Contacts of the helix formed by residues 146 - 161 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA* 4.4 18.2 - - - -
10B GLY* 4.4 4.7 - - - -
139B HIS* 3.7 14.9 - - - +
140B SER* 4.0 16.2 - - - -
143B GLY 3.7 2.8 - - - -
144B GLY 3.1 0.2 - - - -
145B THR* 1.3 86.8 + - - +
147B SER* 1.5 46.5 - - - +
150B GLY* 2.5 31.8 + - - -
500B GDP 3.8 0.4 + - - -
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TRP* 2.6 7.4 + - - -
139B HIS* 4.6 2.1 + - - -
140B SER 2.3 7.4 + - - -
143B GLY* 2.1 35.3 + - - -
144B GLY* 2.9 3.5 + - - -
146B GLY* 1.5 60.5 - - - +
148B GLY* 1.3 51.5 + - - +
151B THR* 3.3 8.8 - - - +
185B TYR* 2.8 18.2 - - - -
189B LEU* 1.1 117.0 - - - +
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Residues in contact with GLY 148 (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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103B TRP* 2.5 41.1 - - - -
107B HIS* 1.6 49.9 - - - +
144B GLY 2.6 12.5 + - - -
147B SER* 1.3 71.7 - - - +
149B MET* 1.4 53.7 + - - +
150B GLY 3.4 0.4 - - - -
151B THR* 3.4 0.2 - - - -
189B LEU* 2.5 0.4 - - - +
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Residues in contact with MET 149 (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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9B ALA* 5.1 2.7 - - + -
68B VAL* 2.6 39.5 - - + -
70B LEU* 4.0 25.6 - - + -
106B GLY 4.3 7.6 - - - -
107B HIS* 3.5 6.9 - - - +
111B GLY* 4.7 2.5 - - - -
114B LEU* 3.5 27.4 - - + -
115B VAL* 4.4 12.3 - - + +
118B VAL* 3.9 13.7 - - + -
144B GLY 3.1 3.2 + - - -
145B THR* 2.1 37.0 + - - +
148B GLY* 1.4 77.5 - - - +
150B GLY* 1.2 65.9 + - - +
151B THR 3.2 0.2 - - - -
152B LEU* 3.1 3.0 + - - +
153B LEU* 3.0 38.3 + - + +
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Residues in contact with GLY 150 (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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9B ALA* 5.2 4.7 - - - -
137B LEU* 4.8 1.2 - - - +
139B HIS* 4.7 8.5 - - - -
146B GLY* 2.5 29.2 + - - -
149B MET* 1.2 75.2 - - - +
151B THR* 1.3 52.0 + - - +
153B LEU* 3.6 10.6 + - - +
154B ILE* 2.4 42.2 + - - +
192B HIS* 3.2 3.1 - - - -
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Residues in contact with THR 151 (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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103B TRP* 2.7 15.9 + - - +
107B HIS* 2.6 30.2 + - - -
139B HIS* 5.5 0.2 - - - +
147B SER 3.3 15.2 + - - +
148B GLY* 3.4 0.4 - - - -
150B GLY* 1.3 68.8 - - - +
152B LEU* 1.1 68.2 + - - +
155B SER* 3.0 17.7 + - - -
189B LEU* 3.3 9.9 - - + +
192B HIS* 1.8 89.2 + - + +
193B GLN* 4.7 0.4 - - - +
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Residues in contact with LEU 152 (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 GLY 3.4 6.1 - - - +
107B HIS* 1.9 113.9 - - + +
108B TYR* 4.9 0.7 - - + -
112B ALA* 4.3 0.4 - - - +
115B VAL* 3.5 30.5 - - + -
148B GLY 3.1 0.7 - - - +
149B MET* 3.1 6.4 + - - +
151B THR* 1.1 77.0 - - - +
153B LEU* 1.3 61.1 + - - +
155B SER* 2.3 26.2 + - - +
156B LYS* 3.3 13.9 + - - +
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Residues in contact with LEU 153 (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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7B ILE* 4.2 22.7 - - + -
9B ALA* 4.5 5.8 - - + -
68B VAL* 4.1 10.1 - - + -
115B VAL* 4.1 18.4 - - + +
118B VAL* 3.2 39.9 - - + -
137B LEU* 5.1 2.5 - - + -
149B MET* 3.0 40.8 + - + +
150B GLY* 3.7 9.0 - - - +
152B LEU* 1.3 75.4 - - - +
154B ILE* 1.3 61.2 + - + +
156B LYS* 3.7 3.9 + - + +
157B ILE* 2.7 40.3 + - + +
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Residues in contact with ILE 154 (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 LEU* 3.8 17.9 - - + -
139B HIS* 5.2 7.2 - - + -
150B GLY* 2.4 23.6 - - - +
152B LEU 3.1 0.6 - - - -
153B LEU* 1.3 77.4 - - - +
155B SER* 1.2 57.0 + - - +
157B ILE* 3.3 8.4 + - - +
158B ARG* 2.9 24.8 + - - +
166B MET* 4.9 3.3 - - + +
168B THR* 4.2 9.4 - - + -
192B HIS* 2.8 39.3 - - + +
193B GLN* 4.8 2.0 - - + -
196B GLU* 2.7 25.9 - - + +
197B ASN* 4.0 2.8 + - - +
198B THR* 2.4 54.1 - - + +
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Residues in contact with SER 155 (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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107B HIS* 5.9 0.7 - - - -
151B THR 3.0 12.0 + - - -
152B LEU* 2.3 32.1 + - - +
154B ILE* 1.2 70.8 - - - +
156B LYS* 1.3 56.9 + - - +
158B ARG* 3.1 3.5 + - - +
159B GLU* 2.6 53.6 + - - +
192B HIS* 5.0 0.2 - - - -
196B GLU* 4.0 27.4 - - - -
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Residues in contact with LYS 156 (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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112B ALA* 5.2 1.0 - - - +
115B VAL* 2.9 43.3 + - + +
116B ASP* 2.9 22.2 + - - +
119B LEU* 3.6 31.1 - - + +
152B LEU* 3.3 12.2 + - - +
153B LEU* 4.2 4.0 - - - +
155B SER* 1.3 83.4 + - - +
157B ILE* 1.3 59.5 + - + +
159B GLU* 3.0 17.3 + - - +
160B GLU* 2.7 43.7 + - - +
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Residues in contact with ILE 157 (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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7B ILE* 3.3 34.1 - - + -
118B VAL* 6.1 0.7 - - + -
119B LEU* 6.5 0.7 - - + -
122B VAL* 4.7 12.3 - - + -
135B PHE* 3.1 35.2 - - + -
137B LEU* 4.4 2.7 - - + -
153B LEU* 2.7 31.2 + - + +
154B ILE 3.6 4.0 - - - +
155B SER 3.2 0.6 - - - -
156B LYS* 1.3 77.4 - - + +
158B ARG* 1.3 52.2 + - - +
161B TYR* 2.7 46.1 + - + +
166B MET* 3.1 28.9 - - + -
197B ASN* 3.2 0.7 - - - -
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Residues in contact with ARG 158 (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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154B ILE 2.9 8.6 + - - +
155B SER* 3.7 3.6 - - - +
157B ILE* 1.3 66.6 - - - +
159B GLU* 1.3 67.9 - - + +
162B PRO* 3.2 24.3 - - + +
194B LEU 4.3 1.6 + - - -
195B VAL* 2.9 35.1 + - - +
196B GLU* 2.9 7.6 - - - +
197B ASN* 1.7 106.9 - - + +
198B THR 5.7 0.2 + - - -
263B PRO 5.7 2.4 + - - -
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Residues in contact with GLU 159 (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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155B SER* 2.6 42.5 + - - +
156B LYS* 3.0 16.7 + - - +
158B ARG* 1.3 83.9 - - + +
160B GLU* 1.3 61.6 + - + +
162B PRO* 3.9 6.9 - - - +
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Residues in contact with GLU 160 (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 LEU* 4.4 20.1 - - - +
122B VAL* 5.8 0.2 - - - +
123B ARG* 5.8 4.7 + - - +
156B LYS* 2.7 29.7 + - - +
159B GLU* 1.3 74.5 - - + +
161B TYR* 1.3 91.1 + - + +
162B PRO* 3.1 10.4 - - - +
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Residues in contact with TYR 161 (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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122B VAL* 3.8 30.3 + - + +
123B ARG* 4.5 5.7 - - - +
126B SER* 3.7 22.7 + - - -
135B PHE* 4.1 20.2 - + + -
157B ILE* 2.7 29.7 + - + +
158B ARG 3.5 1.6 - - - -
160B GLU* 1.3 108.0 + - + +
162B PRO* 1.3 64.8 - - - +
163B ASP* 3.2 3.1 - - - +
164B ARG* 3.2 56.3 + - + +
197B ASN* 3.6 5.9 + - - -
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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