Contacts of the helix formed by residues 183 - 196 (chain P) in PDB entry 5A0Q
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 183 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39P ALA* 4.0 4.5 - - - -
41P ASN* 2.8 24.1 + - + +
42P GLY* 2.8 48.2 - - - +
43P VAL 4.3 1.6 - - - +
44P VAL* 5.1 0.8 - - + +
181P LEU 3.9 4.3 - - - -
182P GLU* 1.3 73.1 - - - +
184P GLU* 1.3 57.8 + - + +
186P ALA* 3.3 4.3 + - - +
187P ILE* 2.9 54.4 + - + +
211P ILE* 3.7 18.4 - - + -
213P ASN* 2.7 35.0 - - - +
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Residues in contact with GLU 184 (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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182P GLU* 2.9 21.9 + - + +
183P LEU* 1.3 75.7 - - + +
185P ASP* 1.3 74.0 + - - +
187P ILE* 3.1 20.3 + - + +
188P HIS* 3.0 23.6 + - - +
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Residues in contact with ASP 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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181P LEU* 2.3 51.7 - - + +
182P GLU* 2.5 46.3 + - - +
184P GLU* 1.3 80.8 - - - +
186P ALA* 1.3 49.4 + - - -
188P HIS* 3.0 27.6 + - + +
189P THR 3.8 1.6 + - - -
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Residues in contact with ALA 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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37P ILE* 3.3 27.8 - - + +
39P ALA* 2.8 41.1 - - + -
44P VAL* 4.7 2.2 - - + -
177P TYR* 4.4 1.8 - - + -
181P LEU* 2.8 17.8 - - + +
182P GLU 3.0 4.6 + - - -
183P LEU 3.3 2.2 + - - +
185P ASP* 1.3 72.8 - - - +
187P ILE* 1.4 58.9 + - - +
188P HIS 3.3 0.9 - - - -
189P THR* 3.0 23.3 - - - +
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Residues in contact with ILE 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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44P VAL* 3.8 21.8 - - + -
183P LEU* 2.9 45.1 + - + +
184P GLU* 3.1 20.1 + - + +
186P ALA* 1.4 72.1 - - - +
188P HIS* 1.3 57.5 + - - +
189P THR 3.3 0.7 - - - -
190P ALA* 2.9 14.3 + - + -
191P ILE* 2.9 39.9 + - + +
209P VAL* 5.4 3.1 - - + -
211P ILE* 3.7 15.7 - - + -
220P LEU* 3.8 24.7 - - + -
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Residues in contact with HIS 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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184P GLU 3.0 8.1 + - - +
185P ASP* 3.0 24.7 + - - +
187P ILE* 1.3 77.0 - - - +
189P THR* 1.3 56.7 + - - +
191P ILE* 3.4 10.4 - - + +
192P LEU* 3.0 67.2 + - + +
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Residues in contact with THR 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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37P ILE* 3.9 16.4 - - + -
172P PHE 4.6 0.5 + - - -
173P LEU* 3.7 8.7 - - + +
176P ARG* 4.0 22.3 - - - +
177P TYR* 4.0 26.7 - - + +
181P LEU* 4.9 1.8 - - + -
185P ASP 3.8 1.9 + - - +
186P ALA* 3.0 31.9 - - - +
188P HIS* 1.3 80.0 - - - +
190P ALA* 1.4 57.2 + - - +
192P LEU* 4.6 4.3 - - - +
193P THR* 2.8 44.6 + - - -
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Residues in contact with ALA 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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35P VAL* 4.0 18.9 - - + +
37P ILE* 3.4 25.1 - - + -
44P VAL* 4.1 7.6 - - + -
46P ALA* 5.0 8.3 - - + -
187P ILE* 2.9 22.3 + - + +
189P THR* 1.4 78.0 - - - +
191P ILE* 1.3 61.8 + - + +
193P THR* 4.2 0.2 - - - -
194P LEU* 3.0 34.6 + - - +
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Residues in contact with ILE 191 (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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187P ILE* 2.9 21.9 + - + +
188P HIS* 3.4 20.2 - - + +
190P ALA* 1.3 78.0 - - + +
192P LEU* 1.4 70.5 + - + +
193P THR 3.6 0.2 - - - -
194P LEU* 4.1 12.3 - - + +
195P LYS* 3.4 23.6 + - - +
207P ILE* 4.3 26.2 - - + -
209P VAL* 6.5 0.7 - - + -
225P VAL* 5.4 10.5 - - + +
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Residues in contact with LEU 192 (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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172P PHE* 5.4 4.0 - - - -
176P ARG* 6.4 3.4 - - + -
188P HIS* 3.0 50.1 + - + +
189P THR* 4.6 3.1 - - - +
191P ILE* 1.4 88.3 - - + +
193P THR* 1.3 61.2 + - - +
194P LEU 3.5 0.2 - - - -
195P LYS* 3.8 21.9 - - + +
196P GLU* 4.1 5.5 + - - +
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Residues in contact with THR 193 (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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35P VAL* 4.3 13.0 - - + -
161P ALA* 5.3 0.7 - - + -
169P GLY* 3.1 39.1 - - - +
172P PHE* 3.5 21.6 - - + +
173P LEU* 4.0 12.5 - - + +
176P ARG* 5.1 1.6 - - - +
189P THR* 2.8 33.4 + - - -
190P ALA 4.2 1.3 - - - -
192P LEU* 1.3 73.8 - - - +
194P LEU* 1.3 65.1 + - - +
195P LYS 3.1 1.6 - - - -
196P GLU* 3.2 20.6 - - - +
197P SER* 4.1 4.7 + - - -
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Residues in contact with LEU 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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33P PRO* 4.0 35.4 - - + +
35P VAL* 4.0 22.8 - - + +
46P ALA* 4.5 5.6 - - + +
47P THR* 4.3 7.2 - - - -
48P GLU* 4.2 12.0 - - + +
190P ALA 3.0 18.8 + - - +
191P ILE* 4.1 14.8 - - + +
193P THR* 1.3 77.3 - - - +
195P LYS* 1.4 60.4 + - - +
196P GLU 3.2 0.2 - - - -
197P SER* 3.3 23.2 + - - -
207P ILE* 4.4 36.8 - - + -
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Residues in contact with LYS 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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191P ILE 3.4 17.5 + - - +
192P LEU* 3.8 22.9 - - + +
193P THR 3.1 0.2 - - - -
194P LEU* 1.4 77.3 - - - +
196P GLU* 1.3 62.4 + - - +
197P SER 3.2 4.3 + - - -
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Residues in contact with GLU 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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165P ASN* 3.9 20.1 + - - +
168P ASN* 4.0 15.1 - - + +
169P GLY* 5.5 0.9 - - - -
172P PHE* 2.4 51.0 - - + -
192P LEU 4.1 3.8 + - - +
193P THR* 3.2 17.0 + - - +
195P LYS* 1.3 77.8 - - - +
197P SER* 1.3 61.4 + - - +
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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