Contacts of the helix formed by residues 120 - 133 (chain B) in PDB entry 2GTP
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 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B LEU* 5.2 4.1 - - + +
118B PHE* 5.8 3.6 - - + -
119B MET* 1.3 77.9 - - - +
121B ALA* 1.3 58.3 + - - +
122B GLU* 3.7 10.9 + - - +
123B LEU* 2.9 34.9 + - + +
124B ALA* 2.9 28.8 + - - +
163B ALA* 5.5 1.3 - - - +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B THR* 1.3 70.8 - - - +
122B GLU* 1.3 61.1 + - - +
124B ALA* 3.4 6.7 + - - +
125B GLY* 2.9 26.3 + - - -
163B ALA 6.1 1.6 - - - -
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLN* 3.9 16.9 + - - +
110B LEU* 3.7 32.9 - - + +
120B THR* 3.2 8.6 + - - +
121B ALA* 1.3 79.5 - - - +
123B LEU* 1.3 57.2 + - - +
125B GLY* 3.3 1.8 + - - -
126B VAL* 3.0 37.1 + - + +
129B ARG* 4.9 0.9 + - - -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ILE* 4.2 23.1 - - + -
107B LEU* 3.9 19.7 - - + +
110B LEU* 4.1 44.2 - - + +
111B ALA* 4.8 2.7 - - - +
113B ALA 5.4 2.7 - - - +
118B PHE 5.7 1.3 - - - +
119B MET* 4.3 12.6 - - + -
120B THR* 2.9 28.1 + - + +
122B GLU* 1.3 73.9 - - - +
124B ALA* 1.3 66.5 + - - +
126B VAL* 3.4 2.5 + - + +
127B ILE* 3.0 40.4 + - + +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B MET* 4.1 9.1 - - + +
120B THR 2.9 17.8 + - - +
121B ALA* 3.7 7.6 - - - +
123B LEU* 1.3 77.4 - - - +
125B GLY* 1.3 57.0 + - - +
127B ILE* 3.0 4.5 + - - +
128B LYS* 2.9 39.8 + - - +
159B LEU* 3.6 24.7 - - + +
163B ALA* 3.7 18.2 - - + -
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ALA 2.9 15.1 + - - -
122B GLU 3.3 2.9 + - - -
124B ALA* 1.3 72.5 - - - +
126B VAL* 1.3 64.6 + - - +
128B LYS* 3.9 11.7 - - - +
129B ARG* 3.0 47.5 + - - +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ASP* 3.2 31.3 - - + +
106B GLN* 4.2 13.7 - - + -
107B LEU* 3.9 24.0 - - + +
110B LEU* 4.2 14.8 - - + -
122B GLU* 3.0 24.0 + - + +
123B LEU* 3.6 8.1 - - + +
125B GLY* 1.3 76.0 - - - +
127B ILE* 1.3 61.6 + - - +
129B ARG* 3.4 22.9 - - - +
130B LEU* 3.2 25.6 + - + +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B THR* 4.7 4.5 - - + -
78B ILE* 4.2 10.1 - - + -
81B ILE* 4.1 16.1 - - + +
107B LEU* 3.7 24.7 - - + -
119B MET* 4.2 22.2 - - + -
123B LEU* 3.0 38.5 + - + +
124B ALA 3.0 3.3 + - - +
126B VAL* 1.3 75.4 - - - +
128B LYS* 1.3 59.6 + - - +
130B LEU* 3.3 6.7 + - - +
131B TRP* 2.9 28.1 + - + +
156B LEU* 3.6 31.4 - - + -
159B LEU* 3.7 12.3 - - + -
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ALA* 2.9 31.1 + - - +
125B GLY* 3.5 9.7 + - - +
127B ILE* 1.3 71.7 - - - +
129B ARG* 1.3 65.1 + - + +
131B TRP* 3.2 8.8 + - - +
132B LYS* 3.0 38.4 + - + +
159B LEU* 3.5 35.7 - - + -
160B ASP* 3.3 34.0 + - - +
163B ALA* 4.9 4.0 - - - +
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Residues in contact with ARG 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ARG* 3.5 31.1 + - - +
103B ASP* 2.8 42.9 + - - +
122B GLU 4.9 0.6 + - - -
125B GLY* 3.0 37.7 + - - +
126B VAL* 3.4 27.8 - - - +
128B LYS* 1.3 75.7 - - + +
130B LEU* 1.3 67.4 + - - +
132B LYS* 3.5 14.5 + - - +
133B ASP* 3.4 14.6 + - - -
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ILE* 4.4 11.7 - - + -
85B ILE* 3.3 27.8 - - + -
95B PHE* 3.8 31.0 - - + -
100B ARG* 3.8 26.9 - - + +
103B ASP* 4.1 11.4 - - + +
104B ALA* 4.1 3.6 - - - +
107B LEU* 4.1 9.6 - - + -
126B VAL* 3.2 34.1 + - + +
127B ILE* 3.8 3.8 - - - +
129B ARG* 1.3 77.0 - - - +
131B TRP* 1.3 63.3 + - - +
133B ASP* 3.1 9.4 + - - +
136B VAL* 3.1 27.2 - - + +
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Residues in contact with TRP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ILE* 4.5 7.6 - - + -
84B ILE* 3.9 20.6 - - + -
127B ILE* 2.9 19.1 + - + +
128B LYS* 3.2 7.6 + - - +
130B LEU* 1.3 78.9 - - - +
132B LYS* 1.3 61.0 + - + +
133B ASP 3.7 1.4 + - - +
136B VAL* 4.3 6.6 - - + +
137B GLN* 2.7 60.8 + - - -
140B PHE* 4.0 26.7 - + + -
152B ALA 5.6 0.2 - - - -
153B ALA* 4.1 14.1 - - + -
156B LEU* 3.5 59.2 + - + -
157B ASN* 2.9 38.2 + - - +
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Residues in contact with LYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LYS* 3.0 31.5 + - + +
129B ARG* 4.1 14.1 - - - +
131B TRP* 1.3 79.5 - - + +
133B ASP* 1.3 63.3 + - - +
134B SER 3.6 1.9 + - - -
137B GLN* 4.9 3.5 - - - +
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B PHE* 3.6 6.8 - - - -
96B GLY* 2.9 15.7 + - - -
97B ASP* 3.1 27.2 + - - +
100B ARG* 3.8 22.6 + - + +
129B ARG 3.4 11.7 + - - +
130B LEU 3.1 13.9 + - - +
131B TRP 4.2 0.3 - - - +
132B LYS* 1.3 77.0 - - - +
134B SER* 1.3 65.4 + - - +
135B GLY* 2.9 21.5 + - - -
136B VAL* 3.3 13.1 + - + +
137B GLN* 3.1 24.0 + - - +
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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