Contacts of the helix formed by residues 218 - 233 (chain A) in PDB entry 1TE6
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 GLU 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A LEU* 4.1 0.4 - - - -
216A ILE* 3.9 8.4 - - - +
217A LEU* 1.3 84.7 - - + +
219A ASN* 1.3 66.2 + - - +
220A SER* 3.7 17.9 + - - +
221A GLU* 3.1 27.8 + - + +
222A ALA 3.5 3.3 + - - -
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Residues in contact with ASN 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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162A LEU* 3.3 21.9 - - - +
163A ALA* 4.0 4.1 - - - +
164A MET* 2.9 71.4 + - - +
167A PHE* 3.5 11.6 - - + -
217A LEU 4.0 6.0 - - - +
218A GLU* 1.3 70.0 - - - +
220A SER* 1.3 64.7 + - - +
222A ALA* 3.2 13.0 + - - +
223A LEU* 3.2 11.6 + - - +
258A LEU* 4.5 14.6 - - - +
278A LEU* 5.4 0.9 - - + +
282A PHE* 4.1 12.8 - - + -
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Residues in contact with SER 220 (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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218A GLU* 3.7 18.4 + - - +
219A ASN* 1.3 79.6 - - - +
221A GLU* 1.3 58.2 + - - +
223A LEU* 3.3 6.7 + - - +
224A GLU* 2.9 23.4 + - - +
282A PHE* 4.0 25.0 - - - -
286A TYR* 3.3 20.5 + - - -
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Residues in contact with GLU 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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198A LYS* 2.7 27.4 + - - +
199A TYR* 2.4 35.7 + - - +
216A ILE* 4.1 17.5 - - + -
218A GLU* 3.1 25.9 + - + +
220A SER* 1.3 80.1 + - - +
222A ALA* 1.3 59.6 + - - +
224A GLU* 3.2 15.1 + - - +
225A LEU* 2.9 39.1 + - + +
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Residues in contact with ALA 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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152A ILE* 4.2 11.1 - - + +
162A LEU* 4.2 2.0 - - + -
167A PHE* 3.5 34.3 - - + -
216A ILE* 3.8 19.7 - - + +
218A GLU 3.5 2.4 + - - -
219A ASN 3.2 12.2 + - - +
221A GLU* 1.3 79.3 - - - +
223A LEU* 1.3 61.5 + - - +
225A LEU* 3.3 9.0 + - - +
226A VAL* 3.0 29.4 + - - +
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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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167A PHE* 3.8 18.2 - - + -
219A ASN 3.2 13.1 + - - +
220A SER 3.5 6.7 - - - +
222A ALA* 1.3 80.4 - - - +
224A GLU* 1.3 56.3 + - - +
226A VAL* 3.3 5.5 + - + +
227A LYS* 2.9 31.0 + - - +
241A ILE* 3.7 35.1 - - + +
243A MET* 4.2 8.3 - - + -
282A PHE* 3.5 44.0 - - + -
286A TYR* 3.7 29.5 - - + -
288A VAL* 4.1 10.3 - - + -
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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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198A LYS* 5.9 2.2 - - - +
220A SER 2.9 13.7 + - - +
221A GLU* 3.2 23.1 + - - +
223A LEU* 1.3 75.7 - - - +
225A LEU* 1.3 58.3 + - + +
227A LYS* 3.3 6.7 + - - +
228A GLU* 2.9 38.5 + - - +
286A TYR* 3.0 31.5 + - - +
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Residues in contact with LEU 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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152A ILE* 5.3 4.9 - - + -
191A LEU* 3.4 13.7 - - + +
194A VAL* 3.9 14.8 - - + +
195A ILE* 3.5 36.8 - - + -
198A LYS* 4.6 8.3 - - + +
199A TYR* 4.2 17.9 - - + -
214A PRO* 4.7 8.7 - - + -
216A ILE* 4.5 8.3 - - + -
221A GLU* 2.9 47.7 + - + +
222A ALA* 3.5 9.6 - - - +
224A GLU* 1.3 78.5 - - + +
226A VAL* 1.3 61.2 + - + +
228A GLU* 3.4 9.6 + - - +
229A ALA 3.0 18.2 + - - -
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Residues in contact with VAL 226 (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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151A VAL* 4.0 20.4 - - + -
152A ILE* 4.1 14.6 - - + -
167A PHE* 4.3 13.2 - - + +
168A MET 5.1 0.7 - - - +
169A ILE* 3.4 32.5 - - + -
187A VAL* 4.8 1.7 - - + +
191A LEU* 4.3 6.3 - - + -
222A ALA 3.0 18.8 + - - +
223A LEU* 3.7 7.4 - - + +
225A LEU* 1.3 75.3 - - - +
227A LYS* 1.3 59.4 + - - +
229A ALA* 3.2 3.8 + - - +
230A ILE* 2.9 40.3 + - + +
241A ILE* 4.0 15.0 - - + -
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Residues in contact with LYS 227 (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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223A LEU 2.9 17.7 + - - +
224A GLU* 3.7 9.0 - - - +
226A VAL* 1.3 76.8 - - - +
228A GLU* 1.3 63.2 + - - +
230A ILE* 3.3 17.9 + - - +
231A ASP* 3.0 61.0 + - - +
236A THR* 4.0 18.0 - - - +
237A GLU 5.3 0.6 - - - +
239A ILE 5.3 2.2 + - - -
241A ILE* 4.5 2.0 - - + +
285A ASP 5.8 0.4 - - - +
286A TYR* 4.4 12.8 - - + -
287A PRO* 3.9 39.7 - - + +
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Residues in contact with GLU 228 (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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194A VAL* 3.6 30.6 - - + +
198A LYS* 6.0 2.1 + - - +
224A GLU* 2.9 25.9 + - - +
225A LEU* 3.6 10.5 - - - +
227A LYS* 1.3 73.4 - - - +
229A ALA* 1.3 61.6 + - - +
231A ASP* 3.4 6.3 + - + +
232A LYS* 2.9 38.0 + - + +
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Residues in contact with ALA 229 (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 VAL* 3.9 13.0 - - + +
190A THR* 3.8 10.8 - - - +
191A LEU* 3.7 39.9 - - + +
194A VAL* 4.4 4.4 - - + +
225A LEU 3.0 13.9 + - - +
226A VAL* 3.2 8.0 + - - +
228A GLU* 1.3 76.3 - - - +
230A ILE* 1.3 63.6 + - - +
232A LYS* 3.3 2.0 + - - +
233A ALA* 2.9 25.6 + - - +
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Residues in contact with ILE 230 (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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169A ILE* 4.2 1.1 - - + -
187A VAL* 4.0 21.7 - - + +
226A VAL* 2.9 38.2 + - + +
227A LYS* 3.5 16.2 - - - +
229A ALA* 1.3 76.8 - - - +
231A ASP* 1.3 66.2 + - - +
233A ALA* 3.3 4.0 + - - +
234A GLY 3.2 3.8 + - - -
235A TYR* 3.0 49.5 + - - +
236A THR* 3.7 8.1 - - - +
239A ILE* 4.0 38.4 - - + +
241A ILE* 4.1 16.4 - - + -
287A PRO* 5.2 0.2 - - + -
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Residues in contact with ASP 231 (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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227A LYS* 3.0 49.2 + - - +
228A GLU* 3.8 5.7 - - - +
230A ILE* 1.3 75.8 - - - +
232A LYS* 1.3 60.2 + - - +
234A GLY* 2.8 20.8 + - - -
236A THR* 2.5 30.6 + - - +
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Residues in contact with LYS 232 (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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190A THR* 3.5 27.8 + - + +
193A GLY* 5.1 2.0 - - - -
194A VAL* 3.9 23.9 - - + +
197A ASP* 4.5 14.1 + - - -
228A GLU* 2.9 24.5 + - + +
229A ALA 3.7 0.2 - - - +
231A ASP* 1.3 76.2 - - - +
233A ALA* 1.3 59.0 + - - +
234A GLY* 3.1 1.5 + - - -
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Residues in contact with ALA 233 (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 GLU* 4.6 4.3 - - + +
187A VAL* 3.9 15.9 - - + +
190A THR* 3.8 18.6 - - - +
229A ALA 2.9 16.4 + - - +
230A ILE 3.6 5.4 - - - +
232A LYS* 1.3 76.7 - - - +
234A GLY* 1.3 60.9 + - - +
235A TYR* 3.4 32.9 - - + -
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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