Contacts of the helix formed by residues 190 - 204 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188C GLY 5.1 5.5 + - - -
189C VAL* 1.3 82.7 + - - +
191C HIS* 1.3 67.2 + - - +
192C VAL* 3.2 17.0 - - + -
193C THR* 3.1 15.6 + - - +
194C VAL* 3.2 9.1 + - - +
145D ASN 5.1 11.2 - - - -
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Residues in contact with HIS 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C GLN* 3.1 41.6 + - + +
181C LYS* 4.8 5.6 + - + -
184C GLY* 6.2 0.7 - - - -
189C VAL 3.8 1.2 + - - -
190C HIS* 1.3 73.4 - - - +
192C VAL* 1.3 56.5 + - - +
194C VAL* 3.2 6.6 + - + +
195C SER* 2.9 49.4 + - - -
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Residues in contact with VAL 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C HIS* 4.1 18.2 - - + -
191C HIS* 1.3 79.0 + - - +
193C THR* 1.3 75.9 + - - +
195C SER* 3.4 5.2 + - - -
196C ARG* 3.0 27.0 + - + +
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Residues in contact with THR 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C PRO* 4.5 9.3 - - + +
150C THR* 4.0 7.9 - - - +
153C ILE* 4.4 2.5 - - + -
189C VAL* 3.5 26.8 - - + +
190C HIS* 3.1 6.0 + - - +
192C VAL* 1.3 84.3 - - - +
194C VAL* 1.3 56.8 + - - +
196C ARG* 3.2 31.8 + - - +
197C VAL* 2.9 48.4 + - + +
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Residues in contact with VAL 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ILE* 4.0 12.6 - - + -
180C GLN* 4.0 25.4 - - + +
183C ILE* 4.0 14.6 - - + -
184C GLY* 4.0 16.2 - - - +
189C VAL* 4.0 24.0 - - + +
190C HIS 3.2 15.6 + - - +
191C HIS* 3.2 10.6 + - + +
193C THR* 1.3 74.5 - - - +
195C SER* 1.3 64.2 + - - +
198C LEU* 3.1 46.0 + - + +
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Residues in contact with SER 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C GLN* 2.4 32.6 + - - +
191C HIS* 2.9 30.2 + - - -
192C VAL* 3.9 4.7 - - - -
194C VAL* 1.3 76.4 - - - +
196C ARG* 1.3 56.8 + - - +
198C LEU* 3.8 1.4 + - - +
199C ALA* 3.0 29.6 + - - +
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Residues in contact with ARG 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C THR* 4.0 9.9 + - - +
192C VAL* 3.0 20.3 + - + +
193C THR* 3.5 33.0 + - - +
195C SER* 1.3 77.1 - - - +
197C VAL* 1.3 77.5 + - - +
199C ALA* 3.4 5.3 + - - +
200C CYS* 3.0 36.4 + - - +
203C ARG* 4.9 2.4 + - - +
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Residues in contact with VAL 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C THR* 3.6 23.1 - - + +
153C ILE* 3.9 33.4 - - + -
154C LEU* 3.9 21.1 - - + -
193C THR* 2.9 28.5 + - + +
194C VAL 3.9 2.5 - - - +
196C ARG* 1.3 93.9 - - - +
198C LEU* 1.3 61.0 + - - +
200C CYS* 3.2 8.1 - - - +
201C LEU* 2.9 37.9 + - + +
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Residues in contact with LEU 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ILE* 4.1 12.3 - - + -
157C PHE* 3.7 28.5 - - + -
180C GLN* 3.2 44.2 - - + +
183C ILE* 3.8 17.3 - - + -
194C VAL* 3.1 21.3 + - + +
195C SER 4.2 1.1 - - - +
197C VAL* 1.3 75.8 - - + +
199C ALA* 1.3 63.3 + - - +
201C LEU* 3.2 7.1 + - + +
202C LYS* 3.0 24.7 + - - +
207C LEU* 4.7 2.5 - - + +
209C LYS* 4.1 27.5 + - + +
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Residues in contact with ALA 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C SER 3.0 20.6 + - - +
196C ARG* 3.6 7.0 - - - +
197C VAL 3.3 0.2 - - - -
198C LEU* 1.3 74.0 - - - +
200C CYS* 1.3 59.5 + - - +
202C LYS* 3.2 8.8 + - - +
203C ARG* 2.9 39.9 + - - +
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Residues in contact with CYS 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ARG* 3.0 22.1 + - - +
197C VAL* 3.2 14.8 - - - +
199C ALA* 1.3 76.5 - - - +
201C LEU* 1.3 65.1 + - + +
203C ARG* 3.5 29.4 + - - +
204C GLU* 2.9 42.9 + - - +
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Residues in contact with LEU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C LEU* 4.4 21.5 - - + -
157C PHE* 3.9 24.0 - - + -
197C VAL* 2.9 30.9 + - + +
198C LEU* 3.2 6.3 + - - +
200C CYS* 1.3 79.8 - - + +
202C LYS* 1.3 59.7 + - - +
204C GLU* 3.8 5.6 - - - +
205C ASN 3.3 1.7 + - - -
206C ILE* 2.9 64.3 + - + +
207C LEU* 3.1 34.7 - - + +
222C LEU* 4.7 2.5 - - + -
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Residues in contact with LYS 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C LEU 3.0 12.8 + - - +
199C ALA* 3.4 9.4 - - - +
201C LEU* 1.3 73.0 - - - +
203C ARG* 1.3 61.7 + - - +
204C GLU 3.2 1.3 - - - -
205C ASN* 3.0 27.2 + - - +
207C LEU 3.0 13.9 + - - +
208C ASP* 3.4 33.4 + - + +
209C LYS 5.7 0.2 - - - +
210C LYS* 3.6 24.5 - - - +
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Residues in contact with ARG 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C ARG* 4.9 3.0 + - - +
199C ALA* 2.9 23.5 + - - +
200C CYS* 3.5 38.8 + - - +
202C LYS* 1.3 76.1 - - - +
204C GLU* 1.3 63.3 + - - +
205C ASN* 3.2 8.4 + - - +
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Residues in contact with GLU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C CYS* 2.9 31.8 + - - +
201C LEU* 4.1 5.2 - - - +
203C ARG* 1.3 80.9 + - + +
205C ASN* 1.3 69.0 + - - +
206C ILE* 3.2 26.5 + - + +
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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