Contacts of the helix formed by residues 215 - 234 (chain A) in PDB entry 4E2E
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 SER 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A HIS* 6.0 0.3 - - - -
170A PRO* 3.8 26.8 - - - +
212A ASN* 3.1 22.4 + - - +
214A ASP* 1.4 80.2 - - - +
216A TYR* 1.4 64.4 + - - +
217A LYS* 3.2 3.8 - - - +
218A ASP* 3.1 15.5 + - - +
219A SER* 3.1 23.5 + - - -
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Residues in contact with TYR 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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211A LEU* 4.1 31.2 - - + -
212A ASN 2.8 20.3 + - - +
213A GLU* 3.5 27.4 - - + -
214A ASP 5.3 0.4 - - - -
215A SER* 1.4 71.4 - - - +
217A LYS* 1.4 89.5 + - + +
219A SER* 3.4 1.2 + - - -
220A THR* 3.0 40.2 + - + +
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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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215A SER* 3.2 1.5 - - - -
216A TYR* 1.4 112.2 - - + +
218A ASP* 1.3 62.7 + - - +
220A THR* 3.3 8.1 + - - +
221A LEU* 3.1 30.6 + - - +
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Residues in contact with ASP 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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170A PRO* 3.8 20.5 - - + +
214A ASP 4.7 2.6 - - - +
215A SER* 3.1 22.3 + - - +
217A LYS* 1.3 74.9 - - - +
219A SER* 1.3 64.7 + - - +
221A LEU* 3.5 9.5 + - - +
222A ILE* 3.2 33.2 + - + +
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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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168A THR 2.7 25.4 + - - -
170A PRO* 3.7 9.8 - - - +
173A LEU* 3.4 14.8 - - - +
211A LEU* 3.4 28.8 - - - +
212A ASN 5.6 0.5 + - - -
215A SER* 3.1 14.4 + - - -
216A TYR 3.5 3.8 - - - -
218A ASP* 1.3 78.0 - - - +
220A THR* 1.4 56.3 + - - +
222A ILE 3.4 0.3 + - - -
223A MSE 3.0 34.9 + - - +
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Residues in contact with THR 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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208A LEU* 5.9 1.3 - - + -
211A LEU* 4.6 15.9 - - + -
216A TYR* 3.0 24.5 + - + +
217A LYS* 3.3 12.8 + - - -
219A SER* 1.4 72.2 - - - +
221A LEU* 1.3 62.0 + - - +
223A MSE 3.5 19.4 + - + +
224A GLN* 3.1 23.7 + - - +
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Residues in contact with LEU 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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217A LYS 3.1 20.1 + - - +
218A ASP* 3.6 9.9 - - - +
219A SER 3.3 0.2 - - - -
220A THR* 1.3 76.3 + - - +
222A ILE* 1.4 68.5 + - + +
224A GLN* 3.3 8.8 + - - +
225A LEU* 3.1 51.5 + - + +
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Residues in contact with ILE 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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170A PRO* 3.4 37.0 - - + +
173A LEU* 3.5 35.7 - - + +
174A GLY* 3.8 10.3 - - - +
177A LEU* 4.2 18.4 - - + -
218A ASP* 3.2 21.0 + - + +
219A SER 4.1 0.7 - - - +
221A LEU* 1.4 82.5 - - + +
223A MSE 1.4 56.5 + - - +
225A LEU* 3.0 10.8 + - + +
226A LEU* 2.8 36.1 + - + +
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Residues in contact with MSE 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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168A THR* 5.2 1.1 - - - -
173A LEU* 3.8 17.2 - - + +
201A PHE* 3.2 33.7 - - + +
204A ALA* 4.1 16.6 - - + -
205A ILE* 3.5 39.5 - - + +
208A LEU* 3.9 20.4 - - + -
211A LEU* 5.2 3.4 - - - -
219A SER* 3.0 30.7 + - - +
220A THR* 3.6 17.3 - - + +
221A LEU 3.4 0.2 - - - -
222A ILE* 1.4 74.9 - - - +
224A GLN* 1.4 56.0 + - - +
226A LEU* 3.5 7.5 + - + +
227A ARG 3.1 21.1 + - - -
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Residues in contact with GLN 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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201A PHE* 5.3 1.2 - - - -
220A THR 3.1 13.8 + - - +
221A LEU* 3.5 11.2 - - - +
223A MSE 1.4 73.4 - - - +
225A LEU* 1.3 56.7 + - + +
227A ARG* 3.2 16.3 + - - +
228A ASP* 2.8 64.3 + - - +
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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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177A LEU* 3.8 27.4 - - + -
221A LEU* 3.1 40.6 + - + +
222A ILE* 3.0 13.1 + - + +
224A GLN* 1.3 77.1 - - + +
226A LEU* 1.4 55.5 + - - +
228A ASP* 3.4 12.8 + - - +
229A ASN* 3.1 25.8 + - - +
301A EDO 3.1 33.7 + - - +
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Residues in contact with LEU 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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173A LEU* 3.8 36.8 - - + +
176A ALA* 4.1 2.9 - - + -
177A LEU* 3.7 39.0 - - + +
180A SER* 4.5 1.1 - - - +
197A ALA* 3.8 36.5 - - + +
200A ALA* 4.1 14.4 - - + -
201A PHE* 4.4 10.5 - - + +
222A ILE 2.8 16.3 + - - +
223A MSE 3.5 11.4 - - - +
225A LEU* 1.4 72.6 - - - +
227A ARG* 1.4 58.1 - - - +
229A ASN* 3.4 4.9 + - + +
230A LEU* 3.0 33.8 + - - +
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Residues in contact with ARG 227 (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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201A PHE* 4.0 32.7 - - + -
223A MSE 3.1 14.3 + - - +
224A GLN* 3.2 21.7 + - - +
226A LEU* 1.4 71.9 - - - +
228A ASP* 1.4 56.2 + - - +
230A LEU* 3.4 20.0 + - - +
231A THR* 2.8 70.4 + - - +
234A THR* 5.6 1.0 + - - -
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Residues in contact with ASP 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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224A GLN* 2.8 54.8 + - - +
225A LEU* 3.4 20.3 - - - +
227A ARG* 1.4 71.4 - - - +
229A ASN* 1.4 57.4 - - - +
231A THR* 3.2 8.7 + - - -
232A LEU* 3.0 27.0 + - - +
301A EDO 4.4 5.2 - - - +
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Residues in contact with ASN 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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177A LEU* 3.5 17.8 + - - +
180A SER* 5.1 0.2 + - - -
181A VAL* 3.8 13.9 - - - +
197A ALA* 5.7 0.9 - - + -
225A LEU 3.1 9.2 + - - +
226A LEU* 3.7 5.4 - - + +
228A ASP* 1.4 71.7 - - - +
230A LEU* 1.4 56.1 + - - +
232A LEU* 3.3 15.4 + - - +
233A TRP* 2.9 68.2 + - + -
301A EDO 3.2 42.9 + - - -
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Residues in contact with LEU 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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194A CYS* 3.3 42.4 - - + +
197A ALA* 3.8 15.3 - - + +
198A LYS* 3.7 35.2 - - + +
201A PHE* 4.8 7.4 - - + -
226A LEU 3.0 22.2 + - - +
227A ARG* 3.5 25.4 - - - +
229A ASN* 1.4 75.6 - - - +
231A THR* 1.3 50.1 + - - +
233A TRP* 4.5 4.7 - - - -
234A THR* 2.5 45.9 + - + +
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Residues in contact with THR 231 (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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227A ARG* 2.8 38.2 + - - +
228A ASP* 3.2 11.1 + - - -
230A LEU* 1.3 74.1 - - - +
232A LEU* 1.3 64.9 + - - +
234A THR* 3.4 6.8 + - - -
235A SER* 3.3 30.7 + - - -
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Residues in contact with LEU 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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184A TYR* 5.4 0.6 + - + -
228A ASP 3.0 14.1 + - - +
229A ASN* 3.3 15.7 + - - +
231A THR* 1.3 78.1 - - - +
233A TRP* 1.3 80.0 + - + +
235A SER* 3.4 18.4 + - - +
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Residues in contact with TRP 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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180A SER* 3.4 32.5 - - - -
181A VAL* 3.9 11.9 - - + -
184A TYR* 3.5 63.4 + + + -
185A GLU* 5.6 3.4 + - - -
190A PRO* 5.7 2.8 - - + +
193A ALA* 3.7 33.4 - - + -
194A CYS* 3.7 25.7 - - - -
197A ALA* 4.3 6.5 - - + -
229A ASN* 2.9 56.3 + - + +
230A LEU* 4.5 1.8 - - - -
232A LEU* 1.3 92.0 - - + +
234A THR* 1.4 58.2 + - - +
235A SER 3.3 7.0 + - - +
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Residues in contact with THR 234 (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 CYS* 3.7 24.7 - - + -
227A ARG* 5.6 0.9 + - - -
230A LEU* 2.5 31.7 + - + +
231A THR* 3.5 7.4 + - - -
232A LEU 3.4 0.2 - - - -
233A TRP* 1.4 72.9 - - - +
235A SER* 1.4 57.6 + - - +
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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