Contacts of the helix formed by residues 172 - 191 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ALA 3.5 19.2 - - - +
169A ASP 4.3 4.0 - - - +
170A ASP 3.5 9.2 - - - +
171A ASP* 1.3 86.7 - - - +
173A ALA* 1.3 62.5 + - + +
175A ALA* 3.5 6.0 + - + +
176A ALA* 3.1 23.7 + - - +
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Residues in contact with ALA 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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171A ASP* 3.1 8.9 - - - +
172A PRO* 1.3 82.1 - - + +
174A TYR* 1.3 62.7 + - - +
176A ALA* 3.3 8.7 + - - +
177A THR* 3.2 24.8 + - - -
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Residues in contact with TYR 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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98A ARG* 3.4 36.0 + - + +
101A ASN* 3.3 23.1 - - + +
102A ASP* 3.0 28.9 + - - -
105A ILE* 4.1 17.0 - - + -
167A PHE* 3.8 41.7 - + - -
171A ASP* 2.9 24.8 + - - +
173A ALA* 1.3 75.3 - - - +
175A ALA* 1.3 67.6 + - - +
177A THR* 3.1 10.1 + - + -
178A LEU* 3.0 38.9 + - + +
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Residues in contact with ALA 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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164A SER* 3.5 36.6 - - - +
167A PHE* 4.2 3.1 - - - -
168A ALA* 3.9 17.9 - - + +
171A ASP 2.9 14.1 + - - +
172A PRO* 3.7 6.7 - - + +
174A TYR* 1.3 77.8 - - - +
176A ALA* 1.3 61.8 + - - +
178A LEU* 3.3 3.9 + - - -
179A VAL* 3.0 28.7 + - + +
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Residues in contact with ALA 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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172A PRO 3.1 13.9 + - - +
173A ALA* 3.4 11.7 - - - +
175A ALA* 1.3 74.9 - - - +
177A THR* 1.3 64.9 + - - +
179A VAL* 3.4 7.0 + - - +
180A GLN* 3.0 25.9 + - - +
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Residues in contact with THR 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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105A ILE* 4.4 17.7 - - + -
173A ALA 3.2 12.4 + - - -
174A TYR* 3.1 15.2 + - + -
176A ALA* 1.3 77.7 - - - +
178A LEU* 1.3 66.0 + - - +
180A GLN* 3.4 13.9 + - - +
181A HIS* 3.1 47.4 + - + +
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Residues in contact with LEU 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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101A ASN* 4.0 18.6 - - + +
105A ILE* 4.1 16.2 - - + -
160A MET* 3.6 46.0 - - + +
163A SER* 4.0 14.1 - - - -
164A SER* 3.9 25.1 - - - +
167A PHE* 4.3 2.0 - - + -
174A TYR* 3.0 42.9 + - + +
175A ALA* 3.5 6.5 - - - +
177A THR* 1.3 77.0 - - - +
179A VAL* 1.3 56.5 + - - +
181A HIS* 3.2 4.0 + - - +
182A ALA* 2.9 28.9 + - - +
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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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160A MET 5.2 0.7 - - - -
161A ALA* 5.2 0.7 - - - +
164A SER* 3.4 23.1 - - - +
175A ALA* 3.0 18.3 + - + +
176A ALA* 3.4 7.4 + - - +
178A LEU* 1.3 76.0 - - - +
180A GLN* 1.3 62.9 + - - +
182A ALA* 3.2 7.3 + - - +
183A LYS* 2.9 38.1 + - + +
223A LEU* 5.0 2.5 - - + -
226A ALA* 4.1 17.5 - - + +
227A THR* 3.7 28.5 - - + -
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Residues in contact with GLN 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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176A ALA 3.0 15.3 + - - +
177A THR* 3.6 17.3 + - - +
179A VAL* 1.3 77.6 - - - +
181A HIS* 1.3 66.3 + - + +
183A LYS* 3.5 12.1 + - + +
184A GLN* 3.3 45.9 + - + +
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Residues in contact with HIS 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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105A ILE* 3.8 33.2 - - + +
108A HIS* 3.0 44.5 + + - +
160A MET* 3.7 22.7 - - + +
177A THR* 3.1 39.2 + - + +
178A LEU 3.5 7.0 - - - +
180A GLN* 1.3 79.4 - - + +
182A ALA* 1.3 62.4 + - - +
184A GLN* 3.2 12.2 + - - +
185A LEU* 2.9 34.7 + - + +
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Residues in contact with ALA 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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157A ALA* 3.3 40.9 - - - +
160A MET* 4.1 4.0 - - + -
161A ALA* 3.9 10.1 - - + +
178A LEU 2.9 17.6 + - - +
179A VAL* 3.5 7.0 - - - +
181A HIS* 1.3 77.8 - - - +
183A LYS* 1.3 56.1 + - - +
185A LEU* 4.5 0.4 - - - -
186A TYR* 3.0 27.4 + - - +
223A LEU* 3.8 17.4 - - + +
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Residues in contact with LYS 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* 2.9 28.1 + - + +
180A GLN* 3.6 11.6 - - + +
181A HIS 3.2 0.2 - - - -
182A ALA* 1.3 73.8 - - - +
184A GLN* 1.3 66.6 + - + +
186A TYR* 3.3 3.1 + - - +
187A THR* 3.0 27.9 + - - -
223A LEU* 4.2 11.0 - - + -
227A THR* 3.9 24.1 - - - +
229A ASP* 5.8 2.2 - - - -
232A TYR* 3.5 27.0 + - - +
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Residues in contact with GLN 184 (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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108A HIS* 3.2 26.7 + - + -
111A PRO* 3.8 33.1 - - + +
112A ASN* 4.7 1.6 - - - +
180A GLN* 3.3 36.0 + - + +
181A HIS* 3.2 10.5 + - - +
183A LYS* 1.3 76.2 - - + +
185A LEU* 1.3 59.3 + - - +
187A THR* 3.2 8.1 + - - -
188A PHE* 2.9 29.1 + - - +
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Residues in contact with LEU 185 (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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104A PHE 5.7 0.2 - - - +
108A HIS* 3.5 38.8 - - + +
114A LEU* 4.0 27.8 - - + -
153A ALA* 3.9 20.3 - - + +
156A THR* 3.7 30.7 - - + -
157A ALA* 3.9 7.0 - - + +
160A MET* 4.0 15.9 - - - -
181A HIS 2.9 19.1 + - - +
182A ALA 3.9 3.8 - - - +
184A GLN* 1.3 78.1 - - - +
186A TYR* 1.3 55.7 + - - +
188A PHE* 3.4 10.7 + - + +
189A ALA* 3.0 28.4 + - - +
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Residues in contact with TYR 186 (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 ALA* 4.5 11.7 - - + -
157A ALA* 3.9 6.2 - - + +
182A ALA 3.0 9.3 + - - +
183A LYS 3.8 2.9 - - - +
184A GLN 3.3 0.2 - - - -
185A LEU* 1.3 74.1 - - - +
187A THR* 1.3 63.7 + - - +
189A ALA* 3.2 4.9 + - - +
190A ASP* 2.8 32.7 + - + +
215A GLU 4.5 0.9 - - - -
216A LEU* 2.8 45.5 + - + +
219A GLY* 3.9 17.0 - - - -
220A ALA* 3.6 21.3 - - + +
223A LEU* 3.4 24.5 - - + -
232A TYR* 4.2 21.5 - + + -
235A LYS* 3.4 39.8 - - + +
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Residues in contact with THR 187 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ASN* 5.7 1.8 - - - +
183A LYS* 3.0 16.2 + - - +
184A GLN* 3.5 10.0 - - - -
186A TYR* 1.3 77.5 - - - +
188A PHE* 1.3 55.1 + - - +
190A ASP* 3.2 5.2 + - + +
191A THR* 2.8 52.3 + - - +
232A TYR* 5.4 1.7 + - - -
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Residues in contact with PHE 188 (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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111A PRO 4.1 4.9 - - - +
112A ASN* 3.5 40.6 + - + +
114A LEU* 4.8 3.6 - - + -
143A VAL* 3.9 22.0 - - + -
144A ASP* 3.6 44.4 - - - -
145A PRO 3.8 3.4 - - - -
148A PRO* 4.2 8.7 - - + -
149A GLY 4.3 4.0 - - - -
153A ALA* 3.7 26.0 - - + -
184A GLN 2.9 11.1 + - - +
185A LEU* 3.4 15.3 - - + +
186A TYR 3.2 0.2 - - - -
187A THR* 1.3 76.3 - - - +
189A ALA* 1.3 55.7 + - - +
191A THR* 4.7 0.7 - - - -
192A TYR* 2.9 55.3 + + + +
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Residues in contact with ALA 189 (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 SER* 2.9 57.7 + - - +
153A ALA* 3.8 4.7 - - + -
154A ALA* 3.7 19.1 - - + +
185A LEU 3.0 17.4 + - - +
186A TYR* 3.6 5.4 - - - +
188A PHE* 1.3 78.9 - - - +
190A ASP* 1.3 60.0 + - - +
192A TYR 3.6 4.5 - - - +
193A ARG* 4.3 3.1 + - - +
216A LEU* 4.3 7.4 - - + +
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Residues in contact with ASP 190 (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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186A TYR* 2.8 32.0 + - + +
187A THR* 3.8 5.2 - - - +
189A ALA* 1.3 72.9 - - - +
191A THR* 1.3 62.9 + - - +
193A ARG* 2.7 53.1 + - - +
216A LEU* 4.3 8.6 - - + +
235A LYS* 2.8 32.1 + - - -
239A GLU* 4.1 0.3 - - - +
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Residues in contact with THR 191 (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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187A THR* 2.8 39.5 + - - +
188A PHE* 4.7 0.2 - - - -
190A ASP* 1.3 77.2 + - - +
192A TYR* 1.3 92.8 + - + +
193A ARG* 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