Contacts of the helix formed by residues 179 - 187 (chain P) in PDB entry 5IYB
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 ASP 179 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178P LEU* 1.3 76.3 - - - +
180P LEU* 1.3 64.8 + - - +
181P LYS* 2.7 41.4 + - - +
182P THR* 2.6 37.1 + - - +
183P ILE* 3.1 15.3 + - - +
246P PHE* 4.7 9.5 - - + -
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Residues in contact with LEU 180 (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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178P LEU* 3.8 10.3 + - + +
179P ASP* 1.3 72.4 + - - +
181P LYS* 1.3 52.7 + - - +
183P ILE* 3.2 17.6 - - + +
184P ALA* 2.7 36.6 + - - +
192P TYR* 3.6 22.1 - - + +
198P ALA 3.2 26.7 - - - +
199P ALA* 4.0 0.4 - - - -
200P VAL* 3.5 24.3 - - + +
213P ILE* 3.4 20.0 - - + +
214P PHE 4.0 6.1 - - - +
215P SER* 3.5 40.8 - - - +
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Residues in contact with LYS 181 (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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68O CYS* 5.5 2.8 - - - +
179P ASP* 2.7 38.1 + - - +
180P LEU* 1.3 78.3 - - - +
182P THR* 1.3 60.9 + - - +
184P ALA* 3.4 3.7 + - - +
185P LEU* 2.8 29.4 + - - +
192P TYR* 4.1 23.2 + - + -
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Residues in contact with THR 182 (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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179P ASP* 2.6 34.8 + - - +
181P LYS* 1.3 76.6 + - - +
183P ILE* 1.3 56.4 + - - +
185P LEU* 3.0 13.6 + - + +
186P ARG* 2.7 49.4 + - + +
246P PHE* 4.2 19.3 - - + -
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Residues in contact with ILE 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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178P LEU* 4.0 32.5 - - + -
179P ASP 3.4 8.5 - - - +
180P LEU* 3.2 28.9 - - + +
182P THR* 1.3 75.7 - - - +
184P ALA* 1.3 55.4 + - - +
186P ARG 3.1 0.5 + - - -
187P ALA* 2.7 45.5 + - + +
200P VAL* 4.6 22.2 - - + -
202P MET* 4.7 12.8 - - - -
213P ILE* 4.9 7.0 - - + -
241P VAL* 5.7 4.3 - - + -
244P LEU* 3.8 20.2 - - + -
246P PHE* 3.7 17.9 - - + -
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Residues in contact with ALA 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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66O ARG* 3.0 27.8 + - + +
67O PHE 4.5 2.5 - - - +
68O CYS* 4.3 15.0 - - + -
180P LEU 2.7 20.1 + - - +
181P LYS* 3.5 7.6 - - - +
183P ILE* 1.3 74.3 - - - +
185P LEU* 1.3 62.6 + - - +
187P ALA* 3.7 7.2 + - - +
190P ALA* 5.2 5.4 - - - +
191P GLU* 5.1 0.9 - - - +
192P TYR* 3.5 30.1 - - + +
200P VAL* 4.7 6.0 - - + +
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Residues in contact with LEU 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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66O ARG* 3.0 33.8 + - - +
68O CYS* 5.1 3.6 - - - -
181P LYS 2.8 15.6 + - - +
182P THR* 3.0 13.7 + - + +
184P ALA* 1.3 77.1 - - - +
186P ARG* 1.3 76.8 + - + +
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Residues in contact with ARG 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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324N GLU* 5.1 13.9 + - - +
327N GLU* 4.2 7.1 - - - +
66O ARG* 3.4 7.6 + - - -
182P THR* 2.7 36.7 + - + +
183P ILE 3.7 1.8 - - - +
185P LEU* 1.3 86.3 - - + +
187P ALA* 1.3 67.2 + - - +
188P ARG* 3.8 1.7 + - - +
243P LYS 4.3 13.5 + - - -
244P LEU* 3.7 47.1 + - + +
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Residues in contact with ALA 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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65O TYR 4.5 1.2 - - - +
66O ARG* 2.8 30.7 + - - +
183P ILE* 2.7 25.8 + - + +
184P ALA 3.7 2.7 - - - +
186P ARG* 1.3 73.2 - - - +
188P ARG* 1.3 61.0 + - - +
189P ASN 4.5 0.2 - - - +
190P ALA* 3.7 27.7 - - + +
202P MET* 4.1 17.5 - - + -
244P LEU* 5.0 6.7 - - + +
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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