Contacts of the helix formed by residues 120 - 135 (chain A) in PDB entry 1T0H
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 SER 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LYS* 5.7 1.3 - - - -
101A ASN 2.7 27.9 + - - -
102A ASP 2.9 18.5 + - - -
104A TRP* 3.7 22.9 - - - -
118A ILE 3.4 2.0 + - - -
119A PRO* 1.3 75.5 - - - +
121A PRO* 1.3 71.1 - - - +
122A VAL* 3.4 4.3 + - - -
123A LYS 3.1 14.6 + - - -
124A LEU* 2.9 27.7 + - - +
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Residues in contact with PRO 121 (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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104A TRP* 3.4 25.1 - - + -
120A SER* 1.3 88.1 - - - +
122A VAL* 1.3 62.4 + - + +
124A LEU* 3.7 2.6 - - + +
125A GLU* 3.0 26.0 + - - +
219B PRO* 4.1 26.7 - - + +
220B TYR* 3.9 20.8 - - + -
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Residues in contact with VAL 122 (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 ASN* 3.8 13.9 - - + +
102A ASP* 3.9 13.5 - - - +
120A SER* 3.2 9.7 + - - +
121A PRO* 1.3 77.5 - - + +
123A LYS* 1.3 58.1 + - - +
125A GLU* 3.5 5.6 + - - +
126A ASN* 3.0 45.3 + - - +
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Residues in contact with LYS 123 (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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75A GLU 5.5 0.2 + - - -
76A ASP* 3.1 31.0 + - - +
77A ASP* 5.2 2.8 - - - +
102A ASP* 3.2 53.4 + - + +
103A TRP* 3.8 14.2 - - + +
119A PRO* 3.9 13.9 - - + -
120A SER* 3.1 9.3 + - - +
122A VAL* 1.3 76.4 - - - +
124A LEU* 1.3 65.0 + - - +
126A ASN* 3.3 7.0 + - + +
127A MSE 3.0 49.7 + - + +
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Residues in contact with LEU 124 (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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68A VAL* 4.5 12.1 - - + -
69A ARG 4.9 2.7 - - - +
70A TYR* 4.3 14.1 - - + -
87A PHE* 4.5 2.5 - - + -
119A PRO* 3.7 23.3 - - + -
120A SER 2.9 17.8 + - - +
121A PRO* 3.7 4.5 - - + +
123A LYS* 1.3 76.5 - - - +
125A GLU* 1.3 56.5 + - - +
127A MSE 3.5 15.9 + - + +
128A ARG* 3.0 27.9 + - - +
219B PRO* 3.5 35.2 - - + -
220B TYR* 3.5 29.6 - - + +
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Residues in contact with GLU 125 (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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121A PRO 3.0 18.1 + - - +
122A VAL* 3.7 6.7 - - - +
124A LEU* 1.3 75.8 - - - +
126A ASN* 1.3 59.8 + - - +
128A ARG* 2.9 41.1 + - - +
129A LEU* 2.9 46.8 + - + +
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Residues in contact with ASN 126 (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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102A ASP* 5.0 3.4 + - - -
122A VAL* 3.0 36.7 + - - +
123A LYS* 3.3 8.8 + - + +
125A GLU* 1.3 74.8 - - - +
127A MSE 1.3 60.8 + - - +
129A LEU* 3.7 17.2 - - - +
130A GLN* 2.9 31.2 + - - +
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Residues in contact with MSE 127 (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 TYR* 3.7 30.7 - - + -
76A ASP* 3.5 33.2 - - - +
119A PRO* 4.2 3.1 - - + -
123A LYS* 3.0 50.1 + - + +
124A LEU* 3.8 24.7 - - + +
126A ASN* 1.3 76.4 - - + +
128A ARG* 1.3 56.2 + - - +
130A GLN* 3.8 8.4 - - - +
131A HIS* 3.0 30.1 + - - +
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Residues in contact with ARG 128 (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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124A LEU 3.0 17.4 + - - +
125A GLU* 2.9 42.8 + - - +
127A MSE 1.3 72.1 - - - +
129A LEU* 1.3 78.3 + - - +
131A HIS* 3.3 7.0 + - - +
132A GLU* 3.0 51.0 + - + +
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Residues in contact with LEU 129 (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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125A GLU* 2.9 38.5 + - + +
126A ASN* 3.7 19.1 - - - +
128A ARG* 1.3 89.6 - - - +
130A GLN* 1.3 63.2 + - - +
132A GLU* 3.3 23.9 + - - +
133A GLN* 3.0 46.4 + - - +
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Residues in contact with GLN 130 (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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126A ASN 2.9 21.2 + - - +
127A MSE 3.8 9.6 - - - +
129A LEU* 1.3 71.3 - - - +
131A HIS* 1.3 63.4 + - - +
133A GLN* 3.3 14.5 + - - +
134A ARG* 3.0 76.5 + - - +
201A CL 4.1 5.2 - - + -
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Residues in contact with HIS 131 (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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127A MSE 3.0 18.3 + - - +
128A ARG* 3.7 5.8 - - - +
129A LEU 3.3 0.2 - - - -
130A GLN* 1.3 77.8 - - - +
132A GLU* 1.3 59.6 + - + +
134A ARG* 3.9 1.5 - - - +
135A ALA* 3.0 37.2 + - + +
201A CL 3.7 22.8 - - + +
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Residues in contact with GLU 132 (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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128A ARG* 3.0 42.0 + - + +
129A LEU* 3.8 23.2 - - - +
131A HIS* 1.3 81.1 - - + +
133A GLN* 1.3 64.2 + - + +
135A ALA* 4.1 4.9 - - - +
136A LYS* 3.3 22.2 + - - +
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Residues in contact with GLN 133 (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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129A LEU* 3.0 40.6 + - - +
130A GLN* 3.6 13.6 - - - +
132A GLU* 1.3 83.7 - - + +
134A ARG* 1.3 62.3 + - + +
136A LYS* 3.1 25.1 - - - +
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Residues in contact with ARG 134 (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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130A GLN* 3.0 61.8 + - - +
131A HIS* 4.0 2.9 - - - +
133A GLN* 1.3 77.6 + - + +
135A ALA* 1.3 60.8 + - - +
136A LYS 3.1 8.8 + - - -
201A CL 3.6 15.3 - - - +
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Residues in contact with ALA 135 (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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131A HIS* 3.0 33.0 + - + +
132A GLU* 4.1 5.6 - - - +
134A ARG* 1.3 76.0 - - - +
136A LYS* 1.3 57.2 + - - +
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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