Contacts of the helix formed by residues 168 - 183 (chain A) in PDB entry 3TG5
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 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A PRO* 1.3 78.9 - - - +
169A ASN* 1.3 67.6 + - - +
170A ASP* 4.3 7.0 - - + +
171A SER* 2.7 42.3 + - - -
172A LEU* 3.4 10.6 + - - +
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Residues in contact with ASN 169 (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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150A GLN* 3.0 43.0 + - - +
153A ILE* 3.9 17.7 - - - +
168A ASP* 1.3 73.8 - - - +
170A ASP* 1.3 64.8 + - - +
172A LEU* 3.1 12.0 + - - +
173A VAL* 3.0 29.7 + - - +
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Residues in contact with ASP 170 (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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138A LEU* 5.7 0.2 - - - +
168A ASP* 3.3 7.9 + - - +
169A ASN* 1.3 88.5 - - - +
171A SER* 1.3 60.4 + - - +
173A VAL* 3.7 10.8 + - - +
174A VAL* 3.4 25.8 + - - +
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Residues in contact with SER 171 (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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167A PRO* 3.9 18.0 - - - +
168A ASP* 2.7 29.7 + - - -
170A ASP* 1.3 75.7 - - - +
172A LEU* 1.3 60.6 + - - +
174A VAL* 3.4 8.8 + - - +
175A LEU* 3.0 27.4 + - - +
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Residues in contact with LEU 172 (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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113A LEU* 3.8 32.1 - - + -
153A ILE* 3.7 32.3 - - + -
156A LEU* 3.8 23.1 - - + -
157A HIS* 4.3 14.8 - - + +
166A PHE* 4.7 2.0 - - + -
167A PRO* 4.0 25.1 - - + +
168A ASP 3.4 10.0 + - - +
169A ASN* 3.1 9.1 + - - +
171A SER* 1.3 77.8 - - - +
173A VAL* 1.3 64.4 + - - +
175A LEU* 4.3 11.2 - - + +
176A PHE* 3.0 33.6 + - + -
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Residues in contact with VAL 173 (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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138A LEU* 3.8 25.4 - - + -
141A LEU* 4.4 11.7 - - + -
146A LYS* 5.4 7.2 - - + -
149A ILE* 3.8 19.6 - - + +
150A GLN* 3.6 15.7 - - - +
153A ILE* 3.8 5.2 - - + -
169A ASN* 3.0 36.2 + - - +
170A ASP* 3.8 15.3 - - - +
172A LEU* 1.3 78.2 - - - +
174A VAL* 1.3 56.8 - - - +
176A PHE* 3.9 1.6 - - - +
177A ALA* 3.0 29.2 + - - +
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Residues in contact with VAL 174 (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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136A SER* 3.8 12.1 - - - +
138A LEU* 4.3 27.8 - - + -
170A ASP 3.4 13.9 + - - +
171A SER* 3.4 11.6 + - - +
172A LEU 3.3 0.2 - - - -
173A VAL* 1.3 77.3 - - - +
175A LEU* 1.3 51.5 - - - +
177A ALA* 3.3 6.9 + - - +
178A GLN* 2.8 61.5 + - + +
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Residues in contact with LEU 175 (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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109A THR* 3.7 24.5 - - + -
112A ILE* 3.9 31.6 - - + -
113A LEU* 3.7 31.0 - - + -
116A GLN* 4.7 6.5 - - - +
131A VAL* 4.3 12.3 - - + -
134A PHE* 6.0 0.2 - - + -
171A SER 3.0 17.7 + - - +
172A LEU* 4.0 9.9 - - + +
173A VAL 3.4 0.2 - - - -
174A VAL* 1.3 75.8 - - - +
176A PHE* 1.3 58.5 + - - +
178A GLN* 3.1 22.8 + - + +
179A VAL* 2.8 34.7 + - + +
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Residues in contact with PHE 176 (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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105A THR* 4.1 16.8 - - + -
106A VAL* 4.1 8.3 - - - -
109A THR* 3.0 41.1 - - + -
149A ILE* 4.1 17.0 - - + -
152A ASP* 3.5 45.8 - - + -
153A ILE* 3.7 30.3 - - + -
156A LEU* 4.2 14.4 - - + -
172A LEU* 3.0 28.9 + - + +
173A VAL 3.9 2.7 - - - +
175A LEU* 1.3 76.6 - - - +
177A ALA* 1.3 60.7 + - - +
179A VAL* 3.4 5.7 + - - +
180A ASN* 3.0 33.4 + - - +
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Residues in contact with ALA 177 (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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136A SER* 3.4 29.4 - - - +
138A LEU* 5.1 0.9 - - + +
141A LEU* 4.3 22.7 - - + -
149A ILE* 4.4 4.8 - - + +
173A VAL 3.0 18.8 + - - +
174A VAL* 3.5 5.8 - - - +
176A PHE* 1.3 74.6 - - - +
178A GLN* 1.3 63.2 + - - +
180A ASN* 3.5 11.0 + - - +
181A CYS* 3.2 23.4 + - - +
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Residues in contact with GLN 178 (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 VAL 3.5 14.9 + - - +
132A LYS* 3.4 22.2 + - - +
134A PHE* 3.0 38.9 + - + +
135A GLU 3.5 15.0 - - - +
136A SER* 3.8 6.9 - - - -
174A VAL* 2.8 37.4 + - - +
175A LEU* 3.3 33.8 - - + +
177A ALA* 1.3 70.6 - - - +
179A VAL* 1.3 63.7 + - - +
181A CYS 3.3 0.7 + - - -
182A ASN* 2.8 31.0 + - - +
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Residues in contact with VAL 179 (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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105A THR* 3.9 25.4 - - + -
108A LEU* 4.3 20.9 - - + -
109A THR* 4.0 13.7 - - + +
112A ILE* 3.6 30.1 - - + -
134A PHE* 5.8 0.4 - - + -
175A LEU* 2.8 22.8 + - + +
176A PHE* 3.5 9.4 - - - +
178A GLN* 1.3 75.7 - - - +
180A ASN* 1.3 56.7 + - - +
183A GLY* 2.7 31.4 + - - -
198A ILE* 4.2 11.7 - - + -
369B LEU* 3.5 8.8 - - + +
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Residues in contact with ASN 180 (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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105A THR* 4.0 20.3 - - - +
149A ILE* 4.6 13.7 - - - +
176A PHE* 3.0 24.4 + - - +
177A ALA* 3.8 8.2 - - - +
178A GLN 3.4 0.2 - - - -
179A VAL* 1.3 77.0 - - - +
181A CYS* 1.3 60.1 + - - +
183A GLY 4.6 1.0 + - - +
257A SER* 4.6 9.1 - - - +
258A TYR* 3.7 16.3 + - - -
368B HIS* 4.8 8.9 + - - +
369B LEU* 4.1 16.5 - - - +
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Residues in contact with CYS 181 (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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135A GLU* 3.6 26.5 - - - +
136A SER 4.8 3.6 - - - +
137A HIS* 3.9 15.7 - - + -
177A ALA 3.2 17.4 + - - +
180A ASN* 1.3 76.3 - - - +
182A ASN* 1.3 60.7 + - - +
257A SER 5.0 3.1 - - - +
258A TYR* 3.6 15.3 - - - -
259A PHE* 6.5 0.4 - - + -
435A SAH 3.4 42.3 - - - +
370B LYS* 3.4 19.1 + - - -
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Residues in contact with ASN 182 (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* 4.9 2.6 - - - +
134A PHE* 3.4 36.1 - - + +
135A GLU 3.2 22.6 + - - +
178A GLN 2.8 22.9 + - - +
179A VAL* 5.2 0.2 - - - -
181A CYS* 1.3 80.9 - - - +
183A GLY* 1.3 67.9 + - - +
184A PHE* 3.3 22.0 - - - -
198A ILE* 5.0 2.0 - - + -
199A PHE 5.4 1.2 + - - -
203A ALA* 3.5 28.3 + - + +
435A SAH 3.5 24.2 + - - +
370B LYS* 3.4 7.6 + - - +
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Residues in contact with GLY 183 (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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179A VAL* 2.7 23.7 + - - -
180A ASN 5.3 0.3 - - - +
181A CYS 3.9 0.4 - - - -
182A ASN* 1.3 76.2 - - - +
184A PHE* 1.3 59.4 + - - -
197A ALA 3.7 9.6 - - - -
198A ILE* 4.0 11.8 - - - +
258A TYR* 4.9 0.3 + - - -
369B LEU* 3.7 17.1 - - - +
370B LYS* 3.1 25.5 + - - +
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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