Contacts of the helix formed by residues 70 - 88 (chain A) in PDB entry 1K9K
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 PHE 70 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU 5.7 0.2 - - - -
13A VAL* 3.8 22.0 - - + -
16A PHE* 3.5 44.5 - + + -
27A HIS 4.2 3.1 + - - +
69A ASN* 1.3 76.0 - - - +
71A GLN* 1.3 63.5 + - - +
73A TYR* 3.2 24.2 + + - +
74A VAL* 2.9 45.4 + - + +
77A LEU* 5.6 1.1 - - + -
81B ALA* 3.5 36.1 - - + -
82B LEU* 3.8 15.0 - - + -
85B ASN* 3.4 36.3 - - + +
89B LYS* 6.1 0.2 - - - +
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Residues in contact with GLN 71 (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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69A ASN* 3.1 29.3 + - - +
70A PHE* 1.3 87.2 - - - +
72A GLU* 1.3 65.2 + - + +
74A VAL* 3.2 11.2 + - - +
75A THR* 3.2 22.6 + - - -
82B LEU* 4.3 23.1 - - + +
85B ASN* 5.0 4.4 - - - +
89B LYS* 5.1 8.7 - - - +
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Residues in contact with GLU 72 (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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60A LEU* 3.3 35.9 - - - +
61A ASP* 4.0 0.4 - - - -
62A ARG* 3.1 25.0 + - + +
63A ASN* 3.2 13.0 + - - +
67A GLU 3.0 4.9 - - - +
68A VAL* 3.2 11.1 - - + -
69A ASN* 2.7 45.9 + - - +
71A GLN* 1.3 72.2 - - + +
73A TYR* 1.3 64.1 + - - +
75A THR* 3.2 11.6 + - - -
76A PHE 3.2 15.6 + - - -
400A CA 2.5 30.7 - - - -
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Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 2.8 34.7 + - - -
15A ILE* 3.7 15.1 - - - +
16A PHE* 3.5 36.3 - + + -
29A LEU* 4.5 8.5 - - + -
34A LEU* 6.1 1.6 - - + -
37A LEU* 4.1 21.3 - - + -
60A LEU* 5.4 0.4 - - + -
68A VAL* 3.8 8.9 - - + +
69A ASN 3.0 13.1 + - - +
70A PHE* 3.4 24.0 - + - +
72A GLU* 1.3 75.1 - - - +
74A VAL* 1.3 65.4 + - - +
76A PHE* 3.1 22.2 + + - +
77A LEU* 2.9 57.7 + - + +
5B LEU* 4.1 5.5 - - + +
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Residues in contact with VAL 74 (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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70A PHE* 2.9 48.1 + - + +
71A GLN* 3.2 10.3 + - - +
73A TYR* 1.3 78.0 - - - +
75A THR* 1.3 57.7 + - - +
77A LEU* 3.2 13.5 + - + +
78A GLY* 3.0 25.3 + - - -
74B VAL* 5.9 1.0 - - + +
78B GLY* 3.8 27.4 - - - +
81B ALA* 4.3 10.1 - - + -
82B LEU* 4.3 11.4 - - + -
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Residues in contact with THR 75 (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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59A ASP* 6.1 0.9 - - - +
60A LEU* 4.8 10.1 - - + -
62A ARG* 6.2 3.1 - - + +
71A GLN 3.2 11.6 + - - -
72A GLU* 3.4 13.2 - - - -
73A TYR 3.2 0.4 - - - -
74A VAL* 1.3 79.3 - - - +
76A PHE* 1.3 63.1 + - - +
78A GLY* 3.3 2.9 + - - -
79A ALA* 3.1 21.9 + - + +
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Residues in contact with PHE 76 (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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34A LEU* 5.9 2.7 - - + -
37A LEU* 5.4 0.7 - - + -
38A ILE* 3.8 31.4 - - + -
42A LEU* 4.4 10.1 - - + -
56A LEU* 3.8 32.5 - - + -
60A LEU* 3.7 28.7 - - + +
72A GLU 3.2 6.9 + - - +
73A TYR* 3.1 25.7 + + - +
75A THR* 1.3 74.0 - - - +
77A LEU* 1.3 69.0 + - + +
79A ALA* 3.1 12.9 + - + +
80A LEU* 3.1 57.1 + - + +
5B LEU* 5.0 9.9 - - + -
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Residues in contact with LEU 77 (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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9A ILE* 6.4 0.7 - - + -
12A LEU* 4.0 36.6 - - + -
70A PHE* 5.6 0.7 - - + -
73A TYR* 2.9 61.6 + - + +
74A VAL* 3.5 16.6 - - + +
76A PHE* 1.3 80.5 - - + +
78A GLY* 1.3 57.9 + - - +
80A LEU* 3.1 8.8 + - - +
81A ALA* 2.9 28.2 + - - +
5B LEU* 4.3 15.7 - - + -
9B ILE* 3.9 13.0 - - + +
81B ALA* 5.3 9.4 - - + -
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Residues in contact with GLY 78 (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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74A VAL 3.0 14.0 + - - -
75A THR* 3.3 4.5 + - - -
76A PHE 3.2 0.2 - - - -
77A LEU* 1.3 77.3 - - - +
79A ALA* 1.3 61.9 + - - +
81A ALA* 3.2 5.8 + - - +
82A LEU* 3.0 30.2 + - - +
74B VAL* 3.8 27.3 - - - +
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Residues in contact with ALA 79 (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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60A LEU* 6.3 0.2 - - + -
75A THR* 3.1 14.0 + - + +
76A PHE* 3.1 16.8 + - + +
78A GLY* 1.3 76.1 - - - +
80A LEU* 1.3 64.0 + - + +
82A LEU* 3.3 12.7 + - - +
83A ILE* 3.2 30.4 + - + +
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Residues in contact with LEU 80 (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 LEU* 3.9 17.5 - - + -
76A PHE* 3.1 56.6 + - + +
77A LEU* 3.1 10.5 + - - +
79A ALA* 1.3 76.5 - - + +
81A ALA* 1.3 64.0 + - - +
83A ILE* 3.3 20.1 + - + +
84A TYR* 3.0 23.0 + - - +
5B LEU* 3.6 27.6 - - + -
9B ILE* 4.0 12.8 - - + +
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Residues in contact with ALA 81 (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 LEU 2.9 13.2 + - - +
78A GLY* 3.2 12.1 + - - +
80A LEU* 1.3 75.1 - - - +
82A LEU* 1.3 60.0 + - - +
84A TYR 3.3 0.9 + - - -
85A ASN* 2.8 30.5 + - - +
9B ILE* 3.6 22.1 - - + +
12B LEU* 6.3 0.9 - - + -
13B VAL* 3.8 5.3 - - + +
70B PHE* 3.5 20.6 - - + -
74B VAL* 4.3 6.5 - - + -
77B LEU* 5.1 9.9 - - + -
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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 GLY 3.0 20.3 + - - +
79A ALA* 3.6 13.2 - - - +
80A LEU 3.3 0.2 - - - -
81A ALA* 1.3 75.6 - - - +
83A ILE* 1.3 65.4 + - + +
85A ASN* 3.2 5.5 + - - +
86A GLU* 3.2 27.6 + - + +
70B PHE* 3.7 26.2 - - + -
71B GLN* 4.1 28.5 - - + +
74B VAL* 4.5 7.6 - - + -
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ALA* 3.2 17.4 + - + +
80A LEU* 3.5 25.6 - - + +
82A LEU* 1.3 80.1 - - + +
84A TYR* 1.3 64.4 + - - +
86A GLU* 3.4 16.6 + - - +
87A ALA* 3.8 6.4 + - - +
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Residues in contact with TYR 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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80A LEU 3.0 15.6 + - - +
81A ALA 3.8 3.8 - - - +
83A ILE* 1.3 78.3 - - - +
85A ASN* 1.3 62.7 + - - +
87A ALA* 3.3 17.9 + - + +
88A LEU* 3.5 29.6 + - + +
6B ASP* 4.8 9.6 - - + -
9B ILE* 4.3 6.3 - - + -
10B GLY* 3.7 35.5 + - - -
13B VAL* 3.7 26.0 - - + -
14B ALA* 6.0 0.4 - - + -
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Residues in contact with ASN 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 2.8 17.7 + - - +
82A LEU* 3.2 6.1 + - - +
84A TYR* 1.3 78.8 - - - +
86A GLU* 1.3 65.4 + - - +
88A LEU* 3.1 12.0 + - - +
89A LYS* 3.0 40.5 + - - +
13B VAL* 3.7 9.6 - - - +
17B HIS* 2.6 35.5 + - - -
70B PHE* 3.5 46.9 - - + +
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Residues in contact with GLU 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 LEU 3.2 13.1 + - - +
83A ILE* 3.7 9.9 - - - +
84A TYR 3.2 0.6 - - - -
85A ASN* 1.3 81.8 + - - +
87A ALA* 1.3 60.9 + - - +
88A LEU 3.0 0.2 - - - -
89A LYS* 3.0 59.9 + - - +
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Residues in contact with ALA 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 ILE 3.8 6.7 + - - +
84A TYR* 3.3 14.1 + - + +
86A GLU* 1.3 77.6 - - - +
88A LEU* 1.3 63.3 + - + +
89A LYS 3.4 2.5 - - - +
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Residues in contact with LEU 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 TYR* 3.5 26.4 + - + +
85A ASN* 3.1 10.7 + - - +
86A GLU 3.0 1.2 - - - -
87A ALA* 1.3 83.9 - - + +
89A LYS* 1.3 59.4 + - - +
90A GLY 4.1 0.2 + - - -
13B VAL* 3.7 17.9 - - + +
14B ALA* 4.3 12.8 - - + +
17B HIS* 3.6 41.2 + - + +
27B HIS* 5.3 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