Contacts of the helix formed by residues 185 - 199 (chain A) in PDB entry 2DH3
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A LEU* 3.8 3.5 - - - +
179A ILE* 3.6 16.2 - - - +
184A GLY* 1.3 74.2 - - - -
186A LYS* 1.3 65.2 + - - +
187A GLU* 3.2 21.3 + - - +
188A ASP* 2.7 28.3 + - - +
189A PHE 3.4 14.7 + - - -
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Residues in contact with LYS 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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177A LEU 6.1 0.4 - - - +
179A ILE* 3.9 18.7 - - + +
185A SER* 1.3 74.7 - - - +
187A GLU* 1.3 72.8 + - - +
189A PHE* 3.3 4.1 + - + +
190A ASP* 2.9 51.6 + - - +
235A PHE* 4.4 23.1 - - + -
236A TRP* 4.7 9.9 - - + -
239A ALA* 4.1 20.7 - - - +
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Residues in contact with GLU 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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185A SER* 3.3 16.7 + - - +
186A LYS* 1.3 85.8 + - - +
188A ASP* 1.3 58.5 + - - +
190A ASP* 3.7 10.9 - - + +
191A SER* 2.8 34.7 + - - -
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Residues in contact with ASP 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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139A ASN* 3.2 22.2 + - - -
140A LEU* 3.9 22.2 - - + +
141A ALA* 3.6 16.0 - - + +
144A LYS* 5.1 1.6 - - - -
184A GLY* 4.7 0.2 - - - -
185A SER* 2.7 42.8 + - - +
187A GLU* 1.3 78.3 - - - +
189A PHE* 1.3 58.1 + - - +
191A SER* 3.4 7.1 + - - -
192A LEU* 2.9 28.2 + - - +
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Residues in contact with PHE 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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140A LEU* 4.2 12.3 - - + +
160A LEU* 3.9 27.1 - - + -
163A ILE* 4.1 22.4 - - + -
179A ILE* 4.2 8.7 - - + -
185A SER 3.4 10.0 + - - +
186A LYS* 3.3 11.3 + - + +
187A GLU 3.3 0.4 - - - -
188A ASP* 1.3 76.1 - - - +
190A ASP* 1.3 71.7 + - - +
192A LEU* 3.0 12.2 + - + +
193A LEU* 2.9 54.5 + - + +
203A VAL* 5.0 3.4 - - + -
205A LEU* 4.3 7.2 - - + -
236A TRP* 3.8 32.1 - + - -
239A ALA* 4.9 2.7 - - + -
241A VAL* 3.6 23.1 - - + -
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Residues in contact with ASP 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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186A LYS* 2.9 54.8 + - - +
187A GLU* 3.7 11.5 - - - +
189A PHE* 1.3 79.7 - - - +
191A SER* 1.3 62.7 + - - +
193A LEU* 3.3 7.3 + - - +
194A GLN* 3.2 24.6 + - - +
239A ALA* 4.2 15.1 - - - +
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Residues in contact with SER 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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144A LYS* 2.9 32.0 + - - -
187A GLU 2.8 22.2 + - - -
188A ASP* 3.5 8.5 - - - -
189A PHE 3.2 0.2 - - - -
190A ASP* 1.3 73.4 - - - +
192A LEU* 1.3 62.6 + - - +
194A GLN* 3.6 12.8 + - - +
195A SER* 3.2 25.5 + - - -
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Residues in contact with LEU 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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140A LEU* 3.8 24.5 - - + +
143A LEU* 3.7 31.0 - - + +
144A LYS* 3.6 41.9 - - + +
147A LEU* 4.4 12.1 - - + -
158A LEU* 6.0 2.7 - - + -
160A LEU* 4.6 10.5 - - + -
188A ASP 2.9 14.9 + - - +
189A PHE* 3.0 14.1 + - + +
191A SER* 1.3 74.5 - - - +
193A LEU* 1.3 67.3 + - + +
195A SER* 3.5 1.9 + - - -
196A ALA* 3.1 27.6 + - + +
203A VAL* 5.4 11.4 - - + -
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Residues in contact with LEU 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 PHE* 2.9 49.2 + - + +
190A ASP* 3.3 10.5 + - - +
192A LEU* 1.3 76.9 - - + +
194A GLN* 1.3 64.8 + - - +
196A ALA* 3.2 5.0 + - - +
197A LYS* 3.0 42.2 + - + +
203A VAL* 3.8 31.9 - - + -
239A ALA 3.1 30.3 - - - +
240A GLY 4.1 17.5 - - - +
241A VAL* 4.7 4.3 - - + -
242A ASP* 5.6 1.6 - - - +
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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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190A ASP 3.2 14.9 + - - +
191A SER* 3.8 11.3 + - - +
192A LEU 3.3 0.2 - - - -
193A LEU* 1.3 79.1 - - - +
195A SER* 1.3 62.7 + - - +
197A LYS* 3.5 6.9 + - - +
198A LYS* 3.3 20.4 + - - +
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Residues in contact with SER 195 (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 LYS* 3.9 18.1 - - - +
147A LEU* 4.0 18.8 - - - -
191A SER* 3.2 16.7 + - - -
192A LEU 4.0 1.1 - - - -
193A LEU 3.3 0.2 - - - -
194A GLN* 1.3 75.6 - - - +
196A ALA* 1.3 65.7 + - - +
198A LYS* 3.2 11.1 + - - +
199A LYS* 3.2 30.9 + - - +
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Residues in contact with ALA 196 (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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147A LEU* 4.2 15.4 - - + +
158A LEU* 6.2 0.4 - - + -
192A LEU* 3.1 19.6 + - + +
193A LEU 3.6 4.7 - - - +
195A SER* 1.3 76.7 - - - +
197A LYS* 1.3 60.5 + - + +
199A LYS* 3.2 9.6 + - - +
201A ILE* 2.8 51.4 + - + +
203A VAL* 4.2 17.5 - - + -
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Residues in contact with LYS 197 (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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193A LEU* 3.0 33.1 + - + +
194A GLN* 4.0 6.3 - - - +
196A ALA* 1.3 73.3 - - - +
198A LYS* 1.3 65.5 + - - +
199A LYS 3.4 0.3 + - - -
200A SER* 3.4 11.6 + - - +
201A ILE 4.4 7.4 - - - +
202A ARG* 5.8 6.3 - - - +
240A GLY* 3.7 31.8 + - - -
242A ASP* 4.6 16.4 - - - +
273A ARG* 6.1 2.5 - - - +
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Residues in contact with LYS 198 (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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194A GLN 3.3 11.1 + - - +
195A SER* 3.2 14.1 + - - +
197A LYS* 1.3 78.3 - - - +
199A LYS* 1.3 61.3 + - + +
200A SER* 3.5 0.9 + - - -
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Residues in contact with LYS 199 (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 LYS 5.5 1.3 - - - -
147A LEU* 3.8 32.5 - - + -
148A ASP* 2.6 33.3 + - - +
151A SER* 5.0 10.3 + - - +
195A SER* 3.2 20.1 + - - +
196A ALA 3.2 5.8 + - - +
197A LYS 3.1 0.4 - - - -
198A LYS* 1.3 83.9 - - + +
200A SER* 1.3 69.5 + - - +
201A ILE* 3.3 17.1 + - + +
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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