Contacts of the helix formed by residues 180 - 195 (chain C) in PDB entry 4OA5
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 SER 180 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C SER* 5.1 1.7 - - - -
178C LYS 4.3 0.4 + - - -
179C VAL* 1.3 74.4 - - - +
181C SER* 1.3 57.5 + - - +
182C ASN* 3.3 12.5 + - - +
183C ALA* 3.0 28.8 + - - +
184C HIS* 2.9 27.5 + - - +
307C IOD 4.3 6.3 - - - -
308C IOD 3.3 13.4 - - - +
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Residues in contact with SER 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C PRO* 3.9 23.6 - - - +
176C THR 5.3 0.9 + - - -
179C VAL 3.4 5.4 + - - -
180C SER* 1.3 68.4 + - - +
182C ASN* 1.3 60.5 + - - +
184C HIS* 3.7 7.4 + - - +
185C ALA* 2.9 32.2 + - - +
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Residues in contact with ASN 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C SER* 3.4 30.2 + - - +
180C SER* 3.3 9.1 + - - +
181C SER* 1.3 79.6 - - - +
183C ALA* 1.3 60.7 + - - +
185C ALA* 3.9 5.0 - - - +
186C SER* 3.0 22.3 + - - -
116E GLU* 3.3 42.9 - - + +
119E ALA* 5.7 2.4 - - - +
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Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LYS* 4.2 10.8 - - + +
140C SER* 4.0 12.5 - - - +
166C LEU* 3.7 8.4 - - + +
180C SER* 3.0 17.7 + - - +
182C ASN* 1.3 76.5 - - - +
184C HIS* 1.3 57.8 + - - +
186C SER* 3.3 2.6 + - - -
187C MET* 2.9 31.2 + - - +
307C IOD 3.6 33.0 - - + -
308C IOD 4.0 7.6 - - + -
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Residues in contact with HIS 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C LEU* 3.4 12.8 - - + +
169C SER* 3.0 35.1 + - - -
170C VAL* 4.2 4.5 - - - -
172C ASP 2.9 29.3 + - - -
173C GLU 3.3 18.6 - - - -
175C PRO* 3.6 39.0 - - + +
179C VAL* 4.1 2.2 - - + -
180C SER 2.9 15.9 + - - +
181C SER 3.7 4.5 - - - +
182C ASN 3.2 0.2 - - - -
183C ALA* 1.3 72.8 - - - +
185C ALA* 1.3 68.3 + - - +
187C MET* 3.2 1.0 + - - +
188C ARG* 2.9 46.9 + - + +
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Residues in contact with ALA 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C SER 2.9 17.9 + - - +
182C ASN* 3.9 5.6 - - - +
184C HIS* 1.3 79.5 + - - +
186C SER* 1.3 62.9 + - - +
188C ARG* 3.7 5.6 + - - +
189C ALA* 3.2 23.0 + - - +
119E ALA* 4.4 20.3 - - + +
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Residues in contact with SER 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LYS 3.2 18.7 + - - -
140C SER* 3.5 19.4 + - - -
142C TYR* 3.6 11.4 + - - +
143C LEU* 3.7 24.4 + - - +
182C ASN* 3.0 20.4 + - - -
183C ALA 3.6 4.0 - - - -
185C ALA* 1.3 76.5 - - - +
187C MET* 1.3 59.2 + - - +
189C ALA 3.4 1.0 + - - -
190C PHE* 2.9 27.6 + - - +
119E ALA* 5.1 3.3 - - - +
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Residues in contact with MET 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LYS* 3.7 30.7 - - + +
142C TYR* 3.6 39.7 - - + -
163C ASN 3.5 17.3 - - - +
164C THR* 3.6 39.3 - - - +
166C LEU* 4.3 13.9 - - + -
170C VAL* 4.0 9.9 - - + -
183C ALA 2.9 15.0 + - - +
184C HIS 4.0 2.5 - - - +
186C SER* 1.3 73.8 - - - +
188C ARG* 1.3 67.2 + - - +
190C PHE* 3.6 6.1 - - - +
191C ASN* 2.9 29.8 + - - +
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Residues in contact with ARG 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 3.6 20.7 + - - -
16B LEU* 5.6 0.3 - - - +
170C VAL* 2.9 37.9 + - + +
171C PHE 3.7 12.9 + - - -
172C ASP 3.8 12.4 + - - -
173C GLU* 3.7 29.5 + - - +
184C HIS* 2.9 41.4 + - + +
185C ALA* 3.9 6.5 - - - +
187C MET* 1.3 77.4 - - - +
189C ALA* 1.3 56.0 + - - +
191C ASN* 4.0 1.6 - - - +
192C ASP* 3.0 29.9 + - - +
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Residues in contact with ALA 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LEU* 3.9 17.8 - - + +
185C ALA 3.2 14.9 + - - +
186C SER 3.9 3.1 - - - +
188C ARG* 1.3 77.5 - - - +
190C PHE* 1.3 61.2 + - - +
192C ASP* 3.7 5.9 - - - +
193C GLU* 2.9 32.2 + - - +
119E ALA* 5.8 2.0 - - + +
122E ASN* 3.5 25.3 - - + +
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Residues in contact with PHE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C ILE* 4.1 15.3 - - + -
142C TYR* 3.5 45.3 - + + -
143C LEU* 3.7 10.9 - - + +
146C LEU* 3.8 25.2 - - + +
159C ILE* 4.6 4.3 - - + -
161C ALA* 3.7 22.2 - - + -
164C THR* 3.9 20.6 - - + -
186C SER 2.9 18.6 + - - +
187C MET* 3.3 9.4 + - - +
189C ALA* 1.3 77.0 - - - +
191C ASN* 1.3 75.4 + - - +
193C GLU* 3.4 2.3 + - - +
194C LEU* 3.1 49.8 + - + +
212C MET* 4.2 2.2 - - + -
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Residues in contact with ASN 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TYR* 3.0 29.8 + - - +
16B LEU* 4.3 1.1 - - - -
17B PHE* 3.5 18.8 - - + -
164C THR* 2.9 33.5 + - - -
170C VAL* 3.7 9.3 - - - +
187C MET* 2.9 14.6 + - - +
188C ARG 4.0 0.9 - - - +
190C PHE* 1.3 90.0 - - - +
192C ASP* 1.3 57.5 + - - +
194C LEU 3.2 2.1 + - - -
195C ALA* 2.9 24.3 + - - +
204C ILE* 3.9 10.3 - - - +
212C MET* 3.5 21.1 - - - +
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Residues in contact with ASP 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.1 22.6 - - + +
188C ARG 3.0 19.9 + - - +
189C ALA* 3.7 7.0 - - - +
191C ASN* 1.3 77.4 - - - +
193C GLU* 1.3 63.1 + - - +
195C ALA* 3.2 17.5 + - - +
196C ASN* 3.7 4.7 + - - +
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Residues in contact with GLU 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LEU* 5.6 0.7 - - + -
146C LEU* 3.5 25.8 - - + -
150C LYS* 3.3 18.6 + - + -
189C ALA 2.9 18.3 + - - +
190C PHE 3.8 3.8 - - - +
192C ASP* 1.3 75.0 + - - +
194C LEU* 1.3 57.3 + - - +
196C ASN* 3.1 27.5 + - - +
199C LYS* 3.9 10.4 - - - +
200C TYR* 2.8 41.9 + - + +
126D GLU* 4.2 1.4 - - - +
122E ASN* 5.4 7.9 - - - +
125E LYS* 3.5 26.2 + - - -
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Residues in contact with LEU 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 4.0 2.0 - - - -
146C LEU* 3.8 18.2 - - + -
159C ILE* 4.2 11.0 - - + -
190C PHE* 3.1 53.1 + - + +
191C ASN 3.6 4.3 - - - +
193C GLU* 1.3 75.0 - - - +
195C ALA* 1.3 58.2 + - - +
196C ASN 3.2 2.4 + - - +
200C TYR* 3.6 44.8 - - + +
202C SER* 2.7 30.3 + - - +
212C MET* 3.7 26.7 - - + -
214C SER* 3.7 11.7 - - - +
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Residues in contact with ALA 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.3 44.0 - - + +
17B PHE* 3.7 13.2 - - + -
191C ASN 2.9 12.8 + - - +
192C ASP* 3.5 11.9 - - - +
193C GLU 3.2 1.0 - - - -
194C LEU* 1.3 74.9 - - - +
196C ASN* 1.3 58.8 + - - +
197C LYS* 3.1 18.9 + - - +
200C TYR 5.4 0.2 - - - -
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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
------------------------------------------------------------
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