Contacts of the helix formed by residues 179 - 192 (chain A) in PDB entry 1OI4
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A GLU* 3.1 35.4 - - - +
174A SER* 3.7 6.7 - - - -
175A ARG* 2.9 55.7 + - - +
176A THR* 2.8 23.0 + - - +
178A ASP* 1.3 81.5 - - - +
180A LEU* 1.3 60.6 + - - +
181A PRO* 3.3 3.4 - - - -
182A ALA* 3.0 6.8 + - - +
183A PHE* 2.8 27.1 + - - +
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Residues in contact with LEU 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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37A SER* 3.6 31.4 - - - +
38A GLU* 4.5 4.9 - - + -
41A SER* 3.8 22.2 - - - +
42A PRO* 4.1 25.4 - - + -
124A ILE* 3.9 18.8 - - + -
176A THR 3.8 0.6 + - - -
177A PRO* 3.0 29.4 + - + +
179A ASP* 1.3 77.3 - - - +
181A PRO* 1.3 69.2 - - + +
183A PHE* 3.9 8.1 - - + -
184A ASN* 2.8 37.1 + - - +
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Residues in contact with PRO 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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177A PRO 4.3 0.9 - - - +
178A ASP* 3.7 13.0 - - - +
179A ASP 3.4 3.8 - - - -
180A LEU* 1.3 95.5 - - + +
182A ALA* 1.3 60.0 + - - +
184A ASN* 4.0 5.9 - - + +
185A ARG* 3.1 23.1 + - - +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A GLU* 3.7 31.6 - - + +
164A VAL* 3.1 31.1 - - + +
179A ASP 3.0 6.7 + - - +
181A PRO* 1.3 77.0 - - - +
183A PHE* 1.3 67.4 + - - +
185A ARG* 3.2 27.3 + - - +
186A GLU* 3.2 14.4 + - - +
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Residues in contact with PHE 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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42A PRO* 4.2 13.9 - - + -
46A PHE* 5.7 0.4 - + - -
91A LEU* 3.8 20.2 - - + -
122A PHE* 3.3 34.3 - - + -
123A ALA 3.7 27.1 - - - -
124A ILE* 3.8 18.2 - - + -
164A VAL* 3.2 7.5 - - - +
172A VAL* 3.7 18.8 - - + +
174A SER* 3.2 30.3 - - - +
179A ASP 2.8 13.3 + - - +
180A LEU* 3.5 13.9 - - + +
182A ALA* 1.3 78.7 - - - +
184A ASN* 1.3 74.7 + - - +
186A GLU* 3.4 2.4 + - - +
187A ALA* 3.1 26.1 + - + +
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Residues in contact with ASN 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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41A SER* 3.1 25.1 + - - -
42A PRO* 3.3 30.5 - - - +
45A GLU* 3.8 29.8 - - + +
46A PHE* 5.2 2.4 - - - -
180A LEU* 2.8 29.7 + - - +
181A PRO* 4.0 5.1 - - + +
183A PHE* 1.3 77.4 - - - +
185A ARG* 1.3 63.5 + - - +
187A ALA* 3.7 5.6 - - - +
188A LEU* 2.9 33.6 + - + +
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Residues in contact with ARG 185 (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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163A GLU* 4.5 9.1 + - - -
164A VAL* 3.6 26.9 - - - +
181A PRO 3.1 16.4 + - - +
182A ALA* 3.2 26.6 + - - +
184A ASN* 1.3 76.9 - - - +
186A GLU* 1.3 81.3 + - - +
188A LEU* 3.7 8.3 - - - +
189A ARG* 3.0 28.9 + - + +
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Residues in contact with GLU 186 (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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164A VAL* 4.2 15.9 - - + -
166A VAL* 3.6 31.0 - - + +
172A VAL* 3.9 15.5 - - + -
182A ALA 3.2 13.6 + - - +
185A ARG* 1.3 103.4 + - - +
187A ALA* 1.3 65.4 + - - +
189A ARG* 2.7 42.4 + - - +
190A LEU* 3.0 27.9 + - - +
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Residues in contact with ALA 187 (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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46A PHE* 3.9 13.7 - - + -
122A PHE* 3.6 48.8 - - + -
172A VAL* 4.5 1.5 - - + +
183A PHE* 3.1 20.4 + - + +
184A ASN* 3.7 6.1 - - - +
186A GLU* 1.3 75.7 - - - +
188A LEU* 1.3 64.6 + - - +
190A LEU* 3.2 2.4 + - - +
191A LEU* 3.1 27.3 + - - +
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Residues in contact with LEU 188 (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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45A GLU* 3.8 32.8 - - + +
46A PHE* 3.8 27.6 - - + -
49A ALA* 4.0 24.9 - - + -
51A HIS* 4.7 7.5 - - + +
184A ASN* 2.9 24.9 + - + +
185A ARG* 3.7 6.7 - - - +
187A ALA* 1.3 76.2 - - - +
189A ARG* 1.3 64.1 + - - +
191A LEU* 2.9 14.9 + - - +
192A GLY* 3.0 12.6 + - - -
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Residues in contact with ARG 189 (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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166A VAL* 4.4 8.1 - - - +
169A ASP* 2.6 31.5 + - - -
185A ARG* 3.0 19.9 + - + +
186A GLU* 2.7 46.7 + - - +
188A LEU* 1.3 77.0 - - - +
190A LEU* 1.3 81.1 + - + +
192A GLY* 3.2 16.9 + - - +
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Residues in contact with LEU 190 (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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120A PRO* 4.0 29.6 - - + +
122A PHE* 4.3 1.6 - - + -
166A VAL* 4.6 1.6 - - + -
169A ASP* 3.5 41.3 - - + +
170A GLN 3.7 13.5 - - - +
172A VAL* 3.5 28.7 - - + -
186A GLU 3.0 16.9 + - - +
187A ALA 3.7 4.5 - - - +
189A ARG* 1.3 100.6 - - + +
191A LEU* 1.3 61.3 + - - +
192A GLY 3.3 5.0 + - - +
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Residues in contact with LEU 191 (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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24A LYS* 3.0 44.4 + - + +
26A ILE* 4.0 17.3 - - + -
46A PHE* 3.9 25.1 - - + -
51A HIS* 3.5 34.6 + - + +
88A ASP* 4.9 6.5 - - + +
89A ALA* 3.6 26.5 - - + -
120A PRO* 5.5 2.0 - - + -
122A PHE* 3.8 12.8 - - + -
187A ALA 3.1 16.3 + - - +
188A LEU* 2.9 9.7 + - - +
190A LEU* 1.3 77.5 - - - +
192A GLY* 1.3 60.5 + - - +
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Residues in contact with GLY 192 (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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24A LYS* 4.8 5.1 + - - -
51A HIS* 5.5 1.6 - - - -
188A LEU 3.0 10.5 + - - -
189A ARG 3.2 12.6 + - - +
190A LEU 4.1 4.3 - - - +
191A LEU* 1.3 83.8 - - - +
193A ALA 1.3 49.6 + - - -
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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