Contacts of the helix formed by residues 211 - 225 (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 ASP 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A SER 5.6 1.5 - - - +
201A VAL* 2.8 18.0 + - + +
202A ILE 4.9 0.2 - - - -
203A GLY* 3.5 16.6 - - - +
210A PRO* 1.3 68.8 - - - +
212A PRO* 1.3 61.2 - - - +
213A VAL* 2.7 24.8 + - - +
214A GLU* 2.8 31.4 + - + +
215A THR* 2.5 36.1 + - - +
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Residues in contact with PRO 212 (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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210A PRO* 3.6 10.0 - - + +
211A ASP* 1.3 86.0 - - - +
213A VAL* 1.3 75.8 + - + +
215A THR* 3.2 7.2 + - - +
216A LEU* 3.2 28.7 + - - +
234A SER* 6.4 0.7 - - - -
239A LEU* 4.0 32.2 - - + +
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Residues in contact with VAL 213 (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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211A ASP* 2.7 16.0 + - - +
212A PRO* 1.3 82.7 - - + +
214A GLU* 1.3 75.5 + - + +
216A LEU* 3.5 11.6 + - + +
217A LYS* 3.1 35.4 + - - +
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Residues in contact with GLU 214 (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 SER 4.4 4.3 - - - +
177A THR* 3.4 17.1 - - - -
178A ALA* 2.9 31.1 + - - +
179A GLU* 3.9 5.9 - - - +
201A VAL* 3.9 21.5 - - + -
211A ASP* 2.8 34.6 + - + +
213A VAL* 1.3 76.5 - - + +
215A THR* 1.3 59.3 + - - +
217A LYS* 2.9 34.6 + - - +
218A ALA* 2.8 30.7 + - - +
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Residues in contact with THR 215 (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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199A VAL* 4.0 13.6 - - + +
201A VAL* 3.5 35.2 - - + +
210A PRO* 4.3 7.6 - - + +
211A ASP 2.5 27.1 + - - +
212A PRO* 3.2 14.2 + - - +
214A GLU* 1.3 73.8 - - - +
216A LEU* 1.3 59.3 + - - +
219A SER* 2.9 30.9 + - - -
231A PRO* 5.4 2.9 - - - -
232A TYR 3.8 23.0 + - - +
233A THR* 5.7 2.0 + - - -
239A LEU* 5.7 1.2 - - - +
243A LEU* 4.0 10.8 - - - +
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Residues in contact with LEU 216 (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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212A PRO 3.2 18.7 + - - +
213A VAL* 3.5 11.2 - - + +
214A GLU 3.1 0.4 - - - -
215A THR* 1.3 76.4 - - - +
217A LYS* 1.3 62.1 + - - +
219A SER 3.5 0.3 + - - -
220A GLU* 3.3 20.1 + - - +
239A LEU* 3.9 22.4 - - + -
242A LYS* 4.3 16.8 - - + +
243A LEU* 3.5 35.9 - - + +
246A LEU* 3.5 29.1 - - + +
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Residues in contact with LYS 217 (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* 3.9 15.3 - - + -
179A GLU* 4.6 8.6 + - - +
213A VAL* 3.1 19.8 + - - +
214A GLU* 2.9 34.2 + - - +
216A LEU* 1.3 76.5 - - - +
218A ALA* 1.3 62.0 + - - +
219A SER 3.1 1.3 - - - -
220A GLU* 3.4 10.8 + - - +
221A GLN* 3.3 24.6 + - - +
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Residues in contact with ALA 218 (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* 3.8 27.1 - - + +
181A ALA* 4.0 15.3 - - + -
182A VAL* 4.5 5.4 - - + -
199A VAL* 4.0 14.8 - - + -
201A VAL* 4.8 0.7 - - + -
214A GLU 2.8 15.2 + - - +
217A LYS* 1.3 75.6 - - - +
219A SER* 1.3 58.9 + - - +
220A GLU 3.4 0.2 - - - -
221A GLN* 3.9 6.0 - - - +
222A LEU* 2.9 38.3 + - + +
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Residues in contact with SER 219 (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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199A VAL* 4.1 5.1 - - - +
215A THR 2.9 20.1 + - - -
216A LEU 3.6 5.8 - - - -
217A LYS 3.1 0.6 - - - -
218A ALA* 1.3 79.6 - - - +
220A GLU* 1.3 58.1 + - - +
222A LEU* 3.6 1.6 + - - +
223A LEU* 3.0 33.6 + - - +
229A VAL* 3.7 24.5 - - - +
231A PRO* 3.7 17.2 - - - +
243A LEU* 4.0 11.7 - - - -
246A LEU* 4.4 3.4 - - - -
248A VAL* 4.3 7.0 - - - -
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Residues in contact with GLU 220 (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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216A LEU 3.3 7.9 + - - +
217A LYS* 3.4 9.3 + - - +
219A SER* 1.3 77.3 - - - +
221A GLN* 1.3 67.1 + - - +
223A LEU* 3.5 8.3 + - - +
224A GLU* 3.2 27.6 + - - +
246A LEU* 3.8 37.6 - - + +
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Residues in contact with GLN 221 (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* 6.3 0.2 - - - +
182A VAL* 3.9 23.1 - - + +
186A ARG* 3.9 12.3 - - - +
217A LYS* 3.3 16.8 + - - +
218A ALA* 3.9 4.3 - - - +
219A SER 3.4 0.2 - - - -
220A GLU* 1.3 78.4 - - - +
222A LEU* 1.3 66.1 + - - +
223A LEU 3.1 0.3 + - - -
224A GLU* 3.2 9.9 + - + +
225A GLU* 3.0 48.0 + - + +
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Residues in contact with LEU 222 (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 ALA 5.0 2.5 - - - +
182A VAL* 3.7 31.9 - - + -
185A ALA* 3.7 33.0 - - + -
197A ILE* 3.8 8.7 - - + -
199A VAL* 3.5 31.4 - - + -
218A ALA* 2.9 17.9 + - + +
219A SER 4.0 0.7 - - - +
221A GLN* 1.3 75.7 - - - +
223A LEU* 1.3 58.5 + - - +
225A GLU* 2.9 16.6 + - - +
226A GLY 3.1 9.4 + - - -
227A PHE* 3.2 29.7 + - + -
229A VAL* 3.7 16.2 - - + -
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Residues in contact with LEU 223 (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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219A SER 3.0 23.7 + - - +
220A GLU* 3.9 5.6 - - - +
221A GLN 3.1 0.4 - - - -
222A LEU* 1.3 71.5 - - - +
224A GLU* 1.3 55.0 + - - +
226A GLY* 2.7 27.1 + - - +
227A PHE 3.9 4.2 - - - +
229A VAL* 3.5 20.2 - - + -
246A LEU* 3.1 39.9 - - + +
247A GLY 3.2 27.8 - - - +
248A VAL* 3.6 7.0 - - + +
249A HIS* 3.4 22.0 - - + +
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Residues in contact with GLU 224 (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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220A GLU* 3.2 18.4 + - - +
221A GLN* 3.3 13.0 - - + +
223A LEU* 1.3 73.4 - - - +
225A GLU* 1.3 60.9 + - + +
226A GLY* 3.3 1.1 + - - -
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Residues in contact with GLU 225 (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* 4.1 2.9 - - - +
186A ARG* 2.8 48.9 + - - +
189A LYS* 4.8 6.2 - - - -
221A GLN* 3.0 32.9 + - + +
222A LEU* 2.9 11.4 + - - +
223A LEU 2.9 0.2 + - - -
224A GLU* 1.3 80.4 - - + +
226A GLY* 1.3 62.2 + - - +
227A PHE* 3.5 22.1 - - + -
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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