Contacts of the helix formed by residues 139 - 151 (chain C) 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 ASP 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B GLN* 6.0 2.5 - - + +
235B ALA* 3.2 28.5 - - + +
236B GLU* 4.5 1.1 - - - +
138C ILE* 1.3 78.1 - - - +
140C PHE* 1.3 66.2 + - - +
141C ARG* 4.1 9.4 - - - +
142C THR* 2.6 35.4 + - - -
143C ARG* 3.0 20.5 + - - +
164C VAL* 5.6 1.6 - - - +
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Residues in contact with PHE 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ALA 2.9 18.3 + - - +
236B GLU* 3.7 17.8 - - - +
237B ASP* 4.1 10.5 - - - +
238B GLU* 4.2 23.3 - - + +
239B GLU* 4.5 17.7 - - - -
139C ASP* 1.3 71.5 - - - +
141C ARG* 1.3 71.8 + - + +
143C ARG* 3.2 28.7 + - - +
144C GLU* 2.8 66.6 + - + +
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Residues in contact with ARG 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ASP* 3.4 10.0 + - - +
140C PHE* 1.3 91.8 - - + +
142C THR* 1.3 57.9 + - - +
144C GLU* 4.0 3.3 - - - +
145C SER* 3.1 30.1 + - - -
160C GLU* 5.8 0.4 - - - -
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Residues in contact with THR 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C ILE* 4.3 15.2 - - + +
139C ASP* 2.6 27.9 + - - -
141C ARG* 1.3 75.9 - - - +
143C ARG* 1.3 55.4 + - - +
145C SER* 3.5 2.1 + - - -
146C THR* 2.7 37.6 + - - +
160C GLU* 4.2 23.1 + - + +
161C ALA* 4.0 34.1 - - + +
164C VAL* 4.4 15.3 - - + +
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Residues in contact with ARG 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B GLU* 3.2 34.3 + - - +
237B ASP* 5.2 2.6 + - - +
124C TYR* 4.0 10.1 + - - +
128C VAL* 3.2 35.9 - - + +
129C HIS* 4.8 0.9 - - - +
130C SER* 3.6 31.4 + - - +
135C GLN* 4.8 10.6 - - - +
138C ILE* 4.0 24.5 + - + +
139C ASP 3.0 15.8 + - - +
140C PHE* 3.6 30.2 - - - +
142C THR* 1.3 76.0 - - - +
144C GLU* 1.3 60.7 + - - +
146C THR* 3.5 3.8 + - - -
147C ALA* 2.9 27.5 + - - +
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Residues in contact with GLU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C PHE* 2.8 59.7 + - + +
141C ARG* 4.0 5.4 - - - +
143C ARG* 1.3 73.1 - - + +
145C SER* 1.3 61.1 + - - +
147C ALA* 3.2 12.9 + - - +
148C LYS* 3.0 36.1 + - + +
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Residues in contact with SER 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C ARG 3.1 18.5 + - - -
142C THR 3.9 0.7 - - - -
144C GLU* 1.3 75.5 - - - +
146C THR* 1.3 64.8 + - - +
148C LYS* 3.6 8.4 + - - +
149C LYS* 3.4 37.0 + - - +
160C GLU* 2.7 28.5 + - - -
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Residues in contact with THR 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C TYR* 4.1 13.5 - - + -
128C VAL* 4.2 11.8 - - + +
142C THR* 2.7 24.0 + - - +
143C ARG* 3.7 4.8 - - - -
145C SER* 1.3 75.6 + - - +
147C ALA* 1.3 67.4 + - - +
149C LYS* 3.0 20.7 + - - +
150C ILE* 3.3 15.2 + - + +
157C CYS* 4.7 7.3 + - - +
158C PHE* 3.9 34.5 - - + -
160C GLU* 4.9 3.6 + - - +
161C ALA* 4.1 18.5 + - + +
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Residues in contact with ALA 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C TYR* 3.5 27.1 - - + +
143C ARG 2.9 15.4 + - - +
144C GLU* 3.3 21.5 - - - +
146C THR* 1.3 78.9 - - - +
148C LYS* 1.3 62.8 + - + +
149C LYS 3.2 0.3 + - - -
150C ILE* 3.2 16.9 + - - +
151C LYS* 4.3 7.1 - - - +
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Residues in contact with LYS 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C GLU* 3.0 21.0 + - + +
145C SER* 3.9 8.3 - - - +
146C THR 3.2 0.4 - - - -
147C ALA* 1.3 77.5 - - + +
149C LYS* 1.3 61.1 + - + +
150C ILE 3.6 0.2 + - - -
151C LYS* 3.9 25.9 + - + +
152C ALA 4.8 0.7 + - - -
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Residues in contact with LYS 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C SER* 3.4 32.8 + - - +
146C THR* 3.0 9.6 + - - +
148C LYS* 1.3 74.9 - - + +
150C ILE* 1.3 64.5 + - - +
151C LYS 3.2 3.8 + - - -
152C ALA 3.4 6.8 - - - +
153C PRO* 3.3 25.0 - - + +
154C THR 6.2 0.2 - - - +
156C THR 5.3 2.4 + - - -
157C CYS* 3.5 40.3 + - + +
160C GLU* 3.6 21.8 + - - +
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Residues in contact with ILE 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PRO* 4.8 4.0 - - - +
120C ALA* 3.7 19.3 - - + +
121C GLU* 4.0 35.0 - - + +
124C TYR* 3.7 27.1 - - + -
146C THR* 3.3 15.5 - - + +
147C ALA* 3.2 10.6 + - - +
149C LYS* 1.3 77.0 - - - +
151C LYS* 1.3 64.6 + - + +
153C PRO* 3.4 18.4 - - - +
157C CYS* 3.8 21.1 - - - -
158C PHE* 3.8 14.8 - - + -
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Residues in contact with LYS 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PRO* 5.7 1.6 - - - +
147C ALA 4.3 6.3 - - - +
148C LYS* 3.9 23.3 - - + +
149C LYS 3.2 0.2 - - - -
150C ILE* 1.3 80.6 - - + +
152C ALA* 1.3 60.7 + - + +
153C PRO* 3.6 4.2 - - - +
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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