Contacts of the helix formed by residues 198 - 210 (chain B) in PDB entry 3EIJ
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 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B PHE* 5.4 5.0 - - - -
195B GLU 3.4 15.4 + - - -
196B MET* 4.3 2.4 - - - -
197B LYS* 1.3 79.7 - - - +
199B GLY* 1.3 60.0 + - - +
200B VAL 3.4 0.2 - - - -
201B PRO* 3.4 0.6 - - - +
202B VAL* 3.3 10.2 - - - +
235B ASP* 3.7 26.5 - - - +
238B LYS* 3.9 28.4 - - - +
239B SER* 2.7 27.2 + - - -
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Residues in contact with GLY 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PHE* 3.5 16.3 - - - -
196B MET* 3.2 11.5 + - - +
197B LYS 3.0 2.4 - - - -
198B SER* 1.3 80.0 + - - +
200B VAL* 1.3 63.6 + - - +
201B PRO 3.5 0.2 - - - -
202B VAL* 3.3 10.7 + - - +
203B LEU* 2.9 24.4 + - - +
242B LYS* 6.1 2.7 - - - -
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PHE* 3.5 7.3 - - + -
168B LEU* 3.7 26.2 - - + -
172B ILE* 4.2 9.9 - - + +
188B LEU* 3.9 23.8 - - + -
193B LEU* 3.8 21.1 - - + -
197B LYS* 3.3 14.1 - - + +
199B GLY* 1.3 77.0 - - - +
201B PRO* 1.3 66.1 - - + +
203B LEU* 3.2 2.6 + - - +
204B ALA* 2.8 34.4 + - + +
222B LEU* 5.5 1.6 - - + -
223B LEU* 5.8 0.4 - - + -
226B LEU* 4.3 15.7 - - + -
231B MET* 4.7 5.2 - - + -
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Residues in contact with PRO 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B LYS 3.5 7.2 - - - +
198B SER 3.4 13.0 - - - +
200B VAL* 1.3 94.6 - - + +
202B VAL* 1.3 60.0 + - - +
204B ALA* 3.8 1.2 - - + +
205B VAL* 3.0 31.9 + - + +
223B LEU* 3.5 33.4 - - + -
231B MET* 3.3 26.0 - - + -
235B ASP 4.9 0.4 - - - +
236B VAL* 4.8 7.4 - - + -
239B SER* 3.2 23.6 - - - +
240B PHE* 5.8 1.1 - - + -
243B LEU* 5.4 1.3 - - - -
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B SER 3.3 22.0 - - - +
199B GLY* 3.3 9.2 + - - +
201B PRO* 1.3 77.6 - - - +
203B LEU* 1.3 52.7 + - - +
206B SER* 2.8 38.5 + - - +
239B SER* 3.6 26.0 - - - +
242B LYS* 4.0 37.2 - - + +
243B LEU* 3.8 25.5 - - + +
246B ASP* 4.7 5.8 - - - +
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PHE* 4.0 15.9 - - + -
165B GLU* 4.1 37.0 - - + +
168B LEU* 3.7 29.6 - - + -
169B THR* 4.2 11.0 - - - +
172B ILE* 4.1 7.2 - - + -
199B GLY 2.9 16.3 + - - +
200B VAL 3.6 3.1 - - - +
202B VAL* 1.3 73.5 - - - +
204B ALA* 1.3 61.3 + - - +
206B SER* 2.8 18.4 + - - +
207B LEU* 2.9 44.9 + - + +
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Residues in contact with ALA 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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172B ILE* 3.9 27.9 - - + +
176B PHE* 4.0 2.4 - - - -
200B VAL* 2.8 22.4 + - + +
201B PRO* 3.8 8.1 - - + +
203B LEU* 1.3 72.7 - - - +
205B VAL* 1.3 58.0 + - - +
207B LEU* 3.9 2.4 - - - +
208B ALA 3.1 19.8 + - - -
219B THR* 3.4 27.9 + - + -
222B LEU* 4.3 14.4 - - + -
223B LEU* 4.6 2.5 - - + -
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Residues in contact with VAL 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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201B PRO* 3.0 20.7 + - + +
202B VAL 4.0 0.7 - - - +
204B ALA* 1.3 75.4 - - - +
206B SER* 1.3 59.9 + - - +
208B ALA* 3.0 4.7 + - - +
209B LEU* 2.8 43.4 + - + +
219B THR* 3.8 18.8 - - + -
223B LEU* 4.3 11.0 - - + -
240B PHE* 5.4 1.6 - - + -
243B LEU* 3.7 30.5 - - + -
261B VAL* 4.7 2.2 - - + -
264B PHE* 3.8 37.7 - - + -
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Residues in contact with SER 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL* 2.8 26.1 + - - +
203B LEU* 2.8 23.0 + - - +
205B VAL* 1.3 76.2 - - - +
207B LEU* 1.3 63.9 + - - +
209B LEU* 3.6 12.4 + - - +
210B GLU* 3.2 32.6 + - - +
243B LEU* 5.2 3.4 - - - -
250B LEU* 3.8 21.3 - - - +
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Residues in contact with LEU 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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169B THR* 4.0 31.6 - - + +
172B ILE* 4.0 25.8 - - + -
173B GLN* 4.2 17.3 - - + +
176B PHE* 4.5 11.0 - - + -
203B LEU* 2.9 42.6 + - + +
204B ALA 3.9 3.8 - - - +
206B SER* 1.3 80.8 + - - +
208B ALA* 1.3 62.1 + - - +
210B GLU* 3.3 13.9 + - - +
211B GLY* 3.3 18.0 + - - -
215B HIS* 5.4 0.7 - - - -
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Residues in contact with ALA 208 (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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176B PHE* 4.1 3.3 - - + -
204B ALA 3.1 9.5 + - - +
205B VAL* 3.0 7.2 + - - +
207B LEU* 1.3 72.5 - - - +
209B LEU* 1.3 64.7 + - - +
210B GLU 3.1 2.0 - - - -
211B GLY* 3.1 17.5 + - - +
212B LYS 4.0 6.1 - - - +
215B HIS* 3.7 24.5 - - - +
216B ARG* 4.2 15.4 + - - +
219B THR* 3.2 30.7 - - - +
264B PHE* 4.3 4.0 - - + -
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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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205B VAL* 2.8 36.8 + - + +
206B SER* 3.7 7.2 - - - +
207B LEU 3.3 0.2 - - - -
208B ALA* 1.3 73.4 - - - +
210B GLU* 1.3 59.9 + - + +
211B GLY 3.4 3.3 + - - +
216B ARG* 5.3 3.4 + - - +
250B LEU* 4.0 35.0 - - + -
254B THR* 3.2 29.9 + - + +
257B ALA* 4.1 22.7 - - + +
260B LEU* 3.6 42.0 - - + +
261B VAL* 4.3 7.2 - - + -
264B PHE* 4.5 10.8 - - + -
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Residues in contact with GLU 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B SER* 3.2 22.9 + - - +
207B LEU* 3.3 16.0 + - - +
208B ALA 3.1 0.8 - - - -
209B LEU* 1.3 79.6 - - + +
211B GLY* 1.3 58.9 + - - +
250B LEU* 5.8 5.9 - - + +
253B ASP* 3.5 29.4 - - + +
254B THR* 4.0 13.2 - - - +
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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