Contacts of the helix formed by residues 184 - 199 (chain P) in PDB entry 5A31
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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472J LEU* 4.0 35.7 - - + +
473J VAL* 4.0 35.9 - - + +
476J PRO* 4.5 2.0 - - + -
155P ARG* 4.3 6.7 - - - -
179P LEU* 2.9 35.9 + - + +
180P ARG* 5.2 0.2 - - - -
182P LEU* 3.7 26.5 - - + +
183P ASP* 1.3 78.2 - - - +
185P VAL* 1.3 52.4 + - - +
186P LYS 3.5 2.0 - - - -
187P GLU* 3.3 17.2 + - + -
188P ALA* 2.8 35.1 + - - +
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Residues in contact with VAL 185 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180P ARG* 5.1 5.4 - - + +
183P ASP* 3.0 23.3 + - + +
184P LEU* 1.3 71.3 - - - +
186P LYS* 1.3 68.6 + - - +
188P ALA* 3.2 7.1 + - - +
189P ILE* 3.1 35.7 + - + +
212P LEU* 3.9 34.2 - - + +
218P MET* 6.5 0.7 - - + -
396P LYS* 5.9 5.2 - - - +
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Residues in contact with LYS 186 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469J ARG* 4.5 34.4 - - - +
184P LEU 3.5 0.2 - - - -
185P VAL* 1.3 81.4 - - - +
187P GLU* 1.3 76.6 + - - +
189P ILE* 3.6 8.5 + - - +
190P ASP* 3.1 36.0 + - - +
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Residues in contact with GLU 187 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473J VAL* 5.1 14.6 - - + -
162P HIS* 6.1 0.2 - - - -
175P TYR* 4.9 4.9 + - - -
179P LEU* 4.4 13.1 - - + +
184P LEU* 3.3 23.2 + - + +
186P LYS* 1.3 88.8 + - - +
188P ALA* 1.3 63.3 + - - +
190P ASP* 3.1 23.7 + - - +
191P VAL* 3.2 22.7 + - - +
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Residues in contact with ALA 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176P GLY 4.0 11.7 - - - +
179P LEU* 3.9 26.2 - - + -
180P ARG* 4.1 8.1 - - - +
184P LEU 2.8 19.5 + - - +
185P VAL* 3.2 5.6 + - - +
187P GLU* 1.3 72.1 - - - +
189P ILE* 1.3 54.0 + - - +
191P VAL* 3.0 4.0 + - - +
192P PHE* 2.7 41.4 + - + -
212P LEU* 4.0 16.2 - - + -
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Residues in contact with ILE 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185P VAL* 3.1 23.2 + - + +
186P LYS* 3.8 7.9 - - - +
187P GLU 3.3 0.2 - - - -
188P ALA* 1.3 74.7 - - - +
190P ASP* 1.3 63.3 + - - +
192P PHE* 3.9 0.3 - - - +
193P VAL* 2.8 35.5 + - - +
209P LEU* 4.1 13.7 - - + -
212P LEU* 3.6 37.9 - - + +
213P ILE* 4.0 4.5 - - + -
218P MET* 3.9 28.7 - - + -
222P LEU* 3.6 39.7 - - + -
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Residues in contact with ASP 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186P LYS* 3.1 28.3 + - - +
187P GLU* 3.1 18.8 + - - +
189P ILE* 1.3 83.1 - - - +
191P VAL* 1.3 61.4 + - + +
193P VAL* 3.7 7.6 + - - +
194P GLU* 3.2 21.7 + - - +
222P LEU* 5.1 4.0 - - - +
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Residues in contact with VAL 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162P HIS* 4.7 10.5 - - + -
172P LEU* 3.4 34.9 - - + +
175P TYR* 3.8 22.7 - - + -
176P GLY* 3.8 14.1 - - - +
179P LEU* 3.5 26.0 - - + -
187P GLU* 3.2 16.2 + - - +
188P ALA* 3.0 7.5 + - - +
190P ASP* 1.3 75.4 - - + +
192P PHE* 1.3 60.5 + - - +
194P GLU* 3.2 7.6 + - - +
195P ALA* 2.9 24.9 + - - +
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Residues in contact with PHE 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173P TYR* 3.7 30.5 - + - -
176P GLY* 3.3 36.3 - - - -
177P VAL* 3.4 4.7 - - + -
180P ARG* 4.7 3.8 - - + -
188P ALA* 2.7 25.7 + - + +
191P VAL* 1.3 71.2 - - - +
193P VAL* 1.3 66.6 + - - +
195P ALA* 3.1 9.2 + - + +
196P THR* 3.0 26.3 + - - +
205P ALA* 3.8 23.1 - - + +
208P GLU* 3.4 34.1 - - + -
209P LEU* 3.4 22.0 - - + -
212P LEU* 3.8 25.4 - - + -
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Residues in contact with VAL 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189P ILE* 2.8 26.3 + - + +
190P ASP* 3.7 7.9 - - - +
192P PHE* 1.3 74.1 - - - +
194P GLU* 1.3 63.3 + - + +
196P THR* 2.8 24.0 + - - -
197P HIS* 3.2 12.0 + - - +
209P LEU* 4.3 7.4 - - + +
222P LEU* 3.7 39.3 - - + -
223P SER* 3.3 31.6 - - - +
224P LEU* 4.3 8.7 - - + -
225P PRO* 5.3 0.2 - - - +
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Residues in contact with GLU 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162P HIS* 5.1 7.6 - - - +
172P LEU* 3.7 20.0 - - + -
190P ASP 3.2 11.2 + - - +
191P VAL* 3.2 10.2 + - - +
192P PHE 3.1 0.4 - - - -
193P VAL* 1.3 79.3 - - + +
195P ALA* 1.3 64.3 + - - +
197P HIS* 3.2 14.7 + - - +
198P VAL* 2.9 40.8 + - + +
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Residues in contact with ALA 195 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169P GLY 4.4 5.5 - - - +
172P LEU* 3.8 27.3 - - + +
173P TYR* 4.2 9.6 - - - +
191P VAL 2.9 13.1 + - - +
192P PHE* 3.1 15.5 + - + +
194P GLU* 1.3 76.0 - - - +
196P THR* 1.3 63.2 + - - +
198P VAL* 3.1 3.9 + - - +
199P LEU* 2.9 26.1 + - - +
205P ALA* 4.3 16.4 - - + -
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Residues in contact with THR 196 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192P PHE 3.0 14.0 + - - +
193P VAL* 2.8 21.7 + - - -
195P ALA* 1.3 78.8 - - - +
197P HIS* 1.3 66.5 + - - +
199P LEU 3.3 24.8 - - - -
200P PRO* 3.3 10.2 - - - +
205P ALA* 4.3 7.2 - - + -
206P TRP* 3.6 62.4 - - + +
209P LEU* 4.7 5.2 - - + -
224P LEU* 4.1 4.9 - - - +
225P PRO* 3.7 16.5 - - - +
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Residues in contact with HIS 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193P VAL* 3.2 10.9 + - + +
194P GLU* 3.2 21.1 + - - +
196P THR* 1.3 84.1 + - - +
198P VAL* 1.3 61.3 + - + +
200P PRO* 4.9 3.3 - - - +
223P SER* 4.8 15.8 + - - -
224P LEU 5.3 2.0 - - - -
225P PRO* 4.2 33.7 - - + +
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Residues in contact with VAL 198 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168P ASP* 3.2 33.7 - - - +
169P GLY* 3.9 12.6 - - - +
172P LEU* 5.3 7.0 - - + -
194P GLU* 2.9 41.6 + - + +
195P ALA* 3.6 8.1 - - - +
197P HIS* 1.3 79.5 - - + +
199P LEU* 1.3 59.5 + - + +
200P PRO* 4.2 4.6 - - - +
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Residues in contact with LEU 199 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P ILE* 4.3 6.3 - - + -
42P LEU* 6.0 1.6 - - + -
168P ASP* 5.5 0.9 - - - +
169P GLY* 3.8 31.9 - - - -
170P PHE* 3.9 29.6 - - + +
195P ALA 2.9 12.6 + - - +
196P THR* 3.3 11.3 + - - +
198P VAL* 1.3 80.3 - - + +
200P PRO* 1.3 73.1 - - + +
202P HIS* 3.3 39.5 + - + +
205P ALA* 5.4 2.7 - - + +
206P TRP* 5.2 0.5 + - - -
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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