Contacts of the helix formed by residues 133 - 142 (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 ASP 133 (chain B).
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Specific contacts
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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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Residues in contact with SER 134 (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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96B GLY* 3.2 23.4 - - - -
132B LYS 3.6 3.5 + - - -
133B ASP* 1.3 75.4 + - - +
135B GLY* 1.3 54.3 + - - +
137B GLN* 3.7 6.3 - - - +
138B ALA* 2.9 24.9 + - - +
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Residues in contact with GLY 135 (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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88B MET* 3.7 9.4 - - - +
93B ILE* 3.9 2.9 - - - +
94B ASP 3.4 23.3 - - - -
96B GLY 3.7 2.3 - - - +
133B ASP* 2.9 12.8 + - - -
134B SER* 1.3 72.7 + - - +
136B VAL* 1.3 61.3 + - - +
137B GLN 3.2 1.3 - - - -
138B ALA* 3.1 9.5 + - - +
139B CYS* 2.8 28.9 + - - +
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Residues in contact with VAL 136 (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* 3.9 19.3 - - + -
84B ILE* 3.5 23.3 - - + +
85B ILE* 5.0 3.1 - - + -
88B MET* 3.8 12.2 - - - +
95B PHE* 3.6 32.3 - - + -
130B LEU* 3.1 36.6 - - + +
131B TRP* 4.3 8.1 - - + -
133B ASP* 3.3 7.8 + - + +
135B GLY* 1.3 73.1 - - - +
137B GLN* 1.3 52.7 + - - +
139B CYS* 3.1 4.7 + - - +
140B PHE* 2.8 31.8 + - - +
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Residues in contact with GLN 137 (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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131B TRP* 2.7 57.1 + - - -
132B LYS* 4.9 3.1 - - - +
133B ASP 3.1 15.0 + - - +
134B SER* 3.7 8.5 - - - +
136B VAL* 1.3 73.9 - - - +
138B ALA* 1.3 64.1 + - - +
140B PHE* 3.1 26.5 + - - +
141B ASN* 3.0 36.6 + - - +
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Residues in contact with ALA 138 (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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93B ILE* 4.3 15.7 - - + -
134B SER 2.9 17.7 + - - +
135B GLY* 3.1 13.0 + - - +
137B GLN* 1.3 75.1 - - - +
139B CYS* 1.3 62.7 + - - +
141B ASN* 3.1 16.8 + - - +
142B ARG* 3.4 17.2 + - - +
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Residues in contact with CYS 139 (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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84B ILE* 3.5 23.6 - - + -
87B ALA* 3.7 20.9 - - - -
88B MET* 3.6 25.8 - - + -
91B LEU* 4.1 4.9 - - - -
93B ILE* 3.6 19.2 - - + +
135B GLY 2.8 11.3 + - - +
136B VAL 3.4 8.5 - - - +
138B ALA* 1.3 72.9 - - - +
140B PHE* 1.3 58.2 + - - +
142B ARG* 3.1 12.1 + - - +
146B TYR* 2.6 30.3 + - - -
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Residues in contact with PHE 140 (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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84B ILE* 4.1 7.8 - - + +
131B TRP* 4.0 26.9 - + + -
136B VAL 2.8 16.1 + - - +
137B GLN* 3.1 34.0 + - - +
139B CYS* 1.3 74.2 - - - +
141B ASN* 1.3 73.3 + - - +
143B SER* 3.1 28.6 + - - -
146B TYR* 3.5 7.2 - - - -
148B LEU* 3.7 25.8 - - + -
152B ALA* 5.0 1.1 - - + -
153B ALA* 4.0 28.3 - - + -
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Residues in contact with ASN 141 (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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137B GLN* 3.0 30.7 + - - +
138B ALA* 3.1 9.5 + - - +
140B PHE* 1.3 92.1 - - - +
142B ARG* 1.3 61.5 + - + +
143B SER* 3.4 2.1 + - - -
144B ARG* 5.3 2.8 + - - +
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Residues in contact with ARG 142 (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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91B LEU* 3.8 32.6 + - + +
93B ILE* 3.8 21.9 - - - +
138B ALA* 3.4 13.2 + - - +
139B CYS 3.1 13.5 + - - +
141B ASN* 1.3 80.3 - - + +
143B SER* 1.3 54.7 + - - +
144B ARG* 3.1 11.0 - - - -
145B GLU* 2.8 69.6 + - - +
146B TYR* 3.5 3.4 - - - -
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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