Contacts of the helix formed by residues 172 - 185 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A MET* 3.6 3.4 - - - -
130B TYR* 4.9 0.3 + - - -
169B PHE 4.2 11.2 - - - +
170B GLN* 3.2 11.3 + - - +
171B ILE* 1.3 76.4 - - - +
173B PRO* 1.3 71.6 - - + +
174B SER* 3.6 10.0 + - - -
175B VAL* 3.2 23.4 + - - +
176B ALA* 2.9 27.5 + - - +
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Residues in contact with PRO 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A SER* 3.6 36.2 - - - +
209A MET* 3.4 21.7 - - + -
212A PRO* 5.1 0.2 - - - +
172B THR* 1.3 88.0 - - + +
174B SER* 1.3 56.2 + - - +
176B ALA* 3.2 3.1 + - + +
177B LYS* 3.0 33.8 + - - +
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Residues in contact with SER 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B TYR* 3.7 15.9 - - - -
172B THR* 3.2 9.3 + - - -
173B PRO* 1.3 79.6 - - - +
175B VAL* 1.3 61.9 + - - +
177B LYS* 3.5 19.5 - - - +
178B LYS* 3.3 32.8 + - - +
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA* 4.1 13.5 - - + -
130B TYR* 3.7 34.8 - - + +
133B PHE* 4.4 4.0 - - + -
170B GLN 3.6 13.5 - - - +
171B ILE* 4.1 19.7 - - + -
172B THR* 3.2 24.2 + - - +
174B SER* 1.3 76.4 - - - +
176B ALA* 1.3 56.7 + - - +
178B LYS* 3.1 4.7 + - - +
179B ILE* 2.9 48.8 + - + +
1277B TRT 4.4 4.3 - - - -
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A MET* 3.7 35.0 - - + +
212A PRO* 4.3 4.0 - - + -
213A PHE* 3.6 12.4 - - + -
171B ILE* 5.0 1.1 - - + +
172B THR 2.9 13.8 + - - +
173B PRO* 3.5 12.6 - - + +
175B VAL* 1.3 77.1 - - - +
177B LYS* 1.3 57.3 + - - +
179B ILE* 3.3 9.8 + - - -
180B ALA* 2.9 30.5 + - - +
1276B TRT 4.7 4.5 - - - -
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Residues in contact with LYS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A PRO* 3.7 25.5 - - + +
173B PRO 3.0 11.9 + - - +
174B SER* 3.5 28.7 + - - +
176B ALA* 1.3 76.9 - - - +
178B LYS* 1.3 70.8 + - + +
180B ALA* 3.6 1.6 + - - +
181B ALA* 3.1 28.4 + - - +
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Residues in contact with LYS 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 3.3 25.1 + - + +
79B GLU 4.6 6.2 + - - -
80B CYS* 3.7 28.7 - - - -
82B GLU* 2.8 28.6 + - - +
83B ILE* 4.2 3.1 - - + -
130B TYR* 3.1 32.7 + - + +
133B PHE* 3.5 19.7 - - + -
174B SER* 3.3 21.2 + - - +
175B VAL* 3.1 8.8 + - - +
177B LYS* 1.3 83.5 - - + +
179B ILE* 1.3 63.2 + - - +
181B ALA* 3.4 7.8 + - - -
182B VAL 3.4 5.2 + - - -
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Residues in contact with ILE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A PHE* 3.9 4.9 - - + -
133B PHE* 3.5 12.5 - - + -
171B ILE* 4.7 1.8 - - + -
175B VAL* 2.9 35.9 + - + +
176B ALA* 3.6 7.0 - - - +
178B LYS* 1.3 73.4 - - - +
180B ALA* 1.3 66.9 + - - +
181B ALA 3.2 0.2 + - - -
182B VAL* 3.3 6.0 - - - +
183B LEU* 3.2 39.7 + - + +
1276B TRT 3.4 54.5 - - - +
1277B TRT 3.6 38.6 - - - +
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Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A PRO* 3.4 45.3 - - + +
213A PHE* 3.6 24.2 - - + -
176B ALA 2.9 14.1 + - - +
177B LYS 3.8 1.1 - - - +
179B ILE* 1.3 72.9 - - - +
181B ALA* 1.3 62.1 + - - +
183B LEU* 3.1 4.6 + - - -
184B THR* 2.8 33.3 + - + +
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Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 3.5 27.8 - - + -
177B LYS 3.1 17.4 + - - +
178B LYS* 3.6 2.0 - - - +
179B ILE 3.2 0.2 - - - -
180B ALA* 1.3 76.3 - - - +
182B VAL* 1.3 59.2 + - - +
184B THR* 3.1 6.5 + - - -
185B ASP 3.0 27.4 + - - -
186B SER* 3.0 19.5 + - - +
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Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 3.5 44.2 - - + +
133B PHE* 3.8 19.3 - - + -
137B LEU* 5.9 2.2 - - + -
178B LYS 3.4 1.3 + - - +
179B ILE* 3.3 14.8 + - - +
181B ALA* 1.3 75.1 - - - +
183B LEU* 1.3 60.5 + - + +
184B THR 3.3 0.9 + - - -
186B SER* 4.9 1.8 - - - +
187B PHE* 4.1 34.0 + - + +
189B LEU 5.3 1.2 - - - +
191B VAL* 4.6 2.3 - - - +
1277B TRT 3.8 49.6 - - + +
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A PHE* 4.2 13.9 - - + -
179B ILE* 3.2 31.4 + - + +
180B ALA* 3.1 8.8 + - - +
182B VAL* 1.3 78.2 - - + +
184B THR* 1.3 63.6 + - + +
191B VAL* 4.3 19.3 - - + +
194B ILE* 4.0 29.6 - - + -
217B LYS* 4.6 8.0 - - - +
218B ILE* 4.0 23.6 - - + +
1275B TRT 4.6 9.4 - - + -
1276B TRT 4.8 1.8 - - - +
1277B TRT 3.5 42.4 - - + -
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Residues in contact with THR 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A PRO 4.9 6.6 + - - +
213A PHE* 5.8 0.9 - - + -
219A LYS* 5.9 1.3 + - - +
59B ARG* 3.2 5.7 + - - -
180B ALA* 2.8 27.5 + - + +
181B ALA* 3.1 9.5 + - - -
182B VAL 3.3 1.5 - - - -
183B LEU* 1.3 87.1 - - + +
185B ASP* 1.3 71.4 + - - +
186B SER 4.0 0.4 - - - -
187B PHE 6.0 1.1 - - - -
215B THR* 4.2 24.5 - - + -
217B LYS* 3.1 37.2 - - + +
218B ILE* 4.9 4.3 - - + -
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Residues in contact with ASP 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG* 2.6 38.3 + - - +
65B LEU 5.0 0.7 - - - +
68B ARG* 2.8 41.6 + - - +
69B LEU* 3.4 18.5 + - - +
72B ASN* 3.0 34.7 + - - +
181B ALA 3.0 1.8 + - - -
184B THR* 1.3 84.9 + - - +
186B SER* 1.3 63.6 + - - +
187B PHE 5.6 0.2 - - - -
217B LYS* 5.9 0.4 - - - -
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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
------------------------------------------------------------
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