Contacts of the helix formed by residues 72 - 88 (chain A) in PDB entry 1KAS
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 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A PHE* 6.3 0.2 - - + -
70A MET 3.8 0.2 + - - -
71A ASP* 1.3 78.2 + - - +
73A PHE* 1.3 57.0 + - - +
75A GLN* 3.2 15.1 + - - +
76A TYR* 2.9 43.4 + - + +
192A LYS* 3.9 31.6 - - + -
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Residues in contact with PHE 73 (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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71A ASP* 3.1 20.4 + - + +
72A ALA* 1.3 76.8 - - - +
74A ILE* 1.3 83.2 + - + +
76A TYR* 3.5 4.1 + - - +
77A GLY* 3.0 23.0 + - - -
106A SER* 3.6 29.2 - - - -
109A GLY* 3.6 13.5 - - - +
110A GLY* 3.2 29.4 - - - -
136A SER 4.2 0.7 - - - -
137A THR 3.6 7.0 - - - -
138A ILE 3.6 18.6 - - - -
139A VAL* 4.1 6.5 - - - -
142A VAL* 3.6 21.5 - - + -
190A ALA* 3.4 18.9 - - - +
191A GLU* 4.1 5.6 - - - -
192A LYS* 3.9 27.8 - - + +
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Residues in contact with ILE 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 MET* 3.7 14.4 - - + -
71A ASP 3.0 9.6 + - - +
73A PHE* 1.3 96.6 - - + +
75A GLN* 1.3 66.7 + - - +
77A GLY* 3.2 1.2 + - - -
78A ILE* 3.0 35.6 + - + +
135A PRO 3.8 3.6 - - - +
136A SER* 3.3 33.4 - - - +
138A ILE 4.5 0.4 - - - +
141A MET* 3.8 27.1 - - + +
142A VAL* 3.8 17.6 - - + +
145A HIS* 3.7 23.3 - - - +
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Residues in contact with GLN 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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56A PHE* 3.7 27.8 - - + -
58A CYS* 4.1 7.9 - - - -
62A ILE* 4.3 4.8 - - + +
67A GLN* 3.2 38.4 + - + +
70A MET* 3.0 42.3 + - - -
71A ASP 3.2 12.3 + - - +
72A ALA* 3.2 14.7 + - - +
74A ILE* 1.3 76.9 - - - +
76A TYR* 1.3 61.5 + - - +
78A ILE* 3.4 1.6 + - - +
79A VAL* 3.2 27.5 + - - +
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Residues in contact with TYR 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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13A LEU* 3.4 19.9 - - + +
53A VAL* 3.6 37.6 + - + +
56A PHE* 3.8 40.0 - + - +
72A ALA* 2.9 25.3 + - + +
73A PHE* 3.6 4.5 - - - +
75A GLN* 1.3 77.8 - - - +
77A GLY* 1.3 62.4 + - - +
80A ALA* 3.1 22.9 + - - +
191A GLU 3.7 16.4 - - - -
192A LYS* 3.4 39.9 - - + +
233A ASP* 3.9 7.8 + - + +
234A GLY* 4.0 11.4 - - - +
235A ALA* 3.9 13.6 - - + +
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Residues in contact with GLY 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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73A PHE 3.0 14.1 + - - -
74A ILE 3.2 4.0 + - - -
76A TYR* 1.3 76.3 - - - +
78A ILE* 1.3 56.4 + - - +
81A GLY* 2.9 26.0 + - - -
142A VAL* 3.7 23.6 - - - +
146A LEU* 4.3 1.7 - - - +
190A ALA* 3.8 12.3 - - - +
235A ALA* 4.3 0.4 - - - -
237A MET* 3.6 14.8 - - - +
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Residues in contact with ILE 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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61A ILE* 4.4 1.3 - - + -
62A ILE* 4.1 19.1 - - + -
70A MET* 3.8 30.3 - - + -
74A ILE* 3.0 25.6 + - + +
75A GLN 3.9 3.1 - - - +
77A GLY* 1.3 71.4 - - - +
79A VAL* 1.3 57.2 + - - +
81A GLY* 2.9 2.8 + - - -
82A VAL* 2.7 42.9 + - + +
142A VAL* 5.0 3.4 - - + +
145A HIS* 3.7 31.2 - - + -
146A LEU* 4.2 13.4 - - + +
149A MET* 3.6 35.0 - - + -
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Residues in contact with VAL 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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13A LEU* 3.5 33.4 - - + -
56A PHE* 3.8 8.1 - - + -
57A ASN 4.9 4.5 - - - +
58A CYS* 3.6 31.2 - - + -
61A ILE* 4.5 14.4 - - + -
62A ILE* 4.3 6.1 - - + -
75A GLN 3.2 14.4 + - - +
78A ILE* 1.3 76.2 - - - +
80A ALA* 1.3 63.2 + - - +
82A VAL* 3.2 8.3 + - - +
83A GLN* 3.0 34.4 + - + +
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Residues in contact with ALA 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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11A GLY* 3.6 9.1 - - - +
12A MET* 3.8 20.4 - - - +
13A LEU* 4.3 2.0 - - + +
76A TYR 3.1 17.0 + - - +
77A GLY 4.0 3.1 - - - +
79A VAL* 1.3 77.9 - - - +
81A GLY* 1.3 61.2 + - - +
83A GLN* 3.5 7.1 + - - +
84A ALA 3.2 16.8 + - - -
235A ALA* 3.8 24.2 - - + +
237A MET* 3.7 17.8 - - + +
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Residues in contact with GLY 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 GLY 2.9 13.6 + - - -
78A ILE 2.9 7.4 + - - -
80A ALA* 1.3 73.5 - - - +
82A VAL* 1.3 64.4 + - - +
84A ALA* 3.1 4.2 + - - +
85A MET* 3.0 26.4 + - - +
146A LEU* 4.0 20.4 - - - -
186A VAL* 4.9 1.4 - - - +
237A MET* 3.9 17.7 - - - +
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Residues in contact with VAL 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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61A ILE* 3.6 42.0 - - + -
78A ILE* 2.7 28.1 + - + +
79A VAL* 3.6 6.7 - - - +
81A GLY* 1.3 70.5 - - - -
83A GLN* 1.3 63.8 + - + +
85A MET* 3.3 2.6 + - - +
86A GLN* 2.9 45.8 + - - +
146A LEU* 4.5 1.1 - - + +
149A MET* 4.2 9.6 - - + -
150A TYR* 3.5 28.7 - - + +
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Residues in contact with GLN 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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10A LEU 3.7 3.5 - - - +
11A GLY* 3.6 7.2 - - - -
12A MET 3.1 29.2 + - - +
13A LEU* 4.6 0.4 - - - +
18A ASN 3.0 24.2 + - - -
19A THR* 4.1 17.2 - - - +
20A VAL* 4.2 3.6 + - - +
79A VAL* 3.0 31.8 + - + +
80A ALA* 3.5 9.6 - - - +
81A GLY 3.3 0.2 - - - -
82A VAL* 1.3 76.4 - - + +
84A ALA* 1.3 56.8 + - - +
86A GLN* 3.7 9.6 - - - +
87A ASP* 2.8 31.0 + - - +
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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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9A GLY* 3.9 2.2 - - - +
10A LEU 3.7 12.3 + - - +
11A GLY 4.0 1.6 - - - +
80A ALA 3.2 7.6 + - - +
81A GLY* 3.1 9.2 + - - +
83A GLN* 1.3 74.9 - - - +
85A MET* 1.3 66.8 + - - +
87A ASP* 3.8 1.2 - - - +
88A SER 3.0 18.5 + - - -
186A VAL* 4.8 2.7 - - + -
237A MET* 3.7 33.0 - - + +
238A LEU* 4.5 2.0 - - - -
239A VAL* 3.2 26.4 - - + +
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Residues in contact with MET 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 GLY 3.0 15.7 + - - +
82A VAL 3.7 7.0 - - - +
84A ALA* 1.3 76.6 - - - +
86A GLN* 1.3 60.6 + - + +
88A SER* 2.6 24.5 + - - -
89A GLY* 3.4 4.0 + - - -
90A LEU* 4.3 13.8 + - + +
92A ILE* 3.9 27.8 - - + -
100A ILE* 5.1 3.4 - - + -
146A LEU* 5.7 1.6 - - + -
150A TYR* 3.8 50.7 - - + +
152A LEU* 4.0 15.0 - - + -
184A VAL* 6.0 1.3 - - - -
186A VAL* 3.9 25.6 - - + -
239A VAL* 4.6 11.2 - - - -
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Residues in contact with GLN 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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61A ILE* 5.6 3.4 - - - +
82A VAL* 2.9 40.0 + - + +
83A GLN* 3.7 9.1 - - - +
85A MET* 1.3 77.7 - - + +
87A ASP* 1.3 63.0 + - - +
88A SER 3.2 0.5 + - - -
89A GLY* 3.4 9.7 + - - -
150A TYR* 5.0 4.0 + - + +
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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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8A THR 4.0 2.6 - - - +
9A GLY* 3.5 0.6 - - - -
10A LEU* 3.0 31.9 + - - +
83A GLN 2.8 22.1 + - - +
84A ALA 3.8 3.1 - - - +
86A GLN* 1.3 72.8 - - - +
88A SER* 1.3 62.5 + - - +
89A GLY 3.6 0.2 + - - -
252A LYS* 3.7 27.5 - - - +
254A TYR* 2.5 34.5 + - - -
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Residues in contact with SER 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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8A THR* 3.0 30.4 + - - +
84A ALA 3.0 14.1 + - - -
85A MET* 2.6 25.3 + - - -
87A ASP* 1.3 76.7 - - - +
89A GLY* 1.3 64.1 + - - +
90A LEU* 3.6 19.7 + - - +
239A VAL* 3.6 19.3 - - - +
251A ALA* 4.3 16.6 - - - +
252A LYS* 4.9 2.4 + - - +
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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