Contacts of the helix formed by residues 182 - 194 (chain P) in PDB entry 5IJO
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 182 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50P PHE 5.2 10.1 - - - +
51P ILE* 6.4 0.7 - - - +
170P THR* 4.8 15.8 + - - +
171P THR* 5.3 4.3 - - - -
174P THR* 3.8 6.6 - - - +
181P GLY* 1.3 68.7 - - - -
183P THR* 1.3 67.4 + - - +
185P LYS* 3.0 9.1 + - - +
186P VAL* 2.9 23.0 + - - +
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Residues in contact with THR 183 (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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174P THR* 3.8 18.5 - - - -
181P GLY 3.3 1.0 - - - -
182P LEU* 1.3 79.8 - - - +
184P TYR* 1.3 65.2 + - - +
185P LYS 3.3 0.2 + - - -
186P VAL* 3.4 14.8 + - - +
187P LEU* 4.5 2.6 + - - +
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Residues in contact with TYR 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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174P THR* 5.2 1.4 - - - +
181P GLY* 3.4 15.4 + - - +
182P LEU 3.2 0.6 - - - -
183P THR* 1.3 80.0 - - - +
185P LYS* 1.3 60.3 + - - +
186P VAL 3.6 0.3 + - - -
187P LEU* 4.1 9.7 + - - +
188P THR* 4.3 5.9 + - - -
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Residues in contact with LYS 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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51P ILE* 3.8 24.9 - - + +
52P SER* 5.6 0.7 - - - -
53P LEU* 6.3 1.3 - - + -
181P GLY 3.4 9.6 + - - +
182P LEU* 3.0 11.8 + - - +
184P TYR* 1.3 77.5 - - + +
186P VAL* 1.3 64.7 + - - +
187P LEU 3.2 2.5 - - - -
188P THR* 2.9 10.8 + - - +
189P LEU* 2.9 22.7 + - + +
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Residues in contact with VAL 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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182P LEU 2.9 14.6 + - - +
183P THR* 3.4 11.0 + - - +
185P LYS* 1.3 74.4 - - - +
187P LEU* 1.3 63.2 + - - +
189P LEU* 3.1 16.3 + - - +
190P VAL* 3.2 12.1 + - - +
231P SER* 6.2 3.8 - - - -
232P LEU* 6.1 6.3 - - + -
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Residues in contact with LEU 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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183P THR 4.5 2.3 + - - +
184P TYR 4.1 8.2 + - - +
185P LYS 3.2 0.6 - - - -
186P VAL* 1.3 78.3 - - - +
188P THR* 1.3 64.3 + - - +
190P VAL* 3.2 8.5 + - - +
191P SER* 3.1 18.5 + - - -
248P LEU* 6.5 1.1 - - + -
252P HIS* 5.5 11.0 - - + -
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Residues in contact with THR 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 TYR 4.3 3.7 + - - -
185P LYS* 2.9 15.5 + - - -
187P LEU* 1.3 79.5 - - - +
189P LEU* 1.3 52.9 + - - +
191P SER* 2.5 40.6 - - - +
192P GLN* 3.9 5.5 - - - +
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Residues in contact with LEU 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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51P ILE 5.5 0.2 - - - +
52P SER* 4.4 27.1 - - - +
53P LEU* 5.9 6.1 - - + -
185P LYS* 2.9 11.7 + - + +
186P VAL* 3.1 13.4 + - - +
188P THR* 1.3 71.8 - - - +
190P VAL* 1.4 55.3 + - - +
191P SER 2.5 18.9 - - - +
192P GLN* 4.5 3.6 - - - +
193P ILE* 3.8 11.6 + - - +
228P LEU* 6.0 5.8 - - + -
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Residues in contact with VAL 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 VAL 3.2 7.5 + - - +
187P LEU* 3.2 10.3 + - - +
189P LEU* 1.4 73.9 - - - +
191P SER* 1.3 66.8 + - - +
193P ILE* 3.6 5.6 + - - +
194P ASP* 3.5 16.6 + - - +
228P LEU* 5.7 11.1 - - + +
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Residues in contact with SER 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 LEU 3.1 12.0 + - - -
188P THR* 2.5 23.7 + - - +
189P LEU 2.5 21.7 - - - +
190P VAL* 1.3 78.2 - - - +
192P GLN* 1.3 59.0 + - - +
193P ILE 2.7 1.4 + - - -
194P ASP* 4.1 10.3 - - - -
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Residues in contact with GLN 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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53P LEU* 6.3 3.4 - - + -
188P THR 3.9 6.3 - - - +
189P LEU* 4.5 3.4 - - - +
191P SER* 1.3 77.5 - - - +
193P ILE* 1.4 64.0 + - - +
194P ASP* 2.9 6.2 - - - +
195P VAL* 3.1 24.8 + - - +
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Residues in contact with ILE 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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189P LEU 3.8 9.1 + - - +
190P VAL* 3.9 10.3 - - - +
191P SER 2.7 9.7 + - - -
192P GLN* 1.4 73.9 - - - +
194P ASP* 1.3 61.9 + - - +
195P VAL 3.4 5.5 + - - +
221P ILE* 5.1 22.8 - - + +
224P CYS* 5.6 6.5 - - + -
225P ARG* 5.9 7.0 - - + +
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Residues in contact with ASP 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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190P VAL 3.5 13.5 + - - +
191P SER* 4.1 5.8 - - - -
192P GLN 4.1 6.7 - - - +
193P ILE* 1.3 78.3 - - - +
195P VAL* 1.4 66.8 + - - +
196P ASN* 3.1 6.8 + - - +
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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