Contacts of the helix formed by residues 122 - 134 (chain D) in PDB entry 2DRP
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 HIS 122 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109D HIS* 5.1 10.3 + + - -
111D TYR* 3.9 7.9 - - - -
120D TYR* 3.3 8.0 - - - +
121D THR* 1.3 105.8 + - - +
123D ILE* 1.3 65.1 + - - +
124D SER* 3.8 16.4 - - - +
125D ASN* 3.4 12.3 + - - +
126D PHE* 3.1 16.5 + - - +
9E G 4.1 0.6 + - + -
10E A 2.9 50.8 + + + +
11E T 3.5 25.2 - - + +
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D PHE* 3.2 33.2 - - + -
111D TYR* 3.2 45.6 - - + +
122D HIS* 1.3 70.0 - - - +
124D SER* 1.3 55.2 + - - +
126D PHE* 2.9 9.7 + - + +
127D CYS* 2.7 41.3 + - - -
28F T 3.8 21.8 - - + -
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Residues in contact with SER 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D HIS* 3.8 3.1 - - - +
123D ILE* 1.3 75.8 - - - +
125D ASN* 1.3 68.2 + - - +
127D CYS* 2.9 6.3 + - - +
128D ARG* 2.8 27.3 + - - +
11E T 2.9 34.6 + - - +
12E A 3.8 4.7 - - - -
28F T 4.2 9.5 - - - +
29F T 3.2 38.4 - - - +
30F A 4.2 3.6 - - - -
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Residues in contact with ASN 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D TYR* 4.0 15.2 - - + -
122D HIS* 3.4 16.6 + - + +
123D ILE 3.3 0.2 - - - -
124D SER* 1.3 85.3 + - - +
126D PHE* 1.3 61.8 + - - +
128D ARG* 3.4 32.5 + - - +
129D HIS* 3.1 20.3 + - - +
8E G 4.9 2.3 + - + +
9E G 3.2 28.0 + - + +
10E A 2.9 52.4 + - - +
30F A 4.4 1.2 + - - -
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Residues in contact with PHE 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D GLU* 3.8 22.7 - - - -
103D PHE* 3.4 45.8 - + + -
111D TYR* 4.6 6.1 - - + -
113D CYS* 3.6 34.3 - - + -
120D TYR* 3.7 34.7 - + + -
122D HIS 3.1 12.8 + - - +
123D ILE* 2.9 15.7 + - + +
125D ASN* 1.3 76.2 - - - +
127D CYS* 1.3 74.8 + - - +
129D HIS* 2.9 23.9 + + - +
130D TYR* 2.9 27.0 + + + -
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Residues in contact with CYS 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ILE* 2.7 39.2 + - - -
124D SER 3.1 7.0 - - - +
126D PHE* 1.3 83.1 - - - +
128D ARG* 1.3 64.7 + - - +
129D HIS 2.9 1.4 + - - -
130D TYR* 3.0 14.0 + - - +
131D VAL* 3.1 19.9 + - - +
27F G 5.5 0.7 - - - -
28F T 4.1 39.7 - - - +
29F T 3.7 17.3 - - + +
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Residues in contact with ARG 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D SER 2.8 14.7 + - - +
125D ASN* 3.4 26.7 + - - +
127D CYS* 1.3 72.2 - - - +
129D HIS* 1.3 59.6 + - - +
131D VAL* 3.7 7.1 - - - +
132D THR* 2.7 33.0 + - - +
152D ARG* 3.6 45.6 - - + +
8E G 3.3 24.1 + - - +
9E G 2.7 50.1 + - - -
10E A 3.7 1.8 - - - +
29F T 4.8 4.8 - - + +
30F A 5.3 1.3 - - - +
31F T 2.9 29.1 + - - +
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Residues in contact with HIS 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D CYS* 3.5 8.5 - - + -
116D CYS* 3.4 2.0 - - - -
118D ARG* 3.6 17.0 + - - -
120D TYR* 2.7 45.5 + + + +
125D ASN 3.1 9.0 + - - +
126D PHE* 2.9 14.7 + + - +
128D ARG* 1.3 75.1 - - - +
130D TYR* 1.3 77.1 + - - +
132D THR* 2.9 14.6 + - - -
133D SER* 3.1 33.5 + - - -
134D HIS* 3.1 3.5 + + - -
173D ZN 2.0 37.3 - - - -
7E A 5.9 0.2 - - - -
8E G 3.5 17.0 + - - +
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Residues in contact with TYR 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D GLU* 5.8 12.8 - - - -
113D CYS* 5.5 0.7 - - - -
115D VAL* 5.0 10.1 - - + -
126D PHE* 2.9 36.4 + + + +
127D CYS* 3.8 6.1 - - - +
129D HIS* 1.3 79.6 - - - +
131D VAL* 1.3 55.7 + - + +
132D THR 2.8 12.3 + - - -
134D HIS* 2.9 70.2 + + + -
135D LYS* 3.4 40.4 + - + +
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Residues in contact with VAL 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D CYS 3.1 15.4 + - - +
128D ARG* 3.7 13.2 - - - +
130D TYR* 1.3 79.3 - - + +
132D THR* 1.3 62.1 + - - +
135D LYS* 4.0 31.3 - - + +
137D ASN 5.2 2.8 - - - +
138D VAL* 4.7 6.4 - - - +
29F T 4.2 25.4 - - - +
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Residues in contact with THR 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ARG* 2.7 27.6 + - - +
129D HIS* 2.9 4.6 + - - -
130D TYR 2.8 2.4 + - - -
131D VAL* 1.3 82.9 + - - +
133D SER* 1.3 62.6 + - - +
134D HIS 3.9 0.4 - - - -
138D VAL* 4.1 17.8 - - - +
151D THR* 4.2 39.9 + - + +
152D ARG* 4.9 11.0 - - + +
7E A 5.1 6.7 - - - +
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Residues in contact with SER 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D HIS* 3.1 41.1 + - - -
130D TYR 3.1 0.2 + - - -
132D THR* 1.3 82.3 - - - +
134D HIS* 1.3 74.0 + - - +
135D LYS 3.8 3.1 - - - -
138D VAL* 5.6 1.1 - - - -
7E A 6.1 0.7 - - - -
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Residues in contact with HIS 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D CYS* 3.4 9.5 - - - -
115D VAL* 3.9 23.4 - - + +
116D CYS* 3.9 16.1 - - + +
129D HIS* 3.1 7.6 + + - -
130D TYR* 2.9 45.1 + + + -
133D SER* 1.3 95.4 + - - +
135D LYS* 1.3 66.4 + - - +
136D ARG* 3.5 2.6 + - - +
173D ZN 2.0 37.1 - - - -
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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