Contacts of the helix formed by residues 190 - 204 (chain B) in PDB entry 3E5X
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 HIS 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A ASN 5.8 2.2 + - - -
188B GLY 4.5 7.9 + - - -
189B VAL* 1.3 84.1 - - - +
191B HIS* 1.3 69.2 + - - +
192B VAL* 3.4 3.1 - - + +
193B THR* 3.2 9.9 + - - +
194B VAL* 3.2 16.1 + - - +
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Residues in contact with HIS 191 (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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180B GLN* 4.7 0.5 - - - +
184B GLY* 6.2 0.2 - - - -
189B VAL 3.9 0.8 + - - -
190B HIS* 1.3 76.2 - - - +
192B VAL* 1.3 87.9 + - + +
194B VAL* 3.1 9.7 + - - +
195B SER* 2.9 37.8 + - - +
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Residues in contact with VAL 192 (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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190B HIS* 3.4 2.5 - - + +
191B HIS* 1.3 103.8 + - + +
193B THR* 1.3 59.3 + - - +
195B SER* 3.4 6.7 + - - -
196B ARG* 2.9 44.2 + - + +
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Residues in contact with THR 193 (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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149B PRO* 4.7 5.4 - - + -
150B THR* 3.7 29.8 - - + -
153B ILE* 4.5 1.1 - - + -
189B VAL* 3.5 27.5 - - + +
190B HIS* 3.2 8.5 + - - +
192B VAL* 1.3 77.2 - - - +
194B VAL* 1.3 64.8 + - - +
196B ARG* 3.3 25.8 + - - +
197B VAL* 2.9 25.0 + - + +
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Residues in contact with VAL 194 (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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153B ILE* 4.2 12.3 - - + -
180B GLN* 3.8 40.2 - - + +
183B ILE* 4.1 15.9 - - + -
184B GLY* 4.0 16.4 - - - +
189B VAL* 3.7 25.8 - - + +
190B HIS 3.2 15.3 + - - +
191B HIS* 3.1 10.4 + - - +
193B THR* 1.3 77.5 - - - +
195B SER* 1.3 63.7 + - - +
197B VAL* 3.9 0.2 - - - -
198B LEU* 3.0 36.9 + - + +
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Residues in contact with SER 195 (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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180B GLN* 2.9 26.4 + - - +
191B HIS* 2.9 22.2 + - - +
192B VAL* 3.6 8.1 - - - -
194B VAL* 1.3 76.3 - - - +
196B ARG* 1.3 56.2 + - - -
198B LEU* 3.4 1.9 + - - +
199B ALA* 2.9 32.7 + - - +
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Residues in contact with ARG 196 (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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150B THR* 5.2 4.6 - - - +
192B VAL* 2.9 37.8 + - + +
193B THR* 3.4 34.7 + - - +
195B SER* 1.3 73.2 - - - +
197B VAL* 1.3 61.6 + - + +
199B ALA* 3.4 5.7 + - - +
200B CYS* 2.9 43.1 + - - -
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Residues in contact with VAL 197 (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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150B THR* 3.4 35.4 - - + +
153B ILE* 3.9 32.1 - - + -
154B LEU* 4.1 23.6 - - + -
193B THR* 2.9 23.9 + - + +
194B VAL 4.0 1.8 - - - +
196B ARG* 1.3 76.9 - - + +
198B LEU* 1.3 67.7 + - + +
200B CYS* 3.1 8.0 + - - +
201B LEU* 3.0 27.2 + - + +
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Residues in contact with LEU 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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153B ILE* 4.0 14.4 - - + -
157B PHE* 3.6 29.2 - - + -
180B GLN* 3.6 40.6 - - + +
183B ILE* 3.9 14.4 - - + -
194B VAL* 3.0 26.7 + - + +
195B SER 3.9 2.9 - - - +
197B VAL* 1.3 77.7 - - + +
199B ALA* 1.3 62.3 + - - +
201B LEU* 3.4 7.7 + - + +
202B LYS* 3.1 23.8 + - - +
207B LEU* 4.5 2.8 - - + +
209B LYS* 3.8 32.6 + - + +
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Residues in contact with ALA 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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195B SER 2.9 19.0 + - - +
196B ARG* 3.7 6.5 - - - +
198B LEU* 1.3 76.8 - - - +
200B CYS* 1.3 62.0 + - - +
202B LYS* 3.5 8.1 + - - +
203B ARG* 3.0 44.2 + - - +
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Residues in contact with CYS 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 ARG* 2.9 36.2 + - - -
197B VAL* 3.1 8.2 + - + +
199B ALA* 1.3 72.9 - - - +
201B LEU* 1.3 58.4 + - + +
203B ARG* 3.2 20.0 + - - +
204B GLU* 2.8 53.9 + - - +
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Residues in contact with LEU 201 (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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154B LEU* 3.7 29.2 - - + -
157B PHE* 3.7 27.8 - - + -
197B VAL* 3.0 22.1 + - + +
198B LEU* 3.7 5.8 - - - +
200B CYS* 1.3 79.2 - - + +
202B LYS* 1.3 60.4 + - - +
204B GLU* 3.7 1.3 + - - +
205B ASN 3.2 2.3 + - - -
206B ILE* 2.9 66.2 + - + +
207B LEU* 3.2 35.6 + - + +
222B LEU* 4.3 4.3 - - + -
225B LEU* 4.4 6.1 - - + -
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Residues in contact with LYS 202 (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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198B LEU 3.1 15.3 + - - +
199B ALA* 3.9 6.3 - - - +
201B LEU* 1.3 79.0 - - - +
203B ARG* 1.3 58.8 + - - +
205B ASN* 3.1 23.6 + - - +
206B ILE 5.0 0.2 - - - +
207B LEU 3.2 14.5 + - - +
208B ASP* 3.5 38.9 + - - +
209B LYS 5.6 0.2 - - - +
217B TYR* 6.0 1.8 - - + -
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Residues in contact with ARG 203 (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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199B ALA* 3.0 35.0 + - - +
200B CYS* 3.6 37.0 - - - +
202B LYS* 1.3 76.8 - - - +
204B GLU* 1.3 64.3 + - + +
205B ASN* 3.3 12.2 + - - +
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Residues in contact with GLU 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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200B CYS* 2.8 35.8 + - + +
201B LEU* 5.0 0.7 - - - +
203B ARG* 1.3 77.4 - - + +
205B ASN* 1.3 74.4 + - - +
206B ILE* 3.3 32.7 + - + +
218B ASN* 5.9 0.5 + - - -
225B LEU* 4.3 9.7 - - - +
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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