Contacts of the helix formed by residues 184 - 199 (chain C) in PDB entry 5G04
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 LEU 184 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155C ARG* 3.8 40.6 - - + +
179C LEU* 2.9 25.5 + - + +
180C ARG 4.3 0.2 + - - -
182C LEU* 3.9 31.2 - - + +
183C ASP* 1.3 78.3 - - - +
185C VAL* 1.3 50.6 + - - +
186C LYS 3.4 2.7 - - - -
187C GLU* 3.3 28.3 + - + +
188C ALA* 2.8 35.2 + - - +
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Residues in contact with VAL 185 (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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58A VAL 5.5 7.2 - - - +
180C ARG* 5.6 2.5 - - + +
183C ASP* 3.1 21.7 + - + +
184C LEU* 1.3 69.6 - - - +
186C LYS* 1.3 66.5 + - - +
188C ALA* 3.3 5.8 + - - +
189C ILE* 3.0 38.5 + - + +
212C LEU* 3.8 38.8 - - + +
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Residues in contact with LYS 186 (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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184C LEU 3.4 0.2 - - - -
185C VAL* 1.3 81.6 - - - +
187C GLU* 1.3 94.3 + - + +
189C ILE* 3.7 7.3 + - - +
190C ASP* 2.9 36.5 + - - +
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Residues in contact with GLU 187 (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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155C ARG* 5.3 4.7 + - - -
179C LEU* 3.6 15.8 - - + +
184C LEU* 3.5 36.5 - - + +
186C LYS* 1.3 101.6 + - + +
188C ALA* 1.3 63.9 + - - +
190C ASP* 3.1 15.9 + - - +
191C VAL* 3.1 18.9 + - - +
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Residues in contact with ALA 188 (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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176C GLY 4.1 4.0 - - - +
179C LEU* 3.4 21.5 - - + +
180C ARG* 4.2 7.2 - - - +
184C LEU 2.8 18.2 + - - +
185C VAL* 3.3 1.5 + - - +
187C GLU* 1.3 73.0 - - - +
189C ILE* 1.3 55.5 - - - +
191C VAL* 2.8 7.2 - - - +
192C PHE* 2.8 48.9 + - + -
212C LEU* 3.6 21.8 - - + -
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Residues in contact with ILE 189 (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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185C VAL* 3.0 26.6 + - + +
186C LYS* 4.0 7.4 - - - +
187C GLU 3.3 0.2 - - - -
188C ALA* 1.3 75.5 - - - +
190C ASP* 1.3 60.6 + - - +
192C PHE* 3.9 1.2 - - - +
193C VAL* 2.8 32.4 + - + +
209C LEU* 4.3 10.8 - - + -
212C LEU* 3.7 37.2 - - + +
213C ILE* 4.0 17.0 - - + -
218C MET* 6.0 5.2 - - + -
222C LEU* 3.7 39.0 - - + -
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Residues in contact with ASP 190 (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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186C LYS* 2.9 31.3 - - - +
187C GLU* 3.1 15.6 + - - +
189C ILE* 1.3 79.1 - - - +
191C VAL* 1.3 63.3 + - + +
193C VAL* 3.9 6.2 - - - +
194C GLU* 3.2 21.8 + - - +
222C LEU* 5.7 1.9 - - - +
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Residues in contact with VAL 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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162C HIS* 4.5 13.9 - - + +
172C LEU* 4.5 11.9 - - + +
175C TYR* 3.6 33.9 - - + -
176C GLY* 3.5 30.1 - - - +
179C LEU* 3.8 8.7 - - + -
187C GLU 3.1 10.4 + - - +
188C ALA* 2.8 31.9 + - - +
190C ASP* 1.3 76.5 - - + +
192C PHE* 1.3 60.0 + - - +
194C GLU* 3.2 7.6 + - - +
195C ALA* 2.9 26.9 + - - +
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Residues in contact with PHE 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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172C LEU 5.0 0.2 - - - -
173C TYR* 3.7 26.7 - + - -
176C GLY* 3.2 42.6 - - - -
177C VAL* 3.4 3.6 - - + -
180C ARG* 4.5 4.5 - - + -
188C ALA* 2.8 37.6 + - + +
189C ILE* 4.4 0.7 - - - -
191C VAL* 1.3 70.0 - - - +
193C VAL* 1.3 67.0 + - - +
195C ALA* 3.2 4.5 + - - +
196C THR* 3.2 27.4 + - - +
205C ALA* 3.9 19.7 - - + +
208C GLU* 3.3 39.5 - - + -
209C LEU* 3.7 22.4 - - + -
212C LEU* 4.2 13.7 - - + -
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Residues in contact with VAL 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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189C ILE* 2.8 25.7 + - + +
190C ASP* 3.9 6.7 - - - +
192C PHE* 1.3 77.0 - - - +
194C GLU* 1.3 62.3 + - - +
196C THR* 2.8 23.2 + - - -
197C HIS* 3.2 10.8 + - + +
209C LEU* 4.2 8.7 - - + +
222C LEU* 3.7 36.1 - - + -
223C SER* 3.3 29.1 - - - +
224C LEU* 4.4 6.3 - - + -
225C PRO* 5.2 0.2 - - - +
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Residues in contact with GLU 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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162C HIS* 5.4 6.1 - - + +
165C ARG* 4.6 13.7 + - - -
172C LEU* 4.4 18.5 - - + +
190C ASP 3.2 12.3 + - - +
191C VAL* 3.6 9.4 - - - +
192C PHE 3.2 0.4 - - - -
193C VAL* 1.3 81.5 - - - +
195C ALA* 1.4 62.4 + - - +
197C HIS* 3.2 16.0 + - - +
198C VAL* 2.9 42.6 + - + +
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Residues in contact with ALA 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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169C GLY 4.3 6.0 - - - +
172C LEU* 3.8 26.7 - - + +
173C TYR* 4.1 11.4 - - + +
191C VAL 2.9 14.1 + - - +
192C PHE* 3.2 13.2 + - - +
194C GLU* 1.4 74.6 - - - +
196C THR* 1.3 53.5 + - - +
198C VAL* 3.1 5.0 + - - +
199C LEU* 2.8 38.0 + - - +
205C ALA* 4.4 15.9 - - + -
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Residues in contact with THR 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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192C PHE 3.2 12.1 + - - +
193C VAL* 2.8 22.9 + - - +
195C ALA* 1.3 76.4 - - - +
197C HIS* 1.3 66.7 + - - +
199C LEU 3.3 24.0 - - - -
200C PRO* 3.4 5.4 - - - +
205C ALA* 4.4 5.4 - - + -
206C TRP* 3.8 49.9 - - + +
209C LEU* 3.8 17.7 - - + -
224C LEU* 4.8 4.3 - - - +
225C PRO* 3.6 21.7 - - - +
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Residues in contact with HIS 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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193C VAL* 3.2 10.6 + - + +
194C GLU* 3.4 22.2 - - - +
196C THR* 1.3 85.0 + - - +
198C VAL* 1.3 64.8 + - + +
200C PRO* 4.9 2.4 - - - +
223C SER* 4.8 14.5 + - - -
224C LEU 4.7 4.0 - - - -
225C PRO* 4.1 31.8 - - + +
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Residues in contact with VAL 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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165C ARG* 5.2 9.2 - - - +
168C ASP* 3.5 33.7 - - - +
169C GLY* 4.1 9.9 - - - +
172C LEU* 4.6 7.9 - - + -
194C GLU* 2.9 44.1 + - + +
195C ALA* 3.7 4.7 - - - +
197C HIS* 1.3 82.2 - - + +
199C LEU* 1.3 58.5 + - + +
200C PRO* 4.1 4.6 - - - +
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Residues in contact with LEU 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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39C ILE* 3.8 18.2 - - + -
42C LEU* 5.7 3.6 - - + -
168C ASP* 5.0 3.8 - - - +
169C GLY* 3.7 27.8 - - - -
170C PHE* 4.3 29.6 - - + +
195C ALA 2.8 19.4 + - - +
196C THR* 3.3 9.1 - - - +
198C VAL* 1.3 76.8 - - + +
200C PRO* 1.3 78.3 - - + +
202C HIS* 4.1 17.2 + - + +
205C ALA* 5.5 2.8 - - - +
206C TRP* 5.4 1.0 + - - -
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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