Contacts of the helix formed by residues 96 - 110 (chain A) in PDB entry 2C60
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 ASN 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A TYR* 3.5 23.3 - - - -
67A GLU* 5.8 0.2 - - - -
95A LYS* 1.3 95.1 - - - +
97A GLN* 1.3 65.1 + - - +
98A ASP* 3.2 13.6 + - - +
99A ASP* 2.9 30.3 + - - +
100A LEU 3.1 17.5 + - - -
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Residues in contact with GLN 97 (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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64A VAL 2.9 22.2 + - - -
65A LYS* 3.4 16.9 - - - +
66A TYR* 2.8 36.4 + - + +
67A GLU* 4.1 8.2 + - - +
96A ASN* 1.3 75.4 - - - +
98A ASP* 1.3 60.7 + - - +
100A LEU* 3.2 6.5 + - - +
101A ASP* 2.8 67.7 + - - +
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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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96A ASN* 3.2 12.7 + - - +
97A GLN* 1.3 79.8 - - - +
99A ASP* 1.3 65.7 + - - +
101A ASP* 3.3 12.1 + - - +
102A LYS* 3.1 29.7 + - + +
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Residues in contact with ASP 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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92A ILE* 6.2 1.6 - - - -
93A LEU 3.7 3.5 - - - +
94A LEU* 3.8 17.5 - - + +
95A LYS* 2.8 59.2 + - - +
96A ASN* 2.9 24.7 + - - +
98A ASP* 1.3 79.2 - - - +
100A LEU* 1.3 61.9 + - - +
102A LYS* 3.3 7.7 + - - +
103A ALA* 3.0 22.5 + - - +
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Residues in contact with LEU 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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47A ILE* 5.1 4.9 - - + -
64A VAL* 4.0 25.8 - - + +
66A TYR* 3.7 42.4 - - + +
69A VAL* 4.1 13.7 - - + -
83A LEU* 5.7 2.2 - - + -
94A LEU* 4.2 23.9 - - + +
96A ASN 3.1 13.0 + - - +
97A GLN* 3.7 8.7 - - - +
99A ASP* 1.3 77.3 - - - +
101A ASP* 1.3 57.3 + - - +
103A ALA* 3.1 1.7 + - - +
104A ILE* 2.9 46.7 + - + +
116A LEU* 4.4 11.4 - - + -
118A ILE* 5.7 0.7 - - + -
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Residues in contact with ASP 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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64A VAL 4.4 2.4 - - - +
97A GLN* 2.8 57.2 + - - +
98A ASP* 3.7 11.4 - - - +
99A ASP 3.3 0.2 - - - -
100A LEU* 1.3 72.1 - - - +
102A LYS* 1.3 59.5 + - + +
104A ILE* 3.4 8.3 + - - +
105A ASP* 2.9 27.4 + - - +
1124A GOL 4.9 7.4 + - - -
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Residues in contact with LYS 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* 3.1 20.9 + - + +
99A ASP* 3.7 7.2 - - - +
100A LEU 3.2 0.2 - - - -
101A ASP* 1.3 77.0 - - + +
103A ALA* 1.3 62.6 + - - +
105A ASP* 3.2 12.5 + - + +
106A ILE* 3.2 26.6 + - - +
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Residues in contact with ALA 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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85A TYR* 4.3 11.7 - - + -
94A LEU* 4.2 25.6 - - + -
99A ASP 3.0 13.5 + - - +
100A LEU 3.6 7.2 - - - +
102A LYS* 1.3 73.6 - - - +
104A ILE* 1.3 65.0 + - - +
106A ILE* 3.1 24.5 + - - +
107A LEU 3.2 8.3 + - - -
116A LEU* 3.5 24.7 - - + +
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Residues in contact with ILE 104 (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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45A VAL* 4.2 17.7 - - + -
47A ILE* 5.9 0.2 - - + -
62A ARG* 3.7 14.8 - - - +
64A VAL* 3.8 34.5 - - + +
100A LEU* 2.9 36.7 + - + +
101A ASP* 3.8 8.5 - - - +
103A ALA* 1.3 75.5 - - - +
105A ASP* 1.3 57.4 + - - +
107A LEU* 3.2 10.8 + - + +
108A ASP* 2.9 42.1 + - - +
116A LEU* 4.2 16.4 - - + -
1124A GOL 3.9 14.8 - - - +
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Residues in contact with ASP 105 (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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101A ASP 2.9 16.9 + - - +
102A LYS* 3.6 14.6 - - + +
103A ALA 3.2 0.8 - - - -
104A ILE* 1.3 75.6 - - - +
106A ILE* 1.3 64.0 + - - +
108A ASP* 4.3 11.8 - - - +
109A ARG* 2.8 59.7 + - - +
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Residues in contact with ILE 106 (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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85A TYR* 3.7 42.0 - - + +
92A ILE* 6.3 1.3 - - + -
102A LYS 3.2 15.7 + - - +
103A ALA* 3.1 13.5 + - - +
105A ASP* 1.3 75.1 - - - +
107A LEU* 1.3 63.4 + - - +
109A ARG* 3.3 7.6 + - - +
110A SER* 3.1 23.1 + - - -
113A MSE 4.2 12.6 - - + -
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Residues in contact with LEU 107 (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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45A VAL* 3.9 34.3 - - + -
46A ARG 4.9 2.2 - - - +
62A ARG* 4.9 1.8 - - - +
103A ALA 3.2 7.4 + - - +
104A ILE* 3.2 11.6 + - + +
106A ILE* 1.3 79.0 - - - +
108A ASP* 1.3 70.4 + - - +
110A SER* 3.2 9.4 + - - +
113A MSE 3.5 50.6 - - + +
114A LYS* 4.0 4.0 - - - +
115A SER* 3.8 19.1 - - - +
116A LEU* 4.2 15.3 - - + +
1123A CA 2.6 28.1 - - - -
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Residues in contact with ASP 108 (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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62A ARG* 2.8 44.6 + - - -
104A ILE* 2.9 24.7 + - - +
105A ASP* 3.9 13.8 - - - +
106A ILE 3.2 0.2 - - - -
107A LEU* 1.3 84.8 - - - +
109A ARG* 1.3 61.3 + - + +
110A SER 3.5 3.6 + - - +
1123A CA 4.3 2.7 - - - -
1124A GOL 4.6 1.7 + - - -
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Residues in contact with ARG 109 (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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105A ASP* 2.8 47.2 + - - +
106A ILE* 3.3 5.6 + - - +
108A ASP* 1.3 77.8 - - - +
110A SER* 1.3 60.6 + - - +
111A SER 3.8 2.1 + - - -
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Residues in contact with SER 110 (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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106A ILE* 3.1 16.9 + - - -
107A LEU 3.2 1.3 + - - -
108A ASP 4.3 1.9 - - - +
109A ARG* 1.3 78.9 - - - +
111A SER* 1.3 59.5 + - - +
112A SER* 3.2 9.9 + - - -
113A MSE 3.0 40.5 + - - +
1123A CA 2.6 28.6 - - - -
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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