHE* 3.7 17.7 - - - -
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Residues in contact with ALA 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 LEU 2.9 18.1 + - - +
88A ILE 3.6 4.3 - - - +
90A SER* 1.3 76.6 - - - +
92A ALA* 1.3 58.1 + - - +
94A GLU* 3.2 7.0 + - - +
95A HIS* 2.8 30.2 + - - +
132A GLU* 3.6 14.8 - - + +
135A PHE* 4.1 9.6 - - + -
136A LEU* 3.5 38.4 - - + -
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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 ILE* 3.0 15.0 + - + +
89A ALA* 3.4 12.1 - - - +
90A SER 3.2 0.2 - - - -
91A ALA* 1.3 77.9 - - - +
93A GLY* 1.3 61.4 + - - +
95A HIS* 3.4 9.2 + - - +
96A HIS* 3.1 21.8 + - - +
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Residues in contact with GLY 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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26A ARG* 5.6 7.6 - - - -
27A TYR* 5.2 2.2 - - - -
89A ALA 3.1 9.4 + - - -
90A SER* 3.1 7.1 + - - -
92A ALA* 1.3 74.4 - - - +
94A GLU* 1.3 64.1 + - - +
96A HIS* 3.3 6.7 + - - +
97A GLU* 3.1 30.0 + - - +
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Residues in contact with GLU 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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27A TYR* 2.6 25.1 + - - +
53A GLU* 3.1 3.8 - - - +
90A SER 3.0 18.8 + - - +
91A ALA 3.5 6.3 - - - +
93A GLY* 1.3 74.5 - - - +
95A HIS* 1.3 63.8 + - - +
97A GLU* 3.1 11.7 + - - +
98A TYR* 3.0 27.1 + - - +
128A GLU* 2.9 33.1 - - - +
131A HIS* 3.2 18.9 - - + +
132A GLU* 3.7 12.8 - - + +
135A PHE* 3.6 8.9 - - + -
600A FE2 2.2 31.7 - - - -
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Residues in contact with HIS 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 ALA 2.8 12.3 + - - +
92A ALA* 3.4 10.1 - - - +
93A GLY 3.2 0.2 - - - -
94A GLU* 1.3 77.5 - - - +
96A HIS* 1.3 59.5 + - - +
98A TYR* 3.5 21.4 + - - -
99A THR* 2.6 62.4 + - + +
132A GLU* 3.2 24.2 + - - +
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Residues in contact with HIS 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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92A ALA 3.1 10.5 + - - +
93A GLY* 3.8 9.0 - - - +
94A GLU 3.3 0.4 - - - -
95A HIS* 1.3 81.5 - - - +
97A GLU* 1.3 60.8 + - + +
99A THR* 4.0 3.8 - - - -
100A GLU* 2.9 50.8 + - + +
101A MET* 3.0 31.3 + - + +
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Residues in contact with GLU 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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19A GLY* 4.9 7.8 - - - +
20A GLU* 4.3 8.8 - - - +
23A ALA* 4.9 12.5 - - - +
26A ARG* 5.8 0.7 + - - -
27A TYR* 5.4 0.6 + - - -
53A GLU* 5.2 0.9 - - - +
93A GLY 3.1 11.8 + - - +
94A GLU* 3.1 21.2 + - - +
96A HIS* 1.3 83.6 - - + +
98A TYR* 1.3 59.3 + - - +
101A MET* 4.1 20.5 - - + +
102A TYR* 2.9 52.8 + - + +
103A PRO* 3.5 0.2 - - - +
128A GLU* 3.3 29.1 - - + +
600A FE2 4.0 1.9 - - - -
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Residues in contact with TYR 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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94A GLU 3.0 26.6 + - - +
95A HIS* 3.5 28.3 + - - -
97A GLU* 1.3 76.4 - - - +
99A THR* 1.3 72.5 + - + +
100A GLU 3.7 0.2 - - - -
103A PRO* 3.1 19.0 - - - +
125A ALA* 3.3 35.3 - - + +
128A GLU* 4.1 4.3 - - + -
129A GLU* 3.6 53.9 + - + +
132A GLU* 2.6 35.0 + - + -
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Residues in contact with THR 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 HIS* 2.6 53.6 + - + +
96A HIS* 4.0 0.3 - - - -
98A TYR* 1.3 105.0 - - + +
100A GLU* 1.3 82.6 + - - +
103A PRO* 3.9 11.7 - - - +
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Residues in contact with GLU 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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96A HIS* 2.9 35.5 + - + +
99A THR* 1.3 98.3 + - - +
101A MET* 1.3 63.3 - - - +
102A TYR 3.7 1.1 - - - -
103A PRO* 3.6 2.1 - - - +
104A SER* 2.7 36.5 + - - -
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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