Contacts of the helix formed by residues 217 - 227 (chain B) in PDB entry 3EWS
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 217 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B SER 3.6 6.3 - - - +
170B PRO 4.0 3.4 - - - +
171B THR* 3.5 40.4 - - - +
172B TYR* 3.7 8.1 - - + +
197B ALA 3.2 8.4 + - - -
198B VAL* 4.2 9.6 - - + +
199B ARG* 2.8 33.1 + - - -
216B GLY* 1.3 75.1 - - - -
218B PRO* 1.3 75.2 - - - -
219B GLY 2.8 2.9 + - - -
220B THR* 2.9 15.6 + - - -
221B VAL* 3.1 9.8 + - - -
253B HIS* 5.0 1.6 - - - -
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Residues in contact with PRO 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LEU* 4.2 8.3 - - + -
169B SER 3.5 14.6 - - - +
216B GLY 3.9 2.6 - - - +
217B THR* 1.3 85.8 - - - +
219B GLY* 1.3 55.1 + - - +
221B VAL* 4.4 2.2 - - + -
222B LEU* 2.9 32.0 + - - +
247B MET* 3.7 21.1 - - - -
253B HIS* 3.6 30.7 - - + +
256B GLN* 3.8 23.0 - - + +
257B SER* 4.1 9.9 - - - +
260B ILE* 3.4 17.9 - - + +
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Residues in contact with GLY 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ARG* 3.2 20.5 - - - +
217B THR 2.8 6.5 + - - -
218B PRO* 1.3 75.5 - - - +
220B THR* 1.3 55.2 + - - -
222B LEU* 3.0 23.4 - - - +
223B ASP* 3.3 11.9 - - - +
253B HIS* 4.9 0.6 - - - -
256B GLN* 3.8 23.0 + - - -
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Residues in contact with THR 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B ALA 3.2 29.8 - - - -
198B VAL* 3.7 8.9 - - - +
199B ARG* 3.0 38.7 + - - +
201B ASN 5.0 2.7 - - - +
217B THR* 2.9 5.9 + - - -
219B GLY* 1.3 69.5 - - - -
221B VAL* 1.3 66.2 + - - +
222B LEU 3.0 2.1 + - - -
223B ASP* 3.2 14.1 + - + +
224B TRP* 2.9 47.8 - - + +
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Residues in contact with VAL 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 3.9 30.7 - - + -
168B LEU* 3.7 27.8 - - + -
197B ALA* 3.6 24.9 - - + -
214B VAL* 4.8 0.9 - - + -
216B GLY* 3.7 20.0 - - - +
217B THR 3.1 9.2 + - - +
220B THR* 1.3 76.3 - - - +
222B LEU* 1.3 64.7 + - - +
224B TRP* 3.3 11.8 + - + +
225B CYS* 3.5 17.1 + - - -
231B ILE* 5.8 0.7 - - + -
260B ILE* 3.5 21.0 - - + +
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Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B PRO 2.9 12.1 + - - +
219B GLY 3.0 15.0 - - - +
221B VAL* 1.3 80.1 - - - +
223B ASP* 1.3 64.0 + - - +
225B CYS* 3.3 8.7 + - - +
226B SER* 3.2 19.8 + - - +
256B GLN* 3.6 32.5 - - + +
259B ARG* 3.3 51.1 - - + +
260B ILE* 3.7 24.7 - - + +
263B MET* 4.6 9.7 - - + +
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Residues in contact with ASP 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B GLY 3.3 16.7 - - - +
220B THR* 3.2 12.0 + - + +
222B LEU* 1.3 79.1 - - - +
224B TRP* 1.3 68.1 + - + +
225B CYS 3.1 0.4 - - - -
226B SER* 3.1 16.6 + - - -
227B LYS* 3.1 21.6 + - + +
230B PHE* 4.2 3.1 - - + -
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Residues in contact with TRP 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A GLU* 5.1 1.6 - - + -
195B ALA* 4.5 14.4 - - + -
196B TYR 3.9 7.9 - - - -
197B ALA* 3.6 35.2 - - + -
201B ASN* 3.9 21.8 + - + -
203B LEU* 3.5 43.0 - - + +
209B ILE* 3.5 25.8 - - + -
214B VAL* 4.6 5.8 - - + -
220B THR* 2.9 37.0 + - + +
221B VAL* 3.7 10.1 - - - +
222B LEU 3.2 0.8 - - - -
223B ASP* 1.3 82.5 - - + +
225B CYS* 1.3 58.7 + - - +
227B LYS 4.9 0.4 - - - -
230B PHE* 3.4 15.3 + + + +
231B ILE* 3.1 50.9 + - + +
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Residues in contact with CYS 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B LEU* 4.4 12.6 - - - -
221B VAL* 3.6 23.6 - - - +
222B LEU* 3.3 5.9 + - - +
223B ASP 3.1 0.8 - - - -
224B TRP* 1.3 79.9 - - - +
226B SER* 1.3 62.9 + - - +
227B LYS 5.2 0.7 - - - -
231B ILE* 4.1 33.0 - - - +
233B PRO* 4.1 21.1 - - + +
236B ILE* 6.4 0.9 - - - -
260B ILE* 5.2 6.5 - - + -
263B MET* 3.5 29.9 - - - +
264B LEU* 6.6 0.2 - - - -
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Residues in contact with SER 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B LEU* 3.2 15.1 + - - +
223B ASP* 3.1 9.5 + - - -
225B CYS* 1.3 81.3 - - - +
227B LYS* 1.3 66.5 + - - +
263B MET* 3.3 20.9 - - - +
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Residues in contact with LYS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ASP* 3.1 10.5 + - + +
224B TRP 4.5 1.2 - - - +
225B CYS 5.2 0.8 - - - -
226B SER* 1.3 84.7 - - - +
230B PHE* 2.7 62.6 + - + +
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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