Contacts of the helix formed by residues 150 - 167 (chain B) in PDB entry 1TF4
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 SER 150 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B GLY* 1.3 73.1 - - - +
151B ASP* 1.3 56.0 + - - -
154B ALA* 3.0 34.5 + - - +
189B ALA* 3.0 35.7 + - - +
192B TYR 3.0 6.6 + - - -
193B ARG* 3.1 4.2 - - - -
194B GLY 2.8 31.4 + - - -
212B TYR* 3.7 23.3 - - - -
215B GLU* 5.0 0.2 - - - -
216B LEU* 5.0 3.9 - - - +
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Residues in contact with ASP 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 3.9 8.7 - - + -
149B GLY 3.7 1.2 - - - -
150B SER* 1.3 73.9 - - - +
152B VAL* 1.3 65.7 + - - -
155B GLU* 3.0 29.6 + - - +
194B GLY 4.4 0.2 - - - -
195B VAL* 3.5 9.7 - - - +
196B TYR* 3.0 40.5 + - - +
208B SER* 2.6 35.2 + - - +
212B TYR* 3.6 10.5 - - + +
215B GLU* 3.4 32.2 - - - +
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY* 4.0 6.1 - - - +
64B PHE* 3.8 41.7 - - + +
114B LEU* 4.4 0.2 - - - -
116B VAL* 3.6 35.2 - - + -
143B VAL* 4.4 4.0 - - + -
149B GLY* 3.5 9.0 - - - +
151B ASP* 1.3 80.9 + - - +
153B ALA* 1.3 61.4 + - - +
155B GLU* 3.4 1.4 + - + +
156B THR* 2.8 38.4 + - - +
196B TYR* 3.5 33.9 - - + -
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 3.8 15.7 - - + -
149B GLY 3.0 19.5 + - - +
152B VAL* 1.3 74.6 - - - +
154B ALA* 1.3 61.1 + - - +
156B THR* 3.3 3.1 + - - -
157B ALA* 2.9 28.1 + - - +
185B LEU* 3.9 11.6 - - + +
188B PHE* 3.7 31.9 - - + -
189B ALA* 3.8 12.3 - - + -
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Residues in contact with ALA 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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150B SER 3.0 20.9 + - - +
153B ALA* 1.3 75.8 - - - +
155B GLU* 1.3 58.1 + - - +
157B ALA* 3.3 8.4 + - - +
158B ALA* 2.9 27.7 + - - +
186B TYR* 4.5 11.9 - - + -
189B ALA* 3.7 13.6 - - + +
215B GLU* 3.4 33.0 - - + +
216B LEU* 4.5 3.6 - - + +
218B TRP* 5.7 0.2 - - - -
219B GLY* 4.0 4.9 - - - -
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PHE* 4.0 15.9 - - + +
67B ALA* 3.6 5.2 - - + -
68B PHE* 3.5 31.1 - - - +
71B THR* 2.8 28.8 + - - -
151B ASP 3.0 19.2 + - - +
152B VAL 3.7 4.3 - - - +
154B ALA* 1.3 75.3 - - - +
156B THR* 1.3 59.3 + - - +
158B ALA* 3.1 3.4 + - - -
159B ALA* 2.9 26.0 + - - +
215B GLU* 4.2 3.7 - - + +
218B TRP* 3.0 23.3 + - - -
263B LYS* 2.8 37.5 + - - +
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Residues in contact with THR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY 4.7 1.0 + - - -
67B ALA* 3.7 16.7 - - - +
104B PHE* 3.9 37.9 - - + -
114B LEU* 3.7 19.6 - - + +
152B VAL* 2.8 26.6 + - - +
153B ALA 3.7 4.5 - - - -
155B GLU* 1.3 76.5 - - - +
157B ALA* 1.3 62.1 + - - +
159B ALA* 3.3 2.6 + - - +
160B MET* 3.0 31.4 + - - +
185B LEU* 3.7 20.4 - - + -
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Residues in contact with ALA 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ALA 2.9 18.7 + - - +
154B ALA* 3.4 7.6 - - - +
156B THR* 1.3 77.6 - - - +
158B ALA* 1.3 57.6 + - - +
160B MET 3.3 1.0 + - - -
161B ALA* 2.8 32.0 + - - +
182B ALA* 3.3 36.4 - - + +
185B LEU* 3.9 4.9 - - + +
186B TYR* 3.9 21.3 - - + +
219B GLY* 5.6 0.2 - - - -
223B LEU* 4.9 3.4 - - + -
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 3.8 4.2 - - - +
154B ALA 2.9 14.0 + - - +
155B GLU 3.4 8.1 - - - +
157B ALA* 1.3 76.7 - - - +
159B ALA* 1.3 56.5 + - - +
161B ALA* 3.7 1.0 - - - +
162B ALA* 2.8 34.0 + - - +
218B TRP* 3.8 30.5 - - + +
219B GLY* 4.0 10.0 - - - -
222B TRP* 3.9 22.1 - - + +
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Residues in contact with ALA 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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67B ALA 3.5 15.0 - - - +
70B ALA* 3.8 14.2 - - + +
71B THR* 3.2 22.8 + - - +
101B ASN* 4.3 1.3 - - - -
104B PHE* 4.0 14.1 - - + -
155B GLU 2.9 10.0 + - - +
156B THR* 3.5 10.1 - - - +
157B ALA 3.3 0.2 - - - -
158B ALA* 1.3 78.4 - - - +
160B MET* 1.3 54.4 + - - +
162B ALA* 4.0 1.0 - - - +
163B SER* 2.7 36.8 + - - -
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Residues in contact with MET 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASN* 3.7 17.3 - - - +
104B PHE* 3.9 28.9 - - + -
105B ILE* 3.7 28.7 - - + +
108B HIS* 6.0 0.2 - - - -
156B THR* 3.0 12.9 + - - +
157B ALA 3.8 3.1 - - - +
159B ALA* 1.3 73.0 - - - +
161B ALA* 1.3 65.8 + - - +
163B SER* 3.5 0.5 + - - -
164B SER* 3.0 24.1 + - - -
178B LEU* 3.6 35.4 - - + +
181B HIS* 3.7 32.8 - - + -
182B ALA* 4.1 4.3 - - + -
185B LEU* 3.9 21.3 - - - -
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ALA 2.8 17.8 + - - +
158B ALA* 3.7 3.4 - - - +
160B MET* 1.3 76.5 - - - +
162B ALA* 1.3 62.2 + - - +
164B SER* 2.5 27.3 + - - -
165B ILE* 3.6 2.8 + - - +
179B VAL* 5.3 1.8 - - - -
182B ALA* 3.9 4.6 - - - +
222B TRP* 3.7 29.4 - - + +
223B LEU* 4.0 17.7 - - + +
226B ALA* 3.4 15.9 - - + +
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Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 4.2 12.1 - - + +
74B ALA* 3.8 17.0 - - + -
78B ILE* 3.6 10.8 - - + +
158B ALA 2.8 22.4 + - - +
159B ALA 4.0 1.8 - - - +
161B ALA* 1.3 74.4 - - - +
163B SER* 1.3 59.5 + - - +
165B ILE* 3.4 19.5 + - - +
166B VAL* 3.7 5.0 + - - +
222B TRP* 3.8 33.5 - - + +
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Residues in contact with SER 163 (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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70B ALA* 4.7 2.4 + - - +
74B ALA* 4.2 9.7 - - - +
97B LEU* 4.1 13.9 - - - +
101B ASN* 3.1 33.4 + - - -
159B ALA 2.7 22.7 + - - -
160B MET 3.9 2.5 - - - -
162B ALA* 1.3 74.9 - - - +
164B SER* 1.3 65.8 + - - +
166B VAL* 3.0 15.3 + - - +
167B PHE* 3.1 26.0 + - - -
178B LEU* 4.0 5.6 - - - -
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Residues in contact with SER 164 (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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160B MET 3.0 13.4 + - - -
161B ALA 2.5 21.1 + - - -
163B SER* 1.3 76.5 - - - +
165B ILE* 1.3 53.9 + - - +
167B PHE* 3.2 1.0 + - - +
168B ALA* 2.7 35.7 + - - +
175B ALA* 3.5 20.8 - - - +
178B LEU* 3.9 10.9 - - - +
179B VAL* 3.4 22.8 - - - +
226B ALA* 3.4 17.2 + - - +
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Residues in contact with ILE 165 (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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78B ILE* 4.0 35.4 - - + -
161B ALA 3.7 14.4 - - - +
162B ALA* 3.5 11.0 - - - +
163B SER 3.2 0.4 - - - -
164B SER* 1.3 81.9 + - - +
166B VAL* 1.3 60.5 + - - +
167B PHE 3.5 0.2 + - - -
168B ALA* 3.5 18.3 - - + +
169B ASP* 4.9 1.7 + - - +
222B TRP* 4.4 4.5 - - + +
225B LYS* 3.7 37.9 - - + +
226B ALA* 3.9 15.0 - - + +
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA* 4.0 29.8 - - + +
77B ALA* 4.3 8.5 - - + -
78B ILE* 4.1 9.4 - - + +
90B MET* 5.1 3.1 - - + -
93B LEU* 4.3 15.5 - - + -
94B LYS* 3.9 38.1 + - + -
97B LEU* 4.3 9.6 - - + -
162B ALA 3.7 14.6 - - - +
163B SER* 3.0 9.3 + - - +
165B ILE* 1.3 78.6 - - - +
167B PHE* 1.3 63.1 + - + +
169B ASP* 4.9 2.3 + - - +
170B ASP* 4.5 2.3 - - - +
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Residues in contact with PHE 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS* 3.3 49.4 - - + -
97B LEU* 4.0 22.9 - - + -
98B ARG* 3.7 41.3 - - + -
101B ASN* 4.9 0.2 - - - -
163B SER* 3.1 31.9 + - - +
164B SER 4.1 2.7 - - - +
166B VAL* 1.3 78.4 - - + +
168B ALA* 1.3 66.8 + - - +
169B ASP 3.3 2.2 - - - -
170B ASP* 2.8 14.8 + - + -
171B ASP* 2.8 28.1 + - + +
174B TYR* 3.9 28.7 - + + -
175B ALA* 4.3 9.6 - - + -
178B LEU* 4.3 2.7 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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