Contacts of the helix formed by residues 197 - 209 (chain B) in PDB entry 3EJW
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 ASN 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 5.4 0.2 - - - +
13B VAL* 3.4 38.6 - - - +
169B ASN* 3.4 32.1 + - - +
170B ASP 4.2 1.6 - - - +
171B ALA* 4.1 18.5 + - - +
174B SER* 3.9 16.1 - - - +
195B ASP* 2.9 9.2 + - - +
196B ALA* 1.3 76.3 - - - +
198B ALA* 1.3 67.4 + - - +
199B LEU 3.3 1.6 - - - -
200B PRO* 3.3 6.2 - - - +
201B ALA* 3.2 24.3 + - - +
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Residues in contact with ALA 198 (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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132B PHE* 3.3 57.4 - - + +
133B TYR* 3.9 7.0 - - - -
167B GLY 5.8 0.2 - - - +
174B SER* 4.2 4.0 + - - +
193B ALA* 4.0 2.5 - - + -
195B ASP* 2.8 24.0 + - + +
197B ASN* 1.3 77.2 - - - +
199B LEU* 1.3 57.3 + - - +
201B ALA 3.3 0.3 + - - -
202B ALA* 2.9 27.0 + - - +
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Residues in contact with LEU 199 (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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193B ALA* 3.7 18.5 - - + +
195B ASP 3.1 10.7 + - - +
198B ALA* 1.3 76.9 - - - +
200B PRO* 1.3 68.9 - - + +
202B ALA* 3.2 2.9 + - - +
203B ALA* 3.0 20.4 + - - +
217B ILE* 3.6 19.7 - - + -
218B VAL* 3.6 28.3 - - - +
219B GLY 3.6 13.5 - - - -
220B PHE 3.9 4.0 - - - +
221B SER* 3.9 8.5 - - - +
226B MET* 3.7 24.9 - - + -
235B ILE* 4.6 2.7 - - + -
238B PHE* 3.5 29.8 - - + -
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Residues in contact with PRO 200 (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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196B ALA 3.1 28.0 - - - +
197B ASN* 3.3 14.4 - - - +
199B LEU* 1.3 91.1 - - + +
201B ALA* 1.3 58.0 + - - +
203B ALA* 3.3 5.4 + - + +
204B GLN* 2.8 32.3 + - - +
221B SER* 3.8 0.9 - - - +
225B VAL* 3.8 27.6 - - + -
226B MET* 3.8 19.1 - - - -
229B TYR* 3.9 14.2 - - + +
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Residues in contact with ALA 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE* 4.3 0.9 - - + -
171B ALA* 5.0 1.3 - - - +
174B SER* 3.4 40.6 - - - +
175B LEU* 3.6 9.3 - - + +
178B ALA* 3.5 3.5 - - - +
197B ASN 3.2 19.3 + - - +
198B ALA 3.5 3.6 - - - +
200B PRO* 1.3 75.3 - - - +
202B ALA* 1.3 55.0 + - - +
204B GLN* 3.3 6.4 + - - +
205B ALA* 2.8 36.2 + - - +
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE* 4.3 5.4 - - + -
178B ALA* 3.8 11.2 - - + +
182B LEU* 4.7 2.1 - - - +
191B ILE* 4.2 28.0 - - + +
193B ALA* 5.0 0.4 - - + -
198B ALA 2.9 13.6 + - - +
199B LEU* 3.5 9.6 - - - +
201B ALA* 1.3 75.1 - - - +
203B ALA* 1.3 57.5 + - - +
205B ALA* 3.3 2.4 + - - +
206B ALA* 2.9 29.6 + - - +
217B ILE* 3.7 22.3 - - + +
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU 3.0 12.6 + - - +
200B PRO* 3.6 8.3 - - + +
202B ALA* 1.3 77.3 - - - +
204B GLN* 1.3 61.7 + - - +
206B ALA* 3.3 4.5 + - - +
207B GLU* 3.1 25.6 + - - +
217B ILE* 4.2 8.5 - - + +
226B MET* 4.4 3.4 - - + -
229B TYR* 3.6 34.1 - - + -
234B THR* 3.6 6.6 - - + +
235B ILE* 4.1 16.2 - - + -
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Residues in contact with GLN 204 (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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175B LEU* 3.8 21.5 - - + -
200B PRO 2.8 21.2 + - - +
201B ALA* 3.6 5.4 - - - +
203B ALA* 1.3 70.2 - - - +
205B ALA* 1.3 60.9 + - - +
207B GLU* 3.2 15.5 + - - +
208B ASN* 2.9 60.4 + - - +
229B TYR* 2.7 35.9 + - - +
232B ARG* 4.6 2.3 + - - -
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Residues in contact with ALA 205 (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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175B LEU* 4.0 7.4 - - + +
178B ALA* 3.4 23.1 - - + -
179B GLU* 3.8 20.0 - - + +
182B LEU* 3.7 14.1 - - + -
201B ALA 2.8 21.1 + - - +
202B ALA 3.6 3.4 - - - +
204B GLN* 1.3 73.7 - - - +
206B ALA* 1.3 58.1 + - - +
208B ASN* 3.3 2.7 + - - +
209B LEU* 3.0 35.7 + - - +
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Residues in contact with ALA 206 (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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182B LEU* 3.7 13.2 - - + +
202B ALA 2.9 17.3 + - - +
203B ALA* 3.4 6.3 - - - +
204B GLN 3.2 0.2 - - - -
205B ALA* 1.3 77.9 - - - +
207B GLU* 1.3 56.9 + - - +
210B LYS* 3.0 8.0 + - - -
211B ARG* 2.8 31.8 + - + +
212B ALA* 3.6 25.2 + - + +
215B VAL* 5.8 0.4 - - + -
217B ILE* 3.6 21.8 - - + -
234B THR* 4.5 0.7 - - + -
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Residues in contact with GLU 207 (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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203B ALA 3.1 9.3 + - - +
204B GLN* 3.2 15.1 + - - +
206B ALA* 1.3 74.6 - - - +
208B ASN* 1.3 67.6 + - - +
209B LEU 3.2 0.5 + - - -
210B LYS* 3.3 21.6 + - - +
212B ALA* 5.3 3.4 - - + -
229B TYR* 3.4 19.0 - - - -
232B ARG* 2.8 45.3 + - - +
234B THR* 2.5 34.9 + - + +
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Residues in contact with ASN 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU* 4.1 11.7 - - - +
179B GLU* 3.0 26.9 + - - +
204B GLN* 2.9 51.3 + - - +
205B ALA 3.3 4.7 + - - +
207B GLU* 1.3 77.7 - - - +
209B LEU* 1.3 66.7 + - + +
210B LYS* 3.8 4.5 + - - +
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Residues in contact with LEU 209 (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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179B GLU* 3.8 41.3 - - + +
182B LEU* 3.8 22.9 - - + -
183B GLN* 3.9 24.2 - - + +
205B ALA 3.0 14.3 + - - +
208B ASN* 1.3 84.8 - - + +
210B LYS* 1.3 72.5 + - - +
211B ARG* 3.3 20.1 + - + +
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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