Contacts of the helix formed by residues 146 - 161 (chain A) in PDB entry 1TUB
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 GLY 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.2 6.3 - - - -
10A GLY* 5.4 1.3 - - - -
139A HIS* 3.7 5.0 + - - -
140A SER* 3.5 21.7 - - - +
143A GLY 1.9 25.9 + - - -
145A THR* 1.3 68.7 + - - +
147A SER* 1.2 55.0 - - - +
150A THR* 2.2 35.6 + - - +
189A LEU* 3.2 10.5 - - - +
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Residues in contact with SER 147 (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 ASN 3.1 1.7 + - - -
103A TYR* 2.4 22.3 - - - -
143A GLY 3.4 0.6 + - - -
144A GLY 3.2 0.3 + - - -
146A GLY* 1.2 75.6 - - - +
148A GLY* 1.3 60.6 + - - +
149A PHE 3.1 0.2 - - - -
150A THR* 2.4 17.3 + - - -
151A SER* 2.5 23.0 + - - -
185A TYR* 2.7 22.4 + - - -
189A LEU* 1.1 151.5 - - - +
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Residues in contact with GLY 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 2.8 9.1 + - - -
107A HIS* 2.2 59.7 - - - +
144A GLY 3.6 0.6 + - - -
147A SER* 1.3 82.6 + - - +
149A PHE* 1.3 49.0 + - - +
151A SER* 2.6 7.0 - - - -
152A LEU* 2.4 22.0 + - - +
189A LEU* 2.5 1.8 - - - +
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Residues in contact with PHE 149 (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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9A VAL* 3.9 11.4 - - + -
68A VAL* 2.5 46.9 - - + -
70A LEU* 3.6 25.8 - - + -
107A HIS* 3.0 10.5 - - - +
111A GLY* 4.2 16.8 - - - -
114A ILE 4.0 18.2 - - - -
115A ILE* 4.8 5.6 - - + -
118A VAL* 4.9 4.3 - - + -
144A GLY 3.6 2.0 + - - +
145A THR* 2.5 40.6 - - - +
147A SER 3.1 0.8 - - - -
148A GLY* 1.3 76.9 - - - +
150A THR* 1.2 59.6 + - - +
152A LEU* 3.5 10.8 - - + +
153A LEU* 2.9 40.1 + - + +
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Residues in contact with THR 150 (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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9A VAL* 2.4 52.0 - - + -
139A HIS* 3.9 23.4 + - + -
146A GLY 2.2 33.3 + - - +
147A SER* 2.4 15.2 + - - -
149A PHE* 1.2 77.4 - - - +
151A SER* 1.3 50.4 + - - +
152A LEU 2.9 4.5 - - - -
153A LEU* 3.7 5.2 - - - +
154A MET* 2.4 39.0 + - - +
189A LEU* 4.7 0.3 - - - +
192A HIS* 2.5 11.4 + - - -
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Residues in contact with SER 151 (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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103A TYR* 2.0 39.3 + - - -
107A HIS* 2.5 27.1 - - - -
147A SER 2.5 10.9 + - - -
148A GLY* 2.6 4.5 + - - -
150A THR* 1.3 64.4 + - - +
152A LEU* 1.3 47.4 + - - +
155A GLU* 1.6 48.0 - - - +
192A HIS* 1.6 46.2 - - - -
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Residues in contact with LEU 152 (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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106A GLY 4.5 0.9 - - - +
107A HIS* 3.8 21.3 - - + +
111A GLY* 3.6 19.5 - - - +
112A LYS* 3.8 1.6 - - + +
115A ILE* 1.9 58.8 - - + -
148A GLY 2.4 26.8 + - - +
149A PHE* 3.5 9.2 - - + +
151A SER* 1.3 75.1 - - - +
153A LEU* 1.3 57.4 + - - +
154A MET 3.4 0.4 - - - -
155A GLU* 3.7 5.7 - - - +
156A ARG* 2.8 60.5 + - + +
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Residues in contact with LEU 153 (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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7A ILE* 3.2 37.0 - - + -
8A HIS 4.2 1.6 - - - +
9A VAL* 4.7 4.7 - - + -
68A VAL* 4.4 5.6 - - + -
115A ILE* 4.0 10.5 - - + -
118A VAL* 4.3 16.2 - - + -
119A LEU* 4.2 14.6 - - + -
122A ILE* 5.2 1.8 - - + -
137A VAL* 5.6 1.1 - - + -
149A PHE* 2.9 41.1 + - + +
150A THR* 4.0 4.3 - - - +
152A LEU* 1.3 76.1 - - - +
154A MET* 1.3 54.9 + - + +
156A ARG* 4.3 1.6 - - - -
157A LEU* 2.4 64.5 - - + +
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Residues in contact with MET 154 (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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137A VAL* 2.8 33.7 - - + -
150A THR* 2.4 44.8 + - - +
153A LEU* 1.3 69.4 - - - +
155A GLU* 1.3 39.8 - - - +
157A LEU* 4.7 1.1 - - - -
158A SER 2.8 2.6 + - - -
166A LYS* 1.4 72.6 + - + +
168A GLU* 1.6 70.2 - - + +
192A HIS* 3.0 18.6 - - + -
193A THR* 4.3 1.1 - - + -
197A HIS* 1.0 112.2 + - + +
198A SER* 4.5 1.6 - - - -
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Residues in contact with GLU 155 (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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103A TYR* 3.6 1.0 + - - -
107A HIS* 3.9 10.3 + - - -
151A SER* 1.6 35.7 + - - +
152A LEU* 3.7 9.1 - - - +
153A LEU 3.3 0.2 - - - -
154A MET* 1.3 70.9 - - - +
156A ARG* 1.3 53.6 + - + +
158A SER* 2.5 16.5 + - - -
159A VAL* 2.6 27.1 + - + +
192A HIS* 2.4 40.2 - - + +
196A GLU* 3.1 31.3 - - + +
197A HIS* 1.7 23.3 - - - -
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Residues in contact with ARG 156 (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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112A LYS* 3.7 13.7 + - - +
115A ILE* 1.7 77.9 - - - +
116A ASP* 2.5 20.0 + - - -
119A LEU* 3.3 32.3 - - + +
152A LEU* 2.8 30.3 + - + +
153A LEU 4.8 1.1 - - - +
155A GLU* 1.3 73.6 - - + +
157A LEU* 1.3 58.2 + - - +
159A VAL* 4.3 6.1 - - - -
160A ASP* 2.6 43.3 + - - +
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Residues in contact with LEU 157 (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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7A ILE* 3.4 30.3 - - + -
119A LEU* 4.1 17.9 - - + -
122A ILE* 2.8 33.0 - - + -
135A PHE* 5.1 9.4 - - + -
137A VAL* 5.1 0.4 - - + -
153A LEU* 2.4 34.5 - - + +
154A MET* 3.3 8.9 + - - +
155A GLU 3.2 0.4 - - - -
156A ARG* 1.3 80.3 - - + +
158A SER* 1.3 51.3 + - - +
160A ASP* 4.5 3.6 - - - +
161A TYR* 2.8 46.7 + - + +
166A LYS* 3.1 21.1 - - + +
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Residues in contact with SER 158 (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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154A MET 2.8 0.2 + - - -
155A GLU 2.5 9.4 + - - -
157A LEU* 1.3 67.2 - - - +
159A VAL* 1.3 67.1 + - - +
161A TYR 4.6 3.6 - - - -
162A GLY* 3.3 23.8 + - - -
166A LYS* 2.4 19.8 - - - +
196A GLU 2.0 9.0 + - - -
197A HIS* 1.4 99.9 + - - -
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Residues in contact with VAL 159 (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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155A GLU* 2.6 27.1 + - + +
156A ARG* 3.8 7.0 - - - +
158A SER* 1.3 87.5 + - - +
160A ASP* 1.3 66.8 + - - +
162A GLY* 4.4 2.6 + - - -
196A GLU* 4.7 10.8 - - - +
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Residues in contact with ASP 160 (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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119A LEU* 4.5 14.7 - - - +
156A ARG* 2.6 31.8 + - - +
157A LEU* 4.5 1.1 - - - +
159A VAL* 1.3 86.5 - - - +
161A TYR* 1.3 82.9 + - + +
162A GLY 3.8 1.5 + - - -
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Residues in contact with TYR 161 (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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122A ILE* 4.9 11.2 - - + -
123A ARG* 4.0 16.8 - - + +
126A ALA* 3.3 26.0 - - + +
127A ASP* 4.3 4.0 + - - -
135A PHE* 4.1 24.9 - + + -
157A LEU* 2.8 30.0 + - + +
158A SER* 3.7 2.8 - - - +
160A ASP* 1.3 95.3 - - + +
162A GLY* 1.3 63.6 + - - +
163A LYS* 3.1 3.6 - - - -
164A LYS* 3.0 59.5 + - + +
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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