Contacts of the helix formed by residues 172 - 191 (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 PRO 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B ALA* 3.6 19.4 - - - +
169B ASP 4.3 4.3 - - - +
170B ASP 3.6 8.5 - - - +
171B ASP* 1.3 86.7 - - - +
173B ALA* 1.3 62.8 + - + +
175B ALA* 3.7 6.9 - - + +
176B ALA* 3.1 22.7 + - - +
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B ASP* 3.0 9.1 + - - +
172B PRO* 1.3 79.4 - - + +
174B TYR* 1.3 65.2 + - - +
176B ALA* 3.3 8.8 + - - +
177B THR* 3.2 23.7 + - - -
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Residues in contact with TYR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ARG* 3.5 37.3 + - + +
101B ASN* 3.3 23.0 - - - +
102B ASP* 3.0 27.7 + - - -
105B ILE* 4.3 11.9 - - + -
167B PHE* 3.9 34.8 - + - -
171B ASP* 2.9 25.2 + - - +
173B ALA* 1.3 75.5 - - - +
175B ALA* 1.3 66.1 + - - +
177B THR* 3.1 10.3 + - + -
178B LEU* 3.0 53.2 + - + +
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B SER* 3.5 36.0 - - - +
167B PHE* 4.3 3.1 - - + -
168B ALA* 3.9 17.7 - - + +
171B ASP 2.9 14.1 + - - +
172B PRO* 3.7 6.7 - - + +
174B TYR* 1.3 75.9 - - - +
176B ALA* 1.3 58.2 + - - +
178B LEU* 3.3 4.4 + - - -
179B VAL* 3.0 34.9 + - + +
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A SER* 4.8 12.9 + - - +
172B PRO 3.1 13.7 + - - +
173B ALA* 3.4 11.9 - - - +
174B TYR 3.1 0.2 - - - -
175B ALA* 1.3 75.1 - - - +
177B THR* 1.3 59.8 + - - +
179B VAL* 3.3 7.5 + - - +
180B GLN* 2.9 31.1 + - - +
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Residues in contact with THR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 4.1 20.2 - - + -
173B ALA 3.2 12.7 + - - -
174B TYR* 3.1 12.9 + - + -
176B ALA* 1.3 76.7 - - - +
178B LEU* 1.3 63.5 + - - +
180B GLN* 3.3 13.7 + - - +
181B HIS* 3.0 47.8 + - + +
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASN* 4.0 19.3 - - + +
105B ILE* 4.2 11.2 - - + -
160B MET* 3.6 42.4 - - + +
163B SER* 4.0 15.9 - - - -
164B SER* 3.9 25.6 - - - +
167B PHE* 4.3 2.9 - - + -
174B TYR* 3.0 47.5 + - + +
175B ALA* 3.5 6.7 - - - +
177B THR* 1.3 77.2 - - - +
179B VAL* 1.3 57.0 + - - +
181B HIS* 3.2 4.0 + - - +
182B ALA* 2.9 28.8 + - - +
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Residues in contact with VAL 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A SER* 4.1 23.8 - - - +
160B MET 5.2 0.4 - - - -
161B ALA* 5.3 0.2 - - - -
164B SER* 3.4 23.6 - - - +
175B ALA* 3.0 23.2 + - + +
176B ALA* 3.7 5.8 - - - +
178B LEU* 1.3 74.7 - - - +
180B GLN* 1.3 64.4 + - - +
182B ALA* 3.2 8.4 + - - +
183B LYS* 3.0 33.9 + - + +
223B LEU* 5.0 2.7 - - + -
226B ALA* 4.1 17.0 - - + +
227B THR* 3.7 28.9 - - + -
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Residues in contact with GLN 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PRO* 6.1 5.8 - - + -
146A SER* 5.7 0.4 + - - +
192A TYR* 4.4 20.9 + - + -
176B ALA 2.9 15.7 + - - +
177B THR* 3.5 17.8 + - - +
178B LEU 3.3 0.2 - - - -
179B VAL* 1.3 78.0 - - - +
181B HIS* 1.3 67.0 + - + +
183B LYS* 3.5 9.1 + - - +
184B GLN* 3.3 42.1 + - + +
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Residues in contact with HIS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ILE* 4.0 32.6 - - + +
108B HIS* 3.0 43.3 + + - +
160B MET* 3.7 22.1 - - + +
177B THR* 3.0 40.3 + - + +
178B LEU 3.5 7.4 - - - +
180B GLN* 1.3 79.9 - - + +
182B ALA* 1.3 61.5 + - - +
184B GLN* 3.3 12.6 + - - +
185B LEU* 2.9 35.3 + - + +
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Residues in contact with ALA 182 (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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157B ALA* 3.3 41.4 - - - +
160B MET* 4.1 4.0 - - + -
161B ALA* 3.9 10.1 - - + +
178B LEU 2.9 16.2 + - - +
179B VAL* 3.2 7.6 + - - +
181B HIS* 1.3 78.0 - - - +
183B LYS* 1.3 56.1 + - - +
185B LEU* 4.5 0.7 - - - -
186B TYR* 3.0 26.3 + - - +
223B LEU* 3.8 16.9 - - + +
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A PRO 3.4 25.4 + - - -
146A SER* 4.0 9.3 + - - +
148A PRO* 4.0 15.0 - - - +
192A TYR* 5.7 5.3 - - - +
193A ARG 5.7 1.0 + - - -
179B VAL* 3.0 21.2 + - + +
180B GLN* 3.9 8.1 - - - +
181B HIS 3.2 0.2 - - - -
182B ALA* 1.3 74.0 - - - +
184B GLN* 1.3 64.9 + - + +
186B TYR* 3.3 2.3 + - - +
187B THR* 2.9 29.0 + - - -
223B LEU* 4.0 11.2 - - + -
227B THR* 4.2 18.6 - - + -
229B ASP* 5.0 4.9 + - - -
232B TYR* 3.3 28.6 + - + +
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Residues in contact with GLN 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B HIS* 3.2 25.4 + - + -
111B PRO* 3.8 33.7 - - + +
112B ASN* 4.7 1.9 - - - +
180B GLN* 3.3 36.3 + - + +
181B HIS* 3.3 10.8 + - - +
183B LYS* 1.3 75.6 - - + +
185B LEU* 1.3 63.5 + - - +
187B THR* 3.2 8.1 + - - -
188B PHE* 3.0 23.6 + - - +
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Residues in contact with LEU 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE 5.7 0.2 - - - +
108B HIS* 3.5 39.3 - - + +
114B LEU* 4.0 28.3 - - + -
153B ALA* 3.9 19.9 - - + +
156B THR* 3.7 30.1 - - + -
157B ALA* 3.9 7.4 - - + +
160B MET* 3.9 15.9 - - - -
181B HIS 2.9 19.1 + - - +
182B ALA 3.9 4.0 - - - +
184B GLN* 1.3 77.6 - - - +
186B TYR* 1.3 56.6 + - - +
188B PHE* 3.4 12.2 + - + +
189B ALA* 3.0 27.7 + - - +
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Residues in contact with TYR 186 (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 ALA* 4.5 11.2 - - + -
157B ALA* 3.9 6.0 - - + +
182B ALA 3.0 9.1 + - - +
183B LYS 3.8 2.5 - - - +
185B LEU* 1.3 73.8 - - - +
187B THR* 1.3 63.8 + - - +
189B ALA* 3.2 4.1 + - - +
190B ASP* 2.8 32.0 + - + +
215B GLU 4.5 0.9 - - - -
216B LEU* 2.8 45.5 + - + +
219B GLY* 3.9 17.3 - - - -
220B ALA* 3.6 20.4 - - + -
223B LEU* 3.4 29.4 - - + -
232B TYR* 4.2 15.0 - + + -
235B LYS* 3.4 39.3 - - + +
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Residues in contact with THR 187 (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 ASN* 5.7 1.8 - - - +
183B LYS 2.9 15.5 + - - -
184B GLN* 3.5 10.0 - - - -
186B TYR* 1.3 79.3 - - - +
188B PHE* 1.3 54.7 - - - +
190B ASP* 3.2 4.9 + - - +
191B THR* 2.8 51.2 + - - +
232B TYR* 5.4 1.9 + - - -
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Residues in contact with PHE 188 (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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111B PRO 4.0 4.0 - - - +
112B ASN* 3.4 40.6 + - + +
114B LEU* 4.8 3.1 - - + -
143B VAL* 3.9 22.9 - - + -
144B ASP* 3.6 45.1 - - - -
145B PRO 3.8 2.7 - - - -
148B PRO* 4.2 8.1 - - + -
149B GLY 4.4 4.9 - - - -
153B ALA* 3.7 26.2 - - + -
184B GLN 3.0 11.9 + - - +
185B LEU* 3.4 16.4 - - + +
187B THR* 1.3 76.8 - - - +
189B ALA* 1.3 55.5 + - - +
191B THR* 4.7 0.7 - - - -
192B TYR* 2.9 55.3 + + + +
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Residues in contact with ALA 189 (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 54.8 + - - +
153B ALA* 3.8 6.3 - - + -
154B ALA* 3.7 20.2 - - + +
185B LEU 3.0 16.4 + - - +
186B TYR* 3.6 5.4 - - + +
188B PHE* 1.3 79.6 - - - +
190B ASP* 1.3 59.7 + - - +
192B TYR 3.5 5.1 - - - +
193B ARG* 4.2 3.3 - - - +
216B LEU* 4.3 6.8 - - + +
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Residues in contact with ASP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B TYR* 2.8 28.2 + - + +
187B THR* 3.8 5.2 - - - +
189B ALA* 1.3 76.7 - - - +
191B THR* 1.3 63.3 + - - +
193B ARG* 2.7 53.8 + - - +
216B LEU* 4.2 8.1 - - + +
235B LYS* 2.8 32.7 + - - -
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Residues in contact with THR 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B THR* 2.8 40.1 + - - +
190B ASP* 1.3 78.1 + - - +
192B TYR* 1.3 90.9 + - + +
193B ARG* 3.7 5.2 + - - +
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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
------------------------------------------------------------
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