Contacts of the helix formed by residues 172 - 185 (chain A) in PDB entry 1OIZ
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 THR 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A TYR* 4.6 4.3 + - - +
169A PHE 4.2 11.7 - - - +
170A GLN* 3.1 10.8 + - - +
171A ILE* 1.3 75.0 - - - +
173A PRO* 1.3 69.7 - - + +
174A SER* 3.5 9.2 + - - -
175A VAL* 3.1 24.9 + - + +
176A ALA* 2.8 27.5 + - - +
209B MET* 3.9 1.8 - - - -
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Residues in contact with PRO 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A THR* 1.3 86.7 - - - +
174A SER* 1.3 60.5 + - - +
176A ALA* 3.6 2.7 - - + +
177A LYS* 3.1 24.4 + - - +
208B SER* 3.6 42.8 - - - +
209B MET* 3.6 17.7 - - - -
212B PRO* 5.1 1.0 - - - +
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Residues in contact with SER 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 4.9 7.0 + - - -
172A THR* 3.1 10.1 + - - -
173A PRO* 1.3 79.4 - - - +
175A VAL* 1.3 61.5 + - - +
177A LYS* 3.4 9.8 + - - +
178A LYS* 3.2 45.0 + - - +
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA* 4.3 19.7 - - + -
130A TYR* 3.8 32.5 - - + +
133A PHE* 4.8 10.5 - - + -
170A GLN 3.5 12.8 - - - +
171A ILE* 4.3 11.4 - - + -
172A THR* 3.1 25.0 + - + +
174A SER* 1.3 71.1 - - - +
176A ALA* 1.3 67.1 + - - +
178A LYS* 3.1 9.7 + - - +
179A ILE* 2.9 41.0 + - + +
1275A TRT 5.2 1.3 - - - -
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Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 4.4 4.2 - - + +
172A THR 2.8 16.3 + - - +
173A PRO* 3.6 9.4 - - + +
175A VAL* 1.3 77.6 - - - +
177A LYS* 1.3 56.2 - - - +
179A ILE* 3.3 10.9 + - - +
180A ALA* 3.0 25.6 + - - +
1276A TRT 4.2 9.6 - - - +
209B MET* 3.8 30.1 - - + +
212B PRO* 4.3 4.0 - - + -
213B PHE* 3.5 16.6 - - + -
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Residues in contact with LYS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 4.7 12.5 + - - -
173A PRO 3.1 17.1 + - - +
174A SER* 3.5 9.2 - - - +
176A ALA* 1.3 75.1 - - - +
178A LYS* 1.3 64.1 + - + +
180A ALA* 3.5 2.8 + - - +
181A ALA* 3.1 22.7 + - - +
212B PRO* 3.7 25.4 - - + +
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Residues in contact with LYS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TRP* 3.4 18.7 + - + +
79A GLU* 3.2 28.9 + - - +
80A CYS* 3.4 25.7 - - - +
82A GLU* 4.7 5.7 + - - -
83A ILE* 4.2 13.2 - - + -
130A TYR* 4.4 20.0 - - + -
133A PHE* 3.5 18.6 - - + -
174A SER* 3.2 31.6 + - - +
175A VAL* 3.1 9.7 + - - +
177A LYS* 1.3 74.3 - - + +
179A ILE* 1.3 66.0 + - - +
181A ALA* 3.4 1.7 + - - -
182A VAL 3.3 17.7 + - - -
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Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PHE* 3.7 21.5 - - + -
171A ILE* 4.3 16.6 - - + -
175A VAL* 2.9 30.6 + - + +
176A ALA* 3.6 8.5 - - - +
178A LYS* 1.3 74.3 - - - +
180A ALA* 1.3 68.1 + - - +
182A VAL* 3.2 7.8 - - + +
183A LEU* 3.2 40.0 + - + +
1274A TRT 5.2 5.8 - - + -
1275A TRT 3.8 42.8 - - + +
1276A TRT 4.7 9.2 - - - -
213B PHE* 4.1 10.3 - - + -
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ALA 3.0 7.7 + - - +
177A LYS 3.8 1.6 - - - +
179A ILE* 1.3 75.9 - - - +
181A ALA* 1.3 58.3 + - - +
183A LEU* 3.2 4.6 + - - -
184A THR* 2.6 38.1 + - + +
212B PRO* 3.5 45.3 - - + +
213B PHE* 3.6 27.1 - - + -
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TRP* 3.6 17.0 - - + -
177A LYS 3.1 17.2 + - - +
178A LYS* 3.6 7.0 - - - +
179A ILE 3.2 0.2 - - - -
180A ALA* 1.3 76.9 - - - +
182A VAL* 1.3 63.5 + - - +
184A THR* 3.1 5.5 + - - -
185A ASP 3.1 9.4 + - - -
186A SER* 3.1 40.0 + - - +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TRP* 3.5 43.3 - - + +
133A PHE* 3.6 18.6 - - + -
137A LEU* 4.8 4.7 - - + -
178A LYS 3.3 0.6 + - - -
179A ILE* 3.2 16.4 - - - +
181A ALA* 1.3 77.3 - - - +
183A LEU* 1.3 60.8 + - + +
184A THR 3.5 1.0 + - - -
186A SER* 4.5 5.1 + - - -
187A PHE* 4.2 23.9 + - + +
189A LEU 5.2 1.4 - - - +
191A VAL* 4.5 1.2 - - - +
1275A TRT 3.0 56.5 - - + +
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Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A PHE* 6.1 2.0 - - + -
179A ILE* 3.2 35.9 + - + +
180A ALA* 3.7 4.9 - - - +
182A VAL* 1.3 75.7 - - + +
184A THR* 1.3 61.5 + - + +
189A LEU 6.1 0.2 - - - -
191A VAL* 3.8 24.3 + - + +
194A ILE* 4.1 29.6 - - + -
217A LYS* 4.8 5.0 - - - +
218A ILE* 4.2 22.0 - - + +
1274A TRT 4.4 10.1 - - + -
1275A TRT 3.8 40.4 - - + -
213B PHE* 4.3 14.8 - - + -
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Residues in contact with THR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ARG* 3.1 17.0 + - - -
180A ALA* 2.6 29.6 + - + +
181A ALA* 3.1 6.7 + - - -
182A VAL 3.3 0.8 - - - -
183A LEU* 1.3 85.1 - - + +
185A ASP* 1.3 68.3 + - - +
186A SER 3.9 0.4 - - - -
187A PHE 6.0 0.9 - - - -
215A THR* 3.9 27.8 - - + -
217A LYS* 3.2 31.8 + - + +
218A ILE* 4.2 9.9 - - + -
212B PRO 5.4 3.6 + - - +
213B PHE* 6.0 0.7 - - + -
219B LYS* 6.0 0.3 + - - -
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Residues in contact with ASP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ARG* 2.8 35.1 + - - +
65A LEU* 4.9 0.9 - - - +
68A ARG* 2.7 40.8 + - - +
69A LEU* 3.4 18.2 + - - +
72A ASN* 3.1 33.1 + - - +
181A ALA* 3.1 0.8 + - - +
184A THR* 1.3 85.2 + - - +
186A SER* 1.3 63.8 + - - +
217A LYS* 4.1 6.5 - - - +
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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