Contacts of the helix formed by residues 172 - 187 (chain A) in PDB entry 1TQN
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 LEU 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A VAL* 4.2 16.4 - - + +
171A THR* 1.3 69.2 - - - +
173A LYS* 1.3 66.8 + - - +
174A ASP 2.9 0.7 + - - -
175A VAL* 3.0 6.8 + - + +
176A PHE* 2.8 41.0 + - + -
315A SER* 3.5 27.4 - - - +
318A MET* 3.7 18.2 - - + -
319A TYR 4.4 0.2 - - - +
465A PHE* 4.5 17.7 - - + -
489A VAL* 3.0 42.9 + - + +
491A LEU* 3.6 26.0 - - + -
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A THR* 3.5 20.4 - - + +
172A LEU* 1.3 76.4 - - - +
174A ASP* 1.3 94.3 + - - +
177A GLY* 2.5 34.0 + - - -
311A SER* 3.6 9.4 + - - +
315A SER* 3.6 11.2 + - - +
488A PRO* 3.9 25.4 - - + -
489A VAL 4.6 2.7 + - - +
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Residues in contact with ASP 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A THR* 3.5 21.8 - - - +
172A LEU 2.9 1.4 + - - -
173A LYS* 1.3 109.4 + - - +
175A VAL* 1.3 66.3 + - + +
177A GLY* 3.6 0.8 - - - -
178A ALA* 2.9 25.6 + - - +
196A LEU* 4.6 12.2 - - + +
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 3.8 25.7 - - + +
159A ASN 5.5 0.2 - - - -
160A LEU* 3.5 31.6 - - + +
163A GLU* 5.1 8.5 - - + +
170A VAL* 3.2 23.1 - - + -
171A THR 3.2 17.9 - - - +
172A LEU* 3.4 16.4 - - + +
174A ASP* 1.3 74.6 - - - +
176A PHE* 1.3 64.0 + - + +
178A ALA* 3.6 5.0 + - - +
179A TYR* 3.1 24.6 + - - +
196A LEU* 4.8 16.7 - - + +
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Residues in contact with PHE 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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156A LEU* 4.3 25.8 - - + -
160A LEU* 6.1 2.5 - - + -
172A LEU* 2.8 36.1 + - + +
175A VAL* 1.3 79.1 - - + +
177A GLY* 1.3 58.8 + - - +
179A TYR* 3.7 4.4 - - + +
180A SER* 2.7 36.7 + - - -
311A SER* 3.7 21.7 - - - +
314A LEU* 3.8 38.8 - - + +
315A SER* 3.5 17.9 - - - -
318A MET* 3.4 37.9 - - + -
455A ALA* 5.5 2.2 - - + -
456A LEU* 5.4 2.2 - - + -
459A VAL* 4.8 9.2 - - + -
465A PHE* 5.5 6.5 - + - -
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Residues in contact with GLY 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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173A LYS 2.5 25.8 + - - -
174A ASP* 3.6 1.3 - - - -
176A PHE* 1.3 73.8 - - - +
178A ALA* 1.3 51.0 + - - +
180A SER* 3.2 2.8 + - - -
181A MET* 2.8 31.6 + - - +
208A LYS* 6.3 0.7 - - - -
307A TYR* 3.4 22.1 - - - -
311A SER* 3.4 13.2 + - - -
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ASP 2.9 15.9 + - - +
175A VAL 3.9 4.0 - - - +
177A GLY* 1.3 74.4 - - - +
179A TYR* 1.3 54.3 + - - +
181A MET* 3.1 6.7 + - - +
182A ASP* 2.7 44.2 + - - +
195A SER* 4.4 2.5 - - - -
196A LEU* 3.6 44.0 - - + +
208A LYS* 6.4 1.8 - - - +
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Residues in contact with TYR 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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149A ILE* 4.3 8.3 + - - +
152A TYR* 3.8 16.8 - - + -
153A GLY* 3.9 25.1 - - - -
156A LEU* 4.0 25.8 - - + +
175A VAL 3.1 15.7 + - - +
176A PHE* 3.3 6.3 + + - +
178A ALA* 1.3 78.1 - - - +
180A SER* 1.3 68.2 + - - +
182A ASP* 3.3 8.0 + - - +
183A VAL* 3.0 43.4 + - + +
310A THR* 5.0 0.7 - - + -
314A LEU* 4.1 20.2 - - + -
451A ASN* 2.6 47.7 + - - -
454A LEU* 4.6 2.9 - - - +
455A ALA* 3.4 25.8 + - + +
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PHE 2.7 22.4 + - - -
177A GLY 3.4 3.6 - - - -
179A TYR* 1.3 79.8 - - - +
181A MET* 1.3 64.6 + - - +
183A VAL* 3.3 4.9 + - - +
184A ILE* 3.1 28.6 + - - +
306A GLY 3.5 6.4 + - - -
307A TYR* 2.7 39.0 + - - -
310A THR* 3.7 10.4 - - - -
311A SER* 4.1 9.6 - - - -
314A LEU* 6.1 0.2 - - - -
451A ASN* 5.3 1.2 + - - -
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Residues in contact with MET 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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177A GLY 2.8 17.6 + - - +
178A ALA* 3.3 10.3 - - - +
180A SER* 1.3 72.4 - - - +
182A ASP* 1.3 58.2 + - - +
184A ILE* 2.8 39.3 + - + +
185A THR* 3.1 27.7 + - + -
195A SER* 2.9 28.9 - - - +
204A VAL* 3.4 15.9 - - + +
207A THR* 3.0 37.2 - - - +
208A LYS* 4.3 20.0 - - + -
303A ILE* 5.1 2.0 - - + -
307A TYR* 4.1 15.6 - - + +
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Residues in contact with ASP 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TYR* 3.3 32.6 - - + +
155A VAL* 4.1 13.7 - - - +
159A ASN* 5.5 0.3 + - - -
178A ALA* 2.7 23.3 + - - +
179A TYR* 3.3 7.8 + - - +
181A MET* 1.3 70.2 - - - +
183A VAL* 1.3 59.8 + - - +
185A THR* 3.1 11.3 + - - -
186A SER* 2.4 30.2 + - - -
193A ILE 3.1 14.4 - - - +
194A ASP* 4.1 1.4 - - - +
195A SER* 2.6 46.5 + - - -
196A LEU* 4.9 1.2 + - - +
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Residues in contact with VAL 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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149A ILE* 3.1 34.8 - - + +
152A TYR* 4.5 9.9 - - + -
179A TYR* 3.0 50.9 + - + +
180A SER 3.8 4.0 - - - +
182A ASP* 1.3 76.1 - - - +
184A ILE* 1.3 54.0 + - + +
186A SER* 4.5 3.1 - - - -
187A THR* 2.6 46.1 + - + +
447A PHE* 4.0 10.1 - - + -
451A ASN* 3.6 20.6 - - - +
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Residues in contact with ILE 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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180A SER* 3.1 19.7 + - - +
181A MET* 2.8 17.7 + - + +
183A VAL* 1.3 76.0 - - + +
185A THR* 1.3 70.3 + - - +
187A THR* 3.1 19.1 + - - -
188A SER* 3.5 10.7 + - - -
302A PHE 5.5 1.3 - - - +
303A ILE* 3.5 43.5 - - + +
306A GLY* 4.1 4.3 - - - -
307A TYR* 3.4 48.9 - - + +
447A PHE* 6.2 1.6 - - + -
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Residues in contact with THR 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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181A MET* 3.1 33.2 + - + +
182A ASP* 3.1 14.6 + - - -
184A ILE* 1.3 75.4 - - + +
186A SER* 1.3 69.0 + - - +
188A SER* 3.0 16.8 + - - +
189A PHE 2.9 17.7 - - - +
191A VAL* 2.9 29.3 + - + +
193A ILE* 4.7 5.8 + - + +
195A SER* 5.1 2.0 + - - +
203A PHE* 3.7 26.5 - - + -
204A VAL* 4.9 4.9 - - + -
207A THR* 4.6 2.9 - - + +
303A ILE* 6.4 0.2 - - - -
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Residues in contact with SER 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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148A ILE* 3.4 32.2 - - - +
152A TYR* 3.0 22.5 + - - -
182A ASP 2.4 25.3 + - - -
183A VAL* 3.9 3.1 - - - -
185A THR* 1.3 83.9 + - - +
187A THR* 1.3 58.0 + - - +
188A SER 3.1 4.7 + - - -
189A PHE 3.8 13.9 + - - +
190A GLY* 4.3 2.4 + - - -
191A VAL 3.5 8.3 + - - +
192A ASN* 3.2 12.7 + - - -
268A ARG* 6.1 0.7 - - - +
270A ASP* 4.1 3.8 - - - +
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Residues in contact with THR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A MET* 3.9 12.6 - - + -
148A ILE* 4.6 11.7 - - + -
149A ILE* 3.6 28.9 - - + -
183A VAL* 2.6 29.1 + - + +
184A ILE* 3.1 9.8 + - - -
186A SER* 1.3 74.7 - - - +
188A SER* 1.3 51.2 + - - +
270A ASP* 3.2 9.2 - - - +
271A PHE* 2.8 54.6 + - - -
447A PHE* 4.0 11.9 - - + -
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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