Contacts of the helix formed by residues 177 - 192 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175C ALA* 3.6 1.6 - - - +
176C SER* 1.3 83.2 - - - +
178C ALA* 1.3 53.2 + - - +
179C GLU* 2.9 39.0 - - - +
180C GLU* 2.9 33.9 + - - +
181C ALA* 2.8 32.4 + - - +
201C VAL* 5.1 1.7 - - - +
214C GLU* 3.4 7.6 - - - +
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Residues in contact with ALA 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C THR* 1.3 69.3 - - - +
179C GLU* 1.3 57.3 + - - +
181C ALA* 3.6 10.2 - - - +
182C VAL* 2.8 36.9 + - - +
201C VAL* 5.2 1.1 - - - -
214C GLU* 3.0 33.9 + - + +
217C LYS* 4.7 13.5 - - + +
218C ALA* 3.3 31.6 - - + +
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Residues in contact with GLU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C THR* 3.3 32.5 - - - +
178C ALA* 1.3 73.7 + - - +
180C GLU* 1.3 56.3 + - - +
181C ALA 2.7 4.6 + - - -
182C VAL* 2.6 33.0 + - - +
183C ARG* 3.3 9.2 + - - +
214C GLU* 4.1 7.6 - - - +
217C LYS* 5.6 4.0 + - - +
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Residues in contact with GLU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C GLY 3.1 24.5 - - - +
175C ALA* 3.4 13.3 - - + -
176C SER* 3.5 14.0 + - - -
177C THR* 2.9 26.1 + - - +
179C GLU* 1.3 76.1 - - - +
181C ALA* 1.3 59.3 + - - +
183C ARG* 3.8 7.8 + - - +
184C ILE* 3.3 27.0 + - + +
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Residues in contact with ALA 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C THR* 2.9 39.3 - - + +
175C ALA* 3.3 13.4 - - + +
177C THR 2.8 16.3 + - - +
178C ALA* 3.6 11.7 - - - +
179C GLU 2.7 3.8 + - - -
180C GLU* 1.3 71.2 - - - +
182C VAL* 1.3 65.4 + - - +
183C ARG 3.1 2.1 + - - -
184C ILE* 3.3 1.4 + - - -
185C ALA* 3.2 9.8 + - - +
199C VAL* 6.0 1.8 - - + -
200C GLU 5.3 0.2 - - - +
201C VAL* 4.9 9.9 - - + -
218C ALA* 4.8 8.5 - - + -
222C LEU* 5.4 2.2 - - + -
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Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C ALA 2.8 18.9 + - - +
179C GLU* 2.6 15.9 + - - +
181C ALA* 1.3 70.5 - - - +
183C ARG* 1.3 57.7 + - - +
185C ALA* 3.1 9.4 - - - +
186C ARG* 3.0 56.1 + - - +
218C ALA* 4.9 6.7 - - + +
221C GLN* 4.8 16.8 - - + -
222C LEU* 3.7 28.2 - - + +
225C GLU* 4.9 4.5 - - - +
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Residues in contact with ARG 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C GLU 3.3 4.7 + - - +
180C GLU* 3.8 11.4 - - - +
181C ALA 3.1 0.6 - - - -
182C VAL* 1.3 75.8 - - - +
184C ILE* 1.3 51.7 + - + +
185C ALA 2.6 11.3 + - - -
186C ARG* 2.7 21.8 + - - +
187C LEU* 2.5 40.2 + - + +
40G ILE* 5.4 4.7 - - + -
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Residues in contact with ILE 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ALA 5.6 7.6 - - - -
170C PRO* 5.5 0.9 - - - +
171C ASN 3.3 25.5 - - - +
172C THR* 3.2 37.7 - - + +
173C ALA 4.4 4.3 - - - +
174C GLY* 4.5 3.6 - - - +
175C ALA* 3.8 16.2 - - + +
180C GLU* 3.3 19.7 + - + +
181C ALA 3.3 0.8 + - - -
183C ARG* 1.3 73.1 - - + +
185C ALA* 1.3 55.1 + - - +
187C LEU* 3.8 17.4 - - + +
188C ALA* 3.3 22.0 + - - +
197C ILE* 5.1 1.8 - - - +
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Residues in contact with ALA 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C THR* 4.1 1.3 - - + +
181C ALA 3.2 8.5 + - - +
182C VAL 3.1 11.0 - - - +
183C ARG 2.6 5.3 + - - -
184C ILE* 1.3 74.2 - - - +
186C ARG* 1.3 58.8 + - - +
187C LEU 3.3 0.2 - - - -
188C ALA* 3.0 24.7 + - - +
189C LYS 3.4 1.9 + - - -
197C ILE* 4.4 12.6 - - + -
222C LEU* 3.6 37.7 - - + -
227C PHE* 3.0 22.3 - - + -
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Residues in contact with ARG 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C VAL* 3.0 39.6 + - - +
183C ARG* 2.7 22.8 + - - +
185C ALA* 1.3 68.3 - - - +
187C LEU* 1.4 64.4 - - - +
188C ALA 3.1 1.3 - - - -
189C LYS* 3.4 6.0 + - - +
190C ALA* 3.3 21.7 + - - +
222C LEU* 5.0 0.7 - - + -
225C GLU* 3.5 25.6 - - + +
227C PHE* 4.4 13.0 - - + -
40G ILE* 4.0 20.4 - - + +
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Residues in contact with LEU 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C ARG* 2.5 23.9 + - + +
184C ILE* 3.8 16.4 - - + +
186C ARG* 1.4 71.6 - - - +
188C ALA* 1.3 63.5 + - - +
190C ALA* 3.5 10.2 - - - +
191C SER 3.9 0.2 + - - -
33G ILE* 3.9 34.4 - - + +
34G VAL 5.5 2.7 - - - +
35G GLU* 5.7 5.2 - - + -
40G ILE* 3.8 36.1 - - + +
60G VAL* 4.3 24.5 - - + -
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Residues in contact with ALA 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C PRO* 4.3 17.5 - - + -
184C ILE 3.3 13.8 + - - +
185C ALA* 3.0 18.1 + - - +
186C ARG 3.1 0.2 - - - -
187C LEU* 1.3 79.1 - - - +
189C LYS* 1.3 55.1 + - - +
190C ALA 3.0 0.7 - - - -
191C SER* 2.9 36.5 + - - -
194C CYS* 3.6 22.2 - - - -
197C ILE* 5.2 0.7 - - + -
227C PHE* 5.2 3.4 - - + -
33G ILE* 5.7 1.3 - - - -
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Residues in contact with LYS 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ALA 3.4 6.0 + - - +
186C ARG* 3.4 8.7 + - - +
188C ALA* 1.3 78.9 - - - +
190C ALA* 1.3 57.2 + - - +
191C SER 3.2 0.2 - - - -
192C GLY* 3.0 21.9 + - - +
194C CYS* 4.3 14.8 - - - +
227C PHE* 4.7 12.8 - - + -
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Residues in contact with ALA 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C ARG 3.3 9.9 + - - +
187C LEU 3.5 11.7 - - - +
188C ALA 3.0 0.4 + - - -
189C LYS* 1.3 75.5 - - - +
191C SER* 1.3 62.6 + - - +
192C GLY* 3.5 0.3 + - - -
33G ILE* 4.5 9.6 - - + +
40G ILE* 3.4 33.7 - - + -
42G GLY* 4.1 21.3 - - - -
43G LYS* 4.4 4.2 + - - +
44G GLU* 5.2 5.2 - - - +
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Residues in contact with SER 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C LEU 3.9 1.0 + - - -
188C ALA* 2.9 18.1 + - - -
190C ALA* 1.3 78.3 - - - +
192C GLY* 1.3 64.4 + - - +
193C LEU* 3.4 41.1 + - - +
194C CYS* 4.5 3.5 + - - +
33G ILE* 4.5 21.6 - - - +
43G LYS* 5.6 7.1 - - - +
62G PHE* 5.8 6.3 - - - -
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Residues in contact with GLY 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C LYS* 3.0 21.1 + - - -
190C ALA 4.4 0.4 - - - -
191C SER* 1.3 81.4 + - - +
193C LEU* 1.3 65.1 + - - +
194C CYS 3.8 4.0 - - - -
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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