Contacts of the helix formed by residues 81 - 96 (chain A) in PDB entry 1K63
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 ALA 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A GLU 4.7 11.2 + - - +
79A ARG 3.4 3.1 - - - +
80A TYR* 1.3 84.1 - - - +
82A TYR* 1.3 67.2 + - - +
83A ALA* 3.3 6.5 - - + +
84A GLU* 3.1 17.2 + - + +
85A HIS* 3.1 11.5 + - - -
206A SER* 5.0 1.3 - - - -
210A GLN* 3.6 25.4 - - - +
219A ASP* 5.9 1.8 - - - +
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Residues in contact with TYR 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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81A ALA* 1.3 71.6 - - - +
83A ALA* 1.3 68.5 + - - +
85A HIS* 3.1 4.9 + - - +
86A ARG* 2.9 32.0 + - - +
109A TRP* 3.6 22.7 - + - -
112A ALA* 3.2 23.0 + - + -
113A LEU* 3.4 27.7 - - + +
116A ASP* 2.5 46.3 + - - +
207A TRP* 4.0 15.9 - + + -
210A GLN* 2.8 23.9 + - + +
219A ASP* 5.7 0.7 - - - +
220A VAL* 3.9 17.5 - - + -
223A ILE* 3.6 34.0 - - + +
227A TYR* 5.7 0.2 - + - -
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Residues in contact with ALA 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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81A ALA* 3.3 4.7 - - + +
82A TYR* 1.3 86.1 - - + +
84A GLU* 1.3 57.5 - - - +
86A ARG* 3.4 21.9 + - - +
87A ASP* 3.0 27.4 + - - +
219A ASP* 5.2 9.9 + - - +
223A ILE* 5.8 2.5 - - + -
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Residues in contact with GLU 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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64A ILE* 5.4 1.3 - - + -
72A LEU* 3.5 17.0 - - + +
78A GLU 4.7 0.2 - - - +
79A ARG* 3.1 35.9 + - - +
80A TYR* 2.6 34.2 + - - -
81A ALA* 3.1 15.5 + - + +
83A ALA* 1.3 74.7 - - - +
85A HIS* 1.3 67.5 + - - +
87A ASP* 3.2 6.2 + - + +
88A TYR* 3.1 46.4 + - + -
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Residues in contact with HIS 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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63A LEU* 3.7 25.1 - - + +
64A ILE* 3.3 36.9 + - + +
66A MET* 4.3 1.8 - - - -
80A TYR* 3.5 42.0 + + + -
81A ALA 3.1 7.4 + - - +
82A TYR 3.1 9.1 + - - +
84A GLU* 1.3 78.0 - - - +
86A ARG* 1.3 57.1 + - - +
88A TYR* 3.2 3.6 + - - +
89A LEU* 2.8 30.9 + - - +
113A LEU* 4.5 7.2 - - + -
203A PRO* 4.8 3.6 - - + -
207A TRP* 3.1 50.9 + + + -
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Residues in contact with ARG 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 TYR* 2.9 26.0 + - + +
83A ALA* 3.6 18.5 + - - +
85A HIS* 1.3 74.2 - - - +
87A ASP* 1.3 60.7 + - - +
89A LEU* 4.4 3.4 - - - +
90A ASP* 2.8 42.3 + - - +
113A LEU* 4.0 17.0 - - + +
116A ASP* 2.8 43.1 + - - -
119A ARG* 5.9 1.2 - - - +
120A ARG* 3.5 30.9 - - - +
223A ILE* 3.9 24.2 - - - +
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Residues in contact with ASP 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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17A LYS* 2.6 38.0 + - - -
83A ALA 3.0 14.1 + - - +
84A GLU* 3.5 12.3 - - - +
85A HIS 3.2 0.2 - - - -
86A ARG* 1.3 80.2 - - - +
88A TYR* 1.3 66.8 + - + +
90A ASP* 4.1 3.5 - - - +
91A ALA* 3.4 20.4 + - - +
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Residues in contact with TYR 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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16A ILE* 3.6 39.9 - - + +
17A LYS* 3.8 23.2 + - + +
19A ARG* 3.9 17.9 + - + +
21A MET* 3.9 13.4 - - + +
64A ILE* 3.8 31.0 - - + +
72A LEU* 3.5 25.4 - - + +
84A GLU* 3.1 45.5 + - + +
85A HIS 3.7 5.4 - - - +
87A ASP* 1.3 83.2 - - + +
89A LEU* 1.3 58.1 + - - +
91A ALA* 3.3 4.7 + - - +
92A LEU* 3.0 27.0 + - - +
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Residues in contact with LEU 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 MET* 4.7 6.8 - - + +
35A GLN* 3.7 16.4 - - - +
61A CYS* 4.4 3.1 - - + -
63A LEU* 4.0 24.9 - - + -
85A HIS 2.8 21.8 + - - +
86A ARG* 4.2 4.3 - - - +
88A TYR* 1.3 71.2 - - - +
90A ASP* 1.3 61.5 + - - +
92A LEU* 3.2 17.9 + - + +
93A TRP* 2.8 82.7 + - + +
113A LEU* 4.1 20.4 - - + -
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Residues in contact with ASP 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 ARG* 2.8 29.8 + - - +
87A ASP* 4.1 5.0 - - - +
89A LEU* 1.3 74.2 - - - +
91A ALA* 1.3 57.6 + - - +
93A TRP* 3.8 2.1 - - - +
94A GLU* 3.0 29.7 + - - +
117A TRP* 3.2 22.9 + - - +
120A ARG* 2.8 46.2 + - - -
121A HIS* 5.2 1.3 - - - -
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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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16A ILE* 3.6 22.5 - - + +
17A LYS* 4.7 12.6 - - + +
87A ASP 3.4 11.9 + - - +
88A TYR 3.3 9.1 + - - +
89A LEU 3.2 0.4 - - - -
90A ASP* 1.3 80.9 - - - +
92A LEU* 1.3 56.6 + - - +
94A GLU* 3.3 6.5 + - - +
95A ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 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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14A ILE* 4.0 35.2 - - + -
16A ILE* 3.7 13.8 - - + +
21A MET* 4.0 35.4 - - + -
22A ALA 4.8 4.5 - - - +
23A TYR* 4.5 9.4 - - + -
61A CYS* 3.5 39.7 - - + -
88A TYR 3.0 17.3 + - - +
89A LEU* 3.7 8.7 - - + +
91A ALA* 1.3 75.6 - - - +
93A TRP* 1.3 62.9 + - + +
95A ALA* 3.1 3.2 + - - +
96A LEU* 3.0 33.8 + - + +
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Residues in contact with TRP 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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33A LEU* 3.7 28.2 - - + +
35A GLN* 3.5 28.5 + - + -
61A CYS* 3.5 30.9 - - - -
89A LEU* 2.8 49.8 + - + +
90A ASP* 3.9 2.9 - - - +
92A LEU* 1.3 72.8 - - - +
94A GLU* 1.3 63.1 + - - +
96A LEU* 3.5 14.1 + - + -
97A ASP 3.9 0.7 + - - -
98A LEU* 3.4 32.6 + - + +
104A LEU* 4.2 17.9 - - + -
113A LEU 4.8 0.9 - - - -
114A GLY* 4.3 14.8 - - - -
117A TRP* 3.6 60.8 - + + +
124A ARG* 5.0 2.6 + - - -
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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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90A ASP 3.0 16.5 + - - +
91A ALA* 3.5 8.1 - - - +
93A TRP* 1.3 75.8 - - - +
95A ALA* 1.3 65.1 + - - +
97A ASP* 3.2 15.6 + - - -
98A LEU 5.0 0.2 + - - -
117A TRP* 5.8 0.4 - - - +
124A ARG* 4.1 21.1 + - - +
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Residues in contact with ALA 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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14A ILE* 4.0 33.5 - - + +
16A ILE* 4.2 5.8 - - + -
91A ALA 2.9 17.1 + - - +
92A LEU 3.1 6.9 + - - +
94A GLU* 1.3 78.4 - - - +
96A LEU* 1.3 59.0 + - - +
97A ASP* 3.4 4.0 + - - +
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Residues in contact with LEU 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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14A ILE* 3.7 11.2 - - + -
23A TYR* 3.5 41.1 - - + +
33A LEU* 4.9 0.2 - - + -
57A ARG* 2.8 44.5 + - - +
59A ILE* 4.2 12.6 - - + -
61A CYS* 3.8 28.5 - - - -
92A LEU* 3.0 22.7 + - + +
93A TRP* 3.8 14.8 - - + +
94A GLU 3.2 1.2 - - - -
95A ALA* 1.3 74.2 - - - +
97A ASP* 1.3 62.3 + - - +
98A LEU* 3.8 18.6 - - + -
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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