Contacts of the helix formed by residues 99 - 113 (chain A) in PDB entry 2DHI
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 THR 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A PRO* 4.8 9.0 - - - +
79A ASP* 4.1 28.1 - - + +
80A CYS* 3.9 9.0 + - - +
98A SER* 1.3 76.6 + - - +
100A ASP* 1.3 56.8 + - - +
102A CYS* 3.1 8.3 + - + +
103A LEU* 2.8 52.2 + - + +
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Residues in contact with ASP 100 (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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98A SER* 2.8 13.2 + - - +
99A THR* 1.3 77.1 - - - +
101A ASP* 1.3 73.2 + - - +
103A LEU* 3.3 10.0 + - - +
104A ALA* 3.1 24.0 + - - +
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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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10A LYS* 4.2 11.4 + - - -
12A GLY* 6.1 0.3 - - - -
13A TRP 4.1 2.9 - - - +
14A LEU* 3.1 32.1 - - - +
96A ALA* 3.5 8.4 - - + +
97A GLU* 4.1 9.4 + - + +
98A SER* 2.7 20.9 + - - +
100A ASP* 1.3 84.4 + - - +
102A CYS* 1.3 61.4 + - - +
104A ALA* 3.3 7.4 + - - +
105A TRP* 3.1 37.2 + - - -
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Residues in contact with CYS 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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63A THR* 4.4 5.4 - - - -
79A ASP 3.2 22.0 - - - +
80A CYS* 3.6 27.1 - - - +
81A LEU 3.4 20.4 - - - -
82A LEU* 3.9 16.3 - - - +
96A ALA* 3.3 8.8 - - + +
98A SER 3.1 5.2 + - - +
99A THR* 3.4 7.9 - - - +
101A ASP* 1.3 76.5 - - - +
103A LEU* 1.3 65.0 + - - +
105A TRP* 3.0 8.3 + - - +
106A LYS* 2.9 25.0 + - - +
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Residues in contact with LEU 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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99A THR* 2.8 41.8 + - + +
100A ASP* 3.6 7.6 - - - +
102A CYS* 1.3 72.4 - - - +
104A ALA* 1.3 61.7 + - - +
106A LYS* 3.6 13.1 - - + +
107A PHE* 2.8 66.1 + - + -
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Residues in contact with ALA 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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10A LYS* 3.9 21.8 - - + +
100A ASP* 3.1 13.0 + - - +
101A ASP* 3.4 11.4 - - - +
102A CYS 3.2 0.2 - - - -
103A LEU* 1.3 79.3 - - - +
105A TRP* 1.3 54.1 + - - +
107A PHE* 3.7 7.0 - - - +
108A THR* 2.6 37.6 + - - +
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Residues in contact with TRP 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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10A LYS* 2.9 55.3 - - + +
12A GLY* 4.0 20.0 - - - -
14A LEU* 3.0 42.2 - - + +
29A PHE* 4.1 17.7 - + + -
31A LEU* 4.2 23.3 - - + -
37A LEU* 4.6 7.9 - - + -
82A LEU* 4.0 16.8 - - + -
96A ALA* 5.1 0.4 - - + -
101A ASP* 3.1 31.0 + - - -
102A CYS* 3.0 9.9 + - - +
104A ALA* 1.3 75.3 - - - +
106A LYS* 1.3 68.2 + - - +
108A THR* 2.8 21.9 + - + -
109A LEU* 2.9 28.7 + - + +
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Residues in contact with LYS 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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61A ILE* 4.8 12.6 + - + +
63A THR* 3.3 34.6 + - + +
82A LEU* 3.7 19.3 - - + +
102A CYS* 2.9 19.8 + - - +
103A LEU* 3.6 15.0 - - + +
105A TRP* 1.3 73.4 - - - +
107A PHE* 1.3 82.2 + - + +
109A LEU* 3.1 9.5 + - - +
110A GLN* 3.0 35.7 + - + +
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Residues in contact with PHE 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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103A LEU* 2.8 62.6 + - + +
104A ALA* 3.7 6.1 - - - +
106A LYS* 1.3 90.8 - - + +
108A THR* 1.3 63.6 + - - +
110A GLN* 3.3 10.5 + - + +
111A ASP* 3.1 22.9 + - - +
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Residues in contact with THR 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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9A VAL* 4.1 18.4 - - + -
10A LYS* 3.9 19.7 - - + +
31A LEU* 3.7 24.9 - - + -
104A ALA* 2.6 23.1 + - - +
105A TRP* 2.8 22.7 + - + -
107A PHE* 1.3 72.4 - - - +
109A LEU* 1.3 60.2 + - - +
111A ASP* 3.3 8.0 + - - +
112A SER* 3.1 20.3 + - - -
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Residues in contact with LEU 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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31A LEU* 4.3 14.4 - - + -
37A LEU* 5.1 8.1 - - + -
54A MET* 3.3 41.1 - - + -
61A ILE* 3.7 10.3 - - + -
82A LEU* 3.7 29.8 - - + -
84A ILE* 4.0 16.4 - - + -
105A TRP* 2.9 30.3 + - + +
106A LYS* 3.5 9.9 - - - +
108A THR* 1.3 73.0 - - - +
110A GLN* 1.3 55.6 + - - +
111A ASP 2.7 14.9 + - - -
112A SER* 2.7 22.9 + - - -
113A ARG* 3.1 12.9 + - - +
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Residues in contact with GLN 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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61A ILE* 3.7 23.9 + - + +
106A LYS* 3.0 33.8 + - + +
107A PHE* 3.3 10.5 + - + +
109A LEU* 1.3 75.4 - - - +
111A ASP* 1.3 57.8 + - - +
113A ARG* 2.6 69.4 + - - +
114A THR* 4.7 4.0 + - - +
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Residues in contact with ASP 111 (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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107A PHE 3.1 11.7 + - - +
108A THR* 3.4 11.9 - - - +
109A LEU 2.7 1.6 + - - -
110A GLN* 1.3 76.4 - - - +
112A SER* 1.3 58.0 + - - +
113A ARG 2.9 6.7 + - - -
114A THR* 2.4 34.3 + - - -
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Residues in contact with SER 112 (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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31A LEU* 4.2 17.9 - - - +
35A GLY* 4.4 17.0 - - - -
54A MET* 4.0 16.3 - - - +
55A PRO* 3.6 10.1 - - - +
108A THR 3.1 7.1 + - - -
109A LEU* 2.7 27.1 + - - -
111A ASP* 1.3 77.2 - - - +
113A ARG* 1.3 60.1 + - - +
114A THR 3.1 1.0 + - - -
115A SER* 3.3 23.6 - - - -
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Residues in contact with ARG 113 (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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54A MET* 4.4 11.2 - - + -
55A PRO* 3.9 22.2 - - + +
58A CYS* 5.9 3.8 - - - -
59A ILE 4.2 17.4 + - - -
60A ASN* 5.2 5.7 + - - +
61A ILE* 4.0 15.2 - - - +
109A LEU 3.1 16.4 + - - +
110A GLN* 2.6 57.2 + - - +
111A ASP 2.9 0.2 - - - -
112A SER* 1.3 79.2 - - - +
114A THR* 1.3 58.4 + - + +
115A SER 3.1 7.0 + - - +
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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