Contacts of the helix formed by residues 183 - 193 (chain A) in PDB entry 3OTB
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 LEU 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A GLY 4.1 8.7 - - - +
182A THR* 1.3 80.1 - - - +
184A ALA* 1.3 67.3 + - - +
185A ALA* 3.4 5.8 - - + +
186A ASP* 3.0 24.8 - - + +
187A LYS* 3.2 24.5 + - - +
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Residues in contact with ALA 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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152A HIS* 6.1 2.9 - - + -
156A LEU* 4.3 20.1 - - + +
183A LEU* 1.3 78.0 - - - +
185A ALA* 1.3 62.0 + - - +
186A ASP 3.2 0.2 + - - -
187A LYS* 3.4 3.1 + - - +
188A ASN* 3.1 24.3 + - - +
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Residues in contact with ALA 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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183A LEU* 4.3 5.6 - - + +
184A ALA* 1.3 79.0 - - - +
186A ASP* 1.3 62.9 + - - +
188A ASN* 3.9 7.7 - - - +
189A GLU* 3.0 26.5 + - - +
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Residues in contact with ASP 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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178A ARG* 4.7 7.8 + - - -
181A GLY 4.8 0.7 - - - +
182A THR* 3.3 27.0 - - - +
183A LEU* 3.0 42.7 + - - +
184A ALA 3.1 0.4 - - - -
185A ALA* 1.3 81.5 - - - +
187A LYS* 1.3 62.0 + - - +
189A GLU* 3.4 3.5 + - - +
190A ILE* 3.1 23.9 + - - +
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Residues in contact with LYS 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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156A LEU* 3.9 33.8 - - + +
157A TYR* 3.8 30.5 - - - +
160A VAL* 4.1 16.9 - - + +
179A LEU* 3.7 14.1 + - + -
182A THR* 2.9 47.4 + - - +
183A LEU 3.2 11.5 + - - +
184A ALA* 4.1 2.6 - - - +
186A ASP* 1.3 71.2 - - - +
188A ASN* 1.3 64.4 + - - +
189A GLU 3.0 4.0 - - - -
190A ILE* 2.9 22.7 + - - +
191A LEU* 3.1 16.1 + - - +
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Residues in contact with ASN 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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156A LEU* 4.4 12.5 - - + +
184A ALA 3.1 17.3 + - - +
185A ALA* 4.0 8.7 - - - +
187A LYS* 1.3 78.5 - - - +
189A GLU* 1.3 61.1 + - - +
191A LEU* 3.6 7.7 - - - +
192A PHE* 3.4 22.3 + - - +
198A ASN* 5.8 0.7 - - - -
199A TYR* 4.0 33.4 + - - +
200A ASN* 4.1 19.9 + - - +
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Residues in contact with GLU 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 ALA 3.0 18.7 + - - +
186A ASP* 3.7 4.9 - - - +
187A LYS 3.0 0.4 - - - -
188A ASN* 1.3 77.7 - - - +
190A ILE* 1.3 56.0 + - - +
191A LEU 2.8 15.0 + - - -
192A PHE* 3.2 17.5 + - - +
193A SER* 2.9 48.4 + - - +
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Residues in contact with ILE 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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160A VAL* 2.9 31.2 - - + -
164A LEU* 4.6 8.3 - - + -
178A ARG* 3.4 44.2 - - + +
179A LEU* 4.1 19.7 - - + -
182A THR* 5.0 2.7 - - + -
186A ASP 3.1 12.2 + - - +
187A LYS* 2.9 7.3 + - - +
189A GLU* 1.3 77.6 - - - +
191A LEU* 1.3 56.7 + - - +
193A SER* 5.5 0.4 - - - -
194A GLU* 2.7 39.8 - - + +
195A PHE* 3.4 12.2 - - + -
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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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156A LEU* 4.9 4.3 - - + +
159A THR* 4.0 22.7 - - + +
160A VAL* 4.1 23.6 - - + -
163A ALA* 4.6 0.4 - - + -
187A LYS 3.1 11.2 + - - +
188A ASN* 3.6 11.2 - - - +
189A GLU 2.8 1.0 + - - -
190A ILE* 1.3 75.8 - - - +
192A PHE* 1.3 68.0 + - - +
193A SER 3.1 1.1 - - - -
195A PHE* 2.9 29.9 + - + -
196A ASN 3.0 5.9 + - - -
197A ILE* 3.2 39.6 + - + +
199A TYR* 3.6 45.8 - - + -
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Residues in contact with PHE 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 ASN* 3.4 16.0 + - - +
189A GLU* 3.2 18.3 + - - +
191A LEU* 1.3 79.6 - - - +
193A SER* 1.3 68.4 + - - +
196A ASN* 3.2 30.0 + - - +
197A ILE 3.1 16.5 + - - +
198A ASN* 4.4 26.2 - - + +
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Residues in contact with SER 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 GLU* 2.9 38.0 + - - -
190A ILE* 5.5 0.4 - - - -
192A PHE* 1.3 84.9 - - - +
194A GLU* 1.3 63.8 + - - +
195A PHE 3.6 0.9 - - - -
196A ASN 4.5 0.9 - - - -
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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