Contacts of the helix formed by residues 177 - 191 (chain A) in PDB entry 1TYG
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 THR 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ALA* 3.7 1.4 - - - +
176A SER* 1.3 92.0 - - - +
178A ALA* 1.3 65.2 + - - +
179A GLU* 3.6 23.2 + - - +
180A GLU* 3.3 22.9 + - - +
181A ALA* 3.1 19.1 + - - +
201A VAL* 4.0 6.7 - - - +
214A GLU* 3.4 14.1 - - - -
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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
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177A THR* 1.3 69.3 - - - +
179A GLU* 1.3 74.2 + - + +
181A ALA* 3.0 6.6 + - - +
182A VAL* 2.9 26.3 + - + +
201A VAL* 5.0 0.4 - - - -
214A GLU* 2.9 27.1 + - - +
217A LYS* 3.9 14.1 - - + -
218A ALA* 3.8 34.0 - - + +
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Residues in contact with GLU 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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177A THR* 3.7 13.1 + - - +
178A ALA* 1.3 89.6 + - + +
180A GLU* 1.3 65.5 + - + +
182A VAL* 3.1 9.0 + - - +
183A ARG* 3.0 22.7 + - - +
214A GLU* 3.9 6.2 - - - +
217A LYS* 4.6 9.0 + - - +
221A GLN* 6.3 0.2 - - - +
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Residues in contact with GLU 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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174A GLY 3.9 3.1 - - - +
175A ALA* 3.3 14.4 - - + -
176A SER* 2.8 36.7 + - - -
177A THR* 3.3 27.2 + - - +
179A GLU* 1.3 77.0 - - + +
181A ALA* 1.3 64.1 + - - +
183A ARG* 3.1 18.2 + - - +
184A ILE* 3.1 17.0 + - + +
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Residues in contact with ALA 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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172A THR* 3.2 36.1 + - + +
175A ALA* 3.0 11.7 - - + +
177A THR 3.1 8.4 + - - +
178A ALA* 3.0 14.3 + - - +
180A GLU* 1.3 79.7 - - - +
182A VAL* 1.3 57.6 + - - +
184A ILE* 3.4 4.0 + - - +
185A ALA* 3.2 17.7 + - - +
199A VAL* 5.1 1.1 - - + -
201A VAL* 4.2 6.5 - - + -
218A ALA* 4.0 16.6 - - + -
222A LEU* 5.0 2.1 - - - +
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Residues in contact with VAL 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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178A ALA* 2.9 17.0 + - + +
179A GLU* 3.1 9.4 + - - +
181A ALA* 1.3 70.8 - - - +
183A ARG* 1.3 68.7 + - - +
184A ILE 2.9 1.8 - - - -
185A ALA* 2.8 2.6 + - - +
186A ARG* 2.8 65.9 + - + +
218A ALA* 4.5 7.0 - - + +
221A GLN* 3.9 29.2 - - + +
222A LEU* 3.7 30.3 - - + -
225A GLU* 4.1 4.3 - - - +
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Residues in contact with ARG 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 GLU 3.0 12.5 + - - +
180A GLU* 3.1 10.5 + - - +
182A VAL* 1.3 78.0 - - - +
184A ILE* 1.3 66.2 + - - +
186A ARG* 4.0 13.9 - - - +
187A LEU* 3.1 45.3 + - - +
35B GLU* 2.7 41.8 + - - -
38B LYS* 6.2 3.8 - - - +
40B ILE* 4.7 2.8 - - - +
58B GLU* 4.2 20.0 + - - +
60B VAL* 5.0 5.1 - - - +
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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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144A VAL* 3.7 36.3 - - + +
171A ASN 3.6 20.6 - - - +
172A THR* 3.5 28.3 - - - +
173A ALA 4.2 8.1 - - - +
174A GLY* 4.9 1.6 - - - -
175A ALA* 4.2 10.5 - - + +
180A GLU* 3.1 14.6 + - + +
181A ALA 3.6 6.5 - - - +
182A VAL 2.9 0.8 - - - -
183A ARG* 1.3 86.4 - - - +
185A ALA* 1.3 59.4 + - - +
187A LEU* 3.3 7.1 + - + +
188A ALA* 3.0 27.3 + - + +
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Residues in contact with ALA 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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172A THR* 5.1 0.2 + - - -
181A ALA 3.2 6.6 + - - +
182A VAL 2.8 6.7 + - - +
184A ILE* 1.3 77.6 - - - +
186A ARG* 1.3 63.6 + - - +
188A ALA* 3.4 1.8 + - - +
189A LYS 3.1 18.5 + - - -
197A ILE* 3.7 37.0 - - + +
222A LEU* 3.7 28.5 - - + -
227A PHE* 3.4 18.9 - - + -
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Residues in contact with ARG 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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182A VAL* 2.8 39.1 + - + +
183A ARG* 4.0 10.4 - - - +
185A ALA* 1.3 77.3 - - - +
187A LEU* 1.3 59.8 + - - +
189A LYS* 3.5 2.7 + - - +
190A ALA* 3.1 23.4 + - - +
221A GLN* 3.9 9.1 - - - +
225A GLU* 2.8 41.0 + - - +
227A PHE* 4.3 9.4 - - + -
40B ILE* 3.7 22.3 - - + +
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Residues in contact with LEU 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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144A VAL* 4.8 8.3 - - + -
183A ARG* 3.1 53.6 + - + +
184A ILE* 3.3 11.3 + - + +
185A ALA 3.2 0.2 - - - -
186A ARG* 1.3 73.5 - - - +
188A ALA* 1.3 67.0 + - - +
190A ALA 3.1 10.4 + - - -
191A SER 3.4 0.2 + - - -
33B ILE* 3.4 35.2 - - + +
35B GLU* 4.1 17.5 - - + +
40B ILE* 3.3 30.1 - - + -
60B VAL* 4.3 29.2 - - + -
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Residues in contact with ALA 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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144A VAL* 4.4 7.6 - - + +
170A PRO* 3.7 35.4 - - + -
184A ILE* 3.0 17.2 + - + +
185A ALA* 3.8 7.9 - - - +
187A LEU* 1.3 74.8 - - - +
189A LYS* 1.3 58.9 - - - +
191A SER* 2.8 28.9 + - - -
194A CYS* 3.1 9.2 - - - -
197A ILE* 4.8 1.6 - - + -
62B PHE* 3.8 16.4 - - + -
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Residues in contact with LYS 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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185A ALA 3.1 16.9 + - - +
186A ARG* 3.8 4.3 - - - +
188A ALA* 1.3 75.6 - - - +
190A ALA* 1.3 57.8 + - - +
191A SER 2.9 10.0 + - - -
192A GLY* 3.1 14.9 + - - -
193A LEU 4.6 0.2 + - - -
194A CYS* 3.8 18.1 - - - +
195A ASP* 3.4 34.3 + - - +
225A GLU 4.8 7.0 - - - -
226A GLY 3.9 19.7 + - - -
227A PHE* 3.8 26.1 - - + -
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Residues in contact with ALA 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 ARG 3.1 9.3 + - - +
187A LEU 3.1 9.8 + - - +
189A LYS* 1.3 70.4 - - - +
191A SER* 1.3 57.0 + - - +
192A GLY* 2.9 11.9 + - - -
33B ILE* 3.8 10.0 - - + +
40B ILE* 3.2 35.4 - - + -
41B ILE 5.4 3.9 - - - +
42B GLY* 5.0 11.3 - - - +
43B LYS* 5.2 3.1 + - - +
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Residues in contact with SER 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 LEU 3.4 2.8 + - - -
188A ALA 2.8 20.4 + - - -
189A LYS 2.9 1.2 - - - -
190A ALA* 1.3 77.6 - - - +
192A GLY* 1.3 54.8 + - - +
193A LEU* 3.0 37.1 + - - +
194A CYS* 3.8 1.4 - - - -
31B ILE* 5.2 6.9 - - - +
32B VAL 5.8 1.1 - - - -
33B ILE* 3.9 15.7 - - - -
62B PHE* 3.5 30.9 - - - -
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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