Contacts of the helix formed by residues 86 - 101 (chain A) in PDB entry 1DCT
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 PRO 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A ASP* 1.3 90.4 - - - +
87A ARG* 1.3 50.7 + - - +
89A LYS* 2.8 13.5 + - + +
90A LEU* 2.7 40.1 + - + +
18G G 3.9 5.4 - - - +
1N T 3.7 18.6 - - - +
2N C 3.1 51.4 - - - +
3N A 4.0 22.7 - - - +
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Residues in contact with ARG 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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70A PRO* 3.6 26.4 - - + +
72A GLN* 3.3 36.4 - - - +
73A SER* 4.1 8.7 - - - +
79A SER* 4.4 1.4 + - - -
81A ARG* 3.4 20.4 - - - +
85A ASP* 2.5 43.3 + - - +
86A PRO* 1.3 72.5 - - - +
88A GLY* 1.3 64.1 + - - +
90A LEU* 3.0 26.3 + - - +
91A PHE 3.9 1.4 + - - -
12F A 2.8 30.7 + - - -
13F C 4.0 4.8 + - - -
1N T 3.3 33.2 - - - +
2N C 3.9 31.7 + - - -
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Residues in contact with GLY 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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73A SER* 3.4 17.9 + - - -
74A TRP* 3.7 25.7 + - - -
82A GLY 4.0 6.7 - - - -
83A ILE* 4.6 4.9 - - - -
85A ASP* 2.9 8.8 + - - +
87A ARG* 1.3 76.1 - - - +
89A LYS* 1.3 65.9 + - - +
91A PHE* 2.9 24.8 + - - +
126A PHE* 4.6 1.0 - - - -
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Residues in contact with LYS 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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83A ILE* 3.4 28.1 + - + +
84A ASP* 4.4 7.1 + - - +
85A ASP 2.8 20.3 + - - +
86A PRO* 2.8 21.1 + - + +
88A GLY* 1.3 70.3 - - - +
90A LEU* 1.3 52.1 + - - +
91A PHE 2.7 13.2 + - - -
92A TYR* 3.0 34.8 + - + +
93A GLU* 5.0 1.7 - - - +
18G G 5.1 14.6 + - - +
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Residues in contact with LEU 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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7A PHE* 4.4 9.5 - - + -
50A ASP* 4.1 20.6 - - - +
51A ILE* 4.3 15.3 - - + -
52A SER* 4.6 7.4 - - - +
69A PRO* 5.0 0.2 - - - -
70A PRO* 4.1 13.9 - - + -
86A PRO* 2.7 33.0 + - + +
87A ARG* 3.0 24.1 + - - +
89A LYS* 1.3 71.2 - - - +
91A PHE* 1.3 52.4 + - - +
92A TYR 3.1 0.2 - - - -
93A GLU* 2.7 43.2 + - + +
94A TYR 3.7 1.7 + - - -
1N T 3.9 40.4 - - + +
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Residues in contact with PHE 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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69A PRO* 3.2 40.9 - - + +
74A TRP* 4.5 6.7 - - + -
87A ARG 3.9 1.4 + - - -
88A GLY 2.9 16.4 + - - +
89A LYS 2.7 5.1 + - - -
90A LEU* 1.3 72.6 - - - +
92A TYR* 1.3 61.3 + - - +
94A TYR* 3.0 25.2 + + + +
95A ILE* 3.4 6.8 + - + +
108A ALA* 4.6 6.1 - - + -
109A GLU 4.6 2.5 - - - -
110A ASN* 4.0 12.3 - - - -
114A MET* 3.9 23.8 - - + -
126A PHE* 3.2 55.4 - + + -
130A PHE* 3.8 17.9 - + - -
158A TYR* 4.1 18.2 - + - -
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Residues in contact with TYR 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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83A ILE* 3.3 22.2 - - + +
89A LYS* 3.0 30.4 + - + +
90A LEU 3.0 0.2 + - - -
91A PHE* 1.3 74.7 - - - +
93A GLU* 1.3 61.3 + - - +
95A ILE* 2.9 23.5 + - + +
96A ARG* 2.6 34.1 + - - +
125A GLU* 2.7 37.8 + - + +
126A PHE* 3.6 26.8 - + - -
129A GLU* 4.8 14.1 - - + -
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 5.1 0.4 - - + -
51A ILE* 3.6 29.4 - - + -
52A SER* 3.9 27.4 - - - +
89A LYS 5.0 2.4 - - - +
90A LEU* 2.7 27.3 + - + +
92A TYR* 1.3 77.8 - - - +
94A TYR* 1.3 64.6 + - - +
96A ARG* 2.6 59.5 + - - +
97A ILE* 2.9 12.0 + - - +
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Residues in contact with TYR 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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6A LEU* 4.1 17.0 - - + -
7A PHE* 4.0 20.5 - + + -
51A ILE* 4.4 1.2 - - - +
65A ILE* 3.0 37.6 + - + +
67A GLY* 3.9 17.5 - - - -
69A PRO* 3.9 19.5 - - + -
90A LEU 3.7 1.2 + - - -
91A PHE* 3.0 15.3 + + + +
93A GLU* 1.3 81.2 - - - +
95A ILE* 1.3 56.3 + - + +
97A ILE* 3.1 4.3 + - - +
98A LEU* 2.8 39.0 + - + -
106A PHE* 3.7 14.3 - + - -
107A LEU 2.4 36.7 + - - -
108A ALA* 3.7 15.3 - - + -
130A PHE* 4.4 11.9 - + - -
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Residues in contact with ILE 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 PHE* 3.6 13.2 - - + +
92A TYR* 3.1 41.5 - - + +
94A TYR* 1.3 76.9 - - + +
96A ARG* 1.3 51.7 + - - +
98A LEU* 3.0 13.9 + - + +
99A LYS* 2.8 65.2 + - + +
126A PHE* 4.1 22.9 - - + +
129A GLU* 3.9 27.8 - - + +
130A PHE* 4.3 16.2 - - + +
133A ALA* 5.8 0.4 - - + -
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Residues in contact with ARG 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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51A ILE* 3.2 20.0 + - - +
52A SER* 4.1 5.5 + - - +
54A ILE 2.6 25.2 + - - -
55A SER* 3.5 3.9 - - - +
56A SER* 3.3 19.8 - - - +
92A TYR 2.6 15.7 + - - +
93A GLU* 2.6 54.1 + - - +
95A ILE* 1.3 71.3 - - - +
97A ILE* 1.3 86.5 + - - +
99A LYS* 3.0 12.8 + - + +
100A GLN* 3.0 32.5 + - + +
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Residues in contact with ILE 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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4A ILE* 3.8 29.6 - - + -
6A LEU* 3.8 14.4 - - + -
51A ILE* 3.6 18.6 - - + -
56A SER* 4.5 7.0 - - - -
59A PHE* 3.9 28.3 - - + -
65A ILE* 3.9 5.6 - - + -
93A GLU 2.9 12.2 + - - +
94A TYR 3.6 4.5 - - - +
96A ARG* 1.3 108.2 - - - +
98A LEU* 1.3 57.0 + - - +
100A GLN* 4.6 4.3 - - - +
101A LYS* 2.9 43.0 + - + +
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Residues in contact with LEU 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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65A ILE* 3.6 11.6 - - + +
94A TYR* 2.8 19.3 + - + +
95A ILE* 3.2 13.7 - - + +
97A ILE* 1.3 78.1 - - - +
99A LYS* 1.3 58.4 + - - +
102A LYS* 2.8 29.3 + - - +
103A PRO* 3.8 17.9 - - + -
106A PHE* 3.8 37.0 - - + -
130A PHE* 3.5 37.5 - - + -
133A ALA* 4.6 13.7 - - + -
135A TYR* 4.0 13.9 + - + -
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Residues in contact with LYS 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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95A ILE* 2.8 39.2 + - + +
96A ARG* 3.0 9.4 + - + +
98A LEU* 1.3 74.5 - - - +
100A GLN* 1.3 70.0 + - + +
101A LYS 3.1 0.9 + - - -
102A LYS* 3.2 37.4 + - - +
129A GLU* 3.1 33.3 + - - -
132A ASN* 5.9 2.2 - - - +
133A ALA* 4.5 17.0 - - + +
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Residues in contact with GLN 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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56A SER* 3.0 40.4 + - - +
96A ARG* 3.0 26.7 + - + +
97A ILE* 4.1 3.8 - - - +
99A LYS* 1.3 80.6 - - - +
101A LYS* 1.3 65.2 + - + +
102A LYS* 5.2 0.2 - - - -
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Residues in contact with LYS 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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4A ILE* 4.3 7.4 - - + -
56A SER* 3.7 28.8 + - - -
57A ASP* 4.8 3.2 - - - +
59A PHE* 3.1 28.6 + - - -
60A PRO 3.5 25.0 + - - +
61A LYS* 4.1 7.9 - - - +
62A CYS* 4.4 13.7 + - - +
65A ILE* 4.1 5.8 - - + -
97A ILE* 2.9 34.3 + - + +
100A GLN* 1.3 83.1 + - + +
102A LYS* 1.3 72.9 + - - +
103A PRO* 3.2 11.2 - - + +
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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