Contacts of the helix formed by residues 87 - 103 (chain A) in PDB entry 1KAO
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 GLN 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ASN* 1.3 71.0 + - - +
88A GLN* 1.3 63.8 + - - +
90A PHE* 3.1 12.9 + - + +
91A GLN* 3.1 26.2 + - + +
125A GLU* 2.8 48.4 + - + +
126A VAL* 3.6 21.8 - - + -
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Residues in contact with GLN 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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86A ASN* 3.3 10.8 + - - +
87A GLN* 1.3 79.3 - - - +
89A SER* 1.3 58.1 + - - +
91A GLN* 3.2 17.8 + - - +
92A ASP* 2.9 54.8 + - - +
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Residues in contact with SER 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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11A SER* 4.1 18.1 + - - -
14A VAL* 3.6 26.0 - - - -
81A VAL 5.0 0.9 - - - +
82A TYR* 3.6 9.6 - - - +
83A SER* 2.9 25.0 + - - -
86A ASN* 2.8 34.9 + - - -
88A GLN* 1.3 75.6 - - - +
90A PHE* 1.3 60.6 + - - +
92A ASP* 3.5 4.5 + - - +
93A ILE* 3.2 18.4 + - - +
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Residues in contact with PHE 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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82A TYR* 3.7 39.0 - + + -
86A ASN 3.5 0.4 + - - -
87A GLN* 3.1 10.0 + - + +
89A SER* 1.3 80.3 + - - +
91A GLN* 1.4 85.9 + - - +
93A ILE* 3.1 23.1 - - + +
94A LYS* 3.9 15.4 + - - -
113A LEU* 4.9 0.2 - - + -
126A VAL* 3.9 22.9 - - + -
130A GLU* 3.6 42.6 - - + -
131A GLY* 4.0 18.2 - - - -
134A LEU* 3.9 27.1 - - + -
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Residues in contact with GLN 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* 3.1 24.3 + - + +
88A GLN* 3.2 22.6 + - - +
90A PHE* 1.4 87.3 - - - +
92A ASP* 1.3 63.3 + - - +
93A ILE 3.3 0.7 + - - -
94A LYS* 2.9 39.5 + - - +
95A PRO* 3.3 16.1 - - - +
130A GLU* 5.4 2.2 + - - -
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Residues in contact with ASP 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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11A SER* 2.9 31.5 + - - +
88A GLN* 2.9 48.9 + - - +
89A SER* 3.6 2.8 - - - +
90A PHE 3.2 0.2 - - - -
91A GLN* 1.3 76.6 - - - +
93A ILE* 1.3 61.3 + - - +
95A PRO* 3.4 19.3 - - - +
96A MET* 4.0 11.3 + - - +
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Residues in contact with ILE 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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9A LEU 4.2 1.3 - - - +
10A GLY* 3.9 17.3 - - - +
11A SER 5.2 0.7 - - - +
80A LEU* 3.8 29.4 - - + -
81A VAL 3.7 31.0 - - - +
82A TYR* 4.5 7.6 - - + -
89A SER 3.2 12.1 + - - +
90A PHE* 3.1 28.2 + - + +
92A ASP* 1.3 75.7 - - - +
94A LYS* 1.4 65.6 + - - +
96A MET* 3.3 15.2 + - + +
97A ARG* 3.1 21.8 + - - +
113A LEU* 4.3 19.5 - - + -
134A LEU* 4.4 7.4 - - + -
138A TRP* 4.1 7.4 - - + -
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Residues in contact with LYS 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 PHE* 4.0 16.2 - - - +
91A GLN* 2.9 48.9 + - - +
93A ILE* 1.4 79.7 - - - +
95A PRO* 1.3 70.1 - - + +
96A MET 3.3 0.3 + - - -
97A ARG* 3.3 3.1 + - - +
98A ASP* 3.2 29.4 + - - +
134A LEU* 3.8 34.8 - - + -
138A TRP* 4.2 7.5 - - + +
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Residues in contact with PRO 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 GLN 3.3 11.9 - - - +
92A ASP* 3.4 18.4 - - - +
94A LYS* 1.3 95.0 - - + +
96A MET* 1.3 54.4 + - + +
98A ASP* 3.3 6.8 + - + +
99A GLN* 2.9 32.4 + - - +
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Residues in contact with MET 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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9A LEU* 4.0 31.6 - - + -
10A GLY* 5.3 4.9 - - - +
68A ARG* 3.6 34.5 - - + +
72A ILE* 3.9 12.1 - - + -
80A LEU* 5.2 2.2 - - + -
92A ASP 4.1 11.2 - - - +
93A ILE* 3.4 24.9 - - + +
94A LYS 3.2 0.4 - - - -
95A PRO* 1.3 77.5 - - + +
97A ARG* 1.3 66.2 + - - +
99A GLN* 3.3 31.7 + - - +
100A ILE* 3.1 29.5 + - - +
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Residues in contact with ARG 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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80A LEU* 3.6 17.2 - - + +
93A ILE 3.1 6.5 + - - -
94A LYS 3.3 2.2 + - - +
96A MET* 1.3 78.1 - - - +
98A ASP* 1.3 85.9 + - - +
100A ILE* 3.1 15.5 + - + +
101A ILE* 3.2 52.8 + - + +
111A VAL* 5.1 7.4 - - + -
137A GLU* 5.1 1.6 + - - -
138A TRP* 3.5 86.8 + - + +
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Residues in contact with ASP 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 LYS* 3.2 19.3 + - - +
95A PRO* 3.9 6.5 - - + +
97A ARG* 1.3 113.5 + - - +
99A GLN* 1.3 62.6 + - - +
101A ILE* 3.4 7.2 + - - +
102A ARG* 3.2 32.0 + - + +
138A TRP* 4.6 2.9 + - - -
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Residues in contact with GLN 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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65A ALA* 3.3 20.4 + - - +
68A ARG* 2.9 43.7 + - - +
69A ASP* 2.9 27.4 + - - +
72A ILE* 3.8 8.3 - - + -
95A PRO 2.9 17.9 + - - +
96A MET* 3.3 16.3 - - - +
98A ASP* 1.3 76.0 - - - +
100A ILE* 1.3 64.1 + - - +
102A ARG* 3.3 7.4 + - + +
103A VAL* 2.9 29.7 + - + +
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Residues in contact with ILE 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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9A LEU* 4.4 4.5 - - + -
72A ILE* 3.8 28.7 - - + -
78A PHE* 4.0 29.2 - - + -
80A LEU* 3.7 31.6 - - + -
96A MET* 3.1 18.5 + - + +
97A ARG* 3.1 10.5 + - + +
99A GLN* 1.3 74.2 - - - +
101A ILE* 1.3 58.3 + - + +
103A VAL 3.8 0.2 - - - -
104A LYS* 2.9 40.6 + - + +
109A VAL* 3.5 31.0 - - + -
111A VAL* 4.7 5.2 - - + -
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Residues in contact with ILE 101 (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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97A ARG* 3.2 54.5 + - + +
98A ASP* 3.4 7.4 + - - +
100A ILE* 1.3 75.6 - - + +
102A ARG* 1.3 70.0 + - - +
104A LYS 3.5 1.7 + - - +
105A ARG* 3.3 22.0 + - - +
109A VAL* 4.3 29.2 - - + +
111A VAL* 5.6 3.8 - - + -
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Residues in contact with ARG 102 (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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98A ASP* 3.2 19.2 + - + +
99A GLN* 3.7 7.4 - - - +
101A ILE* 1.3 82.9 - - - +
103A VAL* 1.3 69.7 + - + +
104A LYS 3.3 0.3 + - - -
105A ARG* 3.3 30.0 + - - +
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Residues in contact with VAL 103 (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 ASP* 3.2 35.0 - - + +
72A ILE* 4.1 21.5 - - + -
73A LYS* 3.9 28.7 - - + +
99A GLN* 2.9 29.9 + - + +
102A ARG* 1.3 74.9 - - + +
104A LYS* 1.3 58.4 + - + +
105A ARG* 3.2 10.9 + - - +
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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