Contacts of the helix formed by residues 180 - 194 (chain A) in PDB entry 4I0A
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A CYS* 1.3 75.9 - - - +
181A ARG* 1.3 59.4 - - - +
182A GLU* 3.3 16.4 + - - +
183A THR* 2.8 32.8 + - - -
184A VAL* 3.0 31.4 + - - +
302A CMP 3.4 23.3 + - - -
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Residues in contact with ARG 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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170A ARG* 3.5 23.8 - - + +
171A GLN* 3.7 40.4 + - - +
180A SER* 1.3 69.4 - - - +
182A GLU* 1.3 66.0 + - - +
184A VAL* 3.1 9.8 + - - +
185A GLY 2.8 30.8 + - - -
302A CMP 3.1 44.1 + - - +
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Residues in contact with GLU 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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170A ARG* 4.7 8.4 + - - +
180A SER* 3.3 22.0 - - - +
181A ARG* 1.3 83.5 + - - +
183A THR* 1.3 60.8 + - - +
185A GLY* 3.2 3.6 + - - -
186A ARG* 3.0 41.4 + - - +
302A CMP 4.2 3.2 + - - -
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Residues in contact with THR 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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140A VAL* 4.4 8.7 - - + -
179A CYS* 4.1 22.5 - - + +
180A SER* 2.8 27.4 + - - -
182A GLU* 1.3 72.8 - - - +
184A VAL* 1.4 66.6 + - - +
186A ARG* 3.2 13.8 + - + +
187A ILE* 3.0 37.0 + - + +
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Residues in contact with VAL 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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144A ILE* 4.2 9.0 - - + -
170A ARG* 3.5 20.2 - - + +
173A ILE* 3.8 24.0 - - + -
174A GLY* 3.5 23.8 - - - +
179A CYS* 3.4 18.6 - - - -
180A SER 3.0 20.4 + - - +
181A ARG* 3.1 7.4 + - - +
183A THR* 1.4 75.9 - - - +
185A GLY* 1.3 58.3 + - - +
187A ILE* 3.1 2.1 + - - +
188A LEU* 2.8 50.5 + - + +
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Residues in contact with GLY 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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170A ARG* 3.5 37.4 + - - +
181A ARG 2.8 14.8 + - - -
182A GLU 3.2 3.3 + - - -
184A VAL* 1.3 72.7 - - - +
186A ARG* 1.3 63.0 + - - +
188A LEU* 3.9 5.4 - - - +
189A LYS* 3.1 23.7 + - - +
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Residues in contact with ARG 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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182A GLU* 3.0 30.4 + - - +
183A THR* 3.2 10.4 + - + +
185A GLY* 1.3 75.7 - - - +
187A ILE* 1.3 65.1 + - + +
189A LYS* 3.6 7.3 - - - +
190A MET* 3.2 25.6 + - - +
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Residues in contact with ILE 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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140A VAL* 4.9 4.3 - - + -
141A THR* 3.1 48.5 - - + +
144A ILE* 3.7 29.8 - - + -
183A THR* 3.0 34.2 + - + +
184A VAL 3.8 0.2 - - - +
186A ARG* 1.3 77.9 - - + +
188A LEU* 1.3 62.9 + - - +
190A MET* 3.1 16.6 + - + +
191A LEU* 2.8 37.6 + - + +
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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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144A ILE* 4.3 13.2 - - + -
148A LEU* 4.1 17.9 - - + -
170A ARG* 4.6 13.2 - - + +
173A ILE* 4.1 15.7 - - + -
184A VAL* 2.8 37.6 + - + +
185A GLY* 3.9 5.2 - - - +
187A ILE* 1.3 76.0 - - - +
189A LYS* 1.3 63.0 + - - +
191A LEU* 3.1 6.8 + - + +
192A GLU* 3.1 24.0 + - - +
197A ILE* 3.9 27.5 - - + +
199A ALA* 5.6 8.5 - - + -
204A ILE* 4.1 15.9 - - + -
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Residues in contact with LYS 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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185A GLY 3.1 13.1 + - - +
186A ARG* 3.6 11.9 - - - +
187A ILE 3.2 0.2 - - - -
188A LEU* 1.3 77.4 - - - +
190A MET* 1.3 62.0 + - + +
192A GLU* 3.3 29.0 + - - +
193A ASP* 3.2 57.9 + - - +
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Residues in contact with MET 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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141A THR* 5.1 13.5 - - + +
186A ARG 3.2 15.3 + - - +
187A ILE* 3.1 25.2 + - + +
189A LYS* 1.3 79.8 - - + +
191A LEU* 1.3 63.5 + - + +
193A ASP* 3.6 8.8 + - - +
194A GLN* 3.1 48.7 + - - +
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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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141A THR* 4.0 21.5 - - + +
144A ILE* 3.8 28.7 - - + -
145A ALA* 4.4 16.4 - - + +
148A LEU* 4.2 15.5 - - + -
187A ILE* 2.8 23.4 + - + +
188A LEU* 3.1 9.4 + - + +
190A MET* 1.3 79.5 - - + +
192A GLU* 1.3 60.1 + - - +
194A GLN* 3.5 13.5 - - - +
195A ASN 3.5 3.5 + - - -
196A LEU* 3.0 53.5 + - + +
197A ILE* 4.0 13.7 - - + -
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Residues in contact with GLU 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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188A LEU 3.1 9.4 + - - +
189A LYS* 3.6 36.8 + - - +
190A MET 3.2 0.2 - - - -
191A LEU* 1.3 76.7 - - - +
193A ASP* 1.3 65.2 + - - +
195A ASN* 3.0 24.1 + - - +
197A ILE* 3.2 32.3 - - + +
198A SER* 3.9 4.7 - - - -
199A ALA* 3.4 34.7 + - - +
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Residues in contact with ASP 193 (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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189A LYS* 3.2 44.5 + - - +
190A MET* 3.8 10.6 - - - +
192A GLU* 1.3 73.6 - - - +
194A GLN* 1.3 53.7 + - + +
195A ASN* 2.7 30.2 + - - +
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Residues in contact with GLN 194 (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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141A THR* 5.4 3.9 - - - +
190A MET* 3.1 48.0 + - - +
191A LEU* 3.5 21.9 - - - +
192A GLU 3.4 0.4 - - - -
193A ASP* 1.3 72.1 - - + +
195A ASN* 1.3 68.9 + - - +
196A LEU* 2.9 22.5 + - + +
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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