Contacts of the helix formed by residues 190 - 204 (chain A) in PDB entry 2H6C
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 HIS 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ILE* 4.8 25.2 - - + +
146A THR* 6.0 0.2 - - + -
188A GLY 4.3 0.2 + - - -
189A ALA* 1.3 74.8 - - - +
191A HIS* 1.3 65.1 + + - +
192A VAL* 3.0 48.7 + - + +
193A THR* 3.0 18.4 + - - +
194A VAL* 2.8 31.7 + - - +
140B GLN* 3.3 35.6 + - + +
143B GLU* 3.0 30.8 + - - +
144B ILE* 4.6 8.7 - - + +
145B ASN* 6.0 2.2 - - - -
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Residues in contact with HIS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A GLN* 4.2 7.9 + - + +
181A LYS* 6.6 0.2 - - - -
184A GLY* 6.1 0.2 - - - -
189A ALA 3.7 1.9 + - - -
190A HIS* 1.3 82.3 + + - +
192A VAL* 1.3 88.7 + - + +
194A VAL* 3.5 11.7 - - + +
195A SER* 2.7 37.9 + - - +
140B GLN* 3.8 3.1 - - - -
143B GLU* 2.9 44.2 + - + +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A HIS* 3.0 28.5 - - + +
191A HIS* 1.3 92.1 + - + +
193A THR* 1.3 70.4 + - - +
195A SER* 3.0 6.6 + - - -
196A LYS* 2.8 33.2 + - + +
136B TYR* 5.8 2.0 - - - +
140B GLN* 4.0 8.7 - - + +
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Residues in contact with THR 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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146A THR* 4.1 27.9 - - - +
149A PRO* 5.4 1.7 - - + +
150A THR* 3.3 28.5 - - - +
153A ILE* 5.2 0.7 - - + -
189A ALA* 4.7 8.5 - - + -
190A HIS* 3.0 29.7 + - - +
192A VAL* 1.3 80.9 - - - +
194A VAL* 1.3 65.8 + - - +
195A SER 3.0 0.3 + - - -
196A LYS* 4.8 7.9 - - + -
197A VAL* 2.7 34.0 + - + +
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE* 3.9 24.5 - - + +
180A GLN* 3.4 51.6 - - + +
183A ILE* 4.1 9.2 - - + -
184A GLY* 4.0 18.6 - - - +
189A ALA* 4.0 4.3 - - + +
190A HIS 2.8 20.4 + - - +
191A HIS* 3.5 11.9 - - - +
193A THR* 1.3 73.5 - - - +
195A SER* 1.3 61.2 + - - +
197A VAL* 4.0 0.9 - - - +
198A LEU* 3.0 30.5 + - + +
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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
----------------------------------------------------------
180A GLN* 3.2 21.7 + - - +
191A HIS* 2.7 24.3 + - - +
192A VAL* 3.0 5.8 + - - -
194A VAL* 1.3 75.2 - - - +
196A LYS* 1.3 59.8 + - - +
198A LEU* 3.4 5.2 + - - +
199A ALA* 2.9 28.5 + - - +
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Residues in contact with LYS 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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192A VAL* 2.8 23.6 + - + +
193A THR* 4.2 8.3 - - + +
195A SER* 1.3 73.7 - - - +
197A VAL* 1.3 73.3 + - + +
199A ALA* 3.8 6.9 - - - +
200A CYS* 3.2 34.0 + - - +
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Residues in contact with VAL 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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150A THR* 3.4 37.5 - - + +
153A ILE* 4.3 25.1 - - + -
154A LEU* 4.7 8.1 - - + -
193A THR* 2.7 32.0 + - + +
194A VAL* 4.0 4.7 - - - +
196A LYS* 1.3 76.4 - - + +
198A LEU* 1.3 71.9 + - + +
200A CYS* 3.6 7.1 + - - -
201A LEU* 3.3 34.4 + - + +
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Residues in contact with LEU 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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153A ILE* 6.0 1.3 - - + -
157A PHE* 4.0 30.1 - - + -
180A GLN* 3.2 37.5 - - + +
183A ILE* 5.5 3.8 - - + -
194A VAL* 3.0 25.9 + - + +
195A SER 3.4 5.2 - - - +
197A VAL* 1.3 82.5 - - + +
199A ALA* 1.3 65.9 + - - +
200A CYS 3.0 0.5 + - - -
201A LEU* 3.0 14.6 + - + +
202A LYS* 3.2 11.4 + - - +
207A LEU* 4.6 13.9 - - + +
209A LYS* 4.7 22.4 - - + +
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Residues in contact with ALA 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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195A SER 2.9 14.7 + - - +
196A LYS* 3.2 7.8 + - - +
198A LEU* 1.3 80.9 - - - +
200A CYS* 1.3 58.3 + - + +
202A LYS* 3.3 13.0 - - - +
203A LYS* 3.0 23.1 + - - +
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Residues in contact with CYS 200 (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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196A LYS* 3.2 24.3 + - - +
197A VAL* 4.1 7.9 - - - -
198A LEU 3.1 0.6 - - - -
199A ALA* 1.3 76.4 - - + +
201A LEU* 1.3 62.3 + - - +
202A LYS 3.4 0.7 - - - -
203A LYS* 3.8 10.5 - - + -
204A GLU* 3.1 41.5 + - + +
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Residues in contact with LEU 201 (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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154A LEU* 4.0 31.0 - - + -
157A PHE* 4.8 13.5 - - + -
197A VAL* 3.3 28.4 + - + +
198A LEU* 3.0 11.4 + - - +
200A CYS* 1.3 77.0 - - - +
202A LYS* 1.3 60.7 + - - +
204A GLU 3.8 0.5 + - - -
205A ASN 3.5 2.9 + - - -
206A ILE* 3.0 70.5 + - + +
207A LEU* 3.4 31.5 + - + -
222A LEU* 4.8 3.8 - - + -
225A LEU* 4.7 3.1 - - + -
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Residues in contact with LYS 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A LEU 3.2 7.2 + - - +
199A ALA* 3.3 13.9 - - - +
201A LEU* 1.3 75.1 - - - +
203A LYS* 1.3 69.5 + - - +
205A ASN* 3.4 11.6 + - - -
207A LEU 3.1 14.0 + - - +
208A ASP* 3.3 35.1 + - + +
217A TYR* 5.8 2.9 - - + -
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Residues in contact with LYS 203 (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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199A ALA 3.0 11.9 + - - +
200A CYS* 3.9 13.0 - - + +
201A LEU 3.4 0.2 - - - -
202A LYS* 1.3 81.0 - - - +
204A GLU* 1.3 62.6 + - + +
205A ASN* 2.8 18.9 + - - -
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Residues in contact with GLU 204 (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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200A CYS* 3.1 27.7 + - + +
201A LEU 3.8 1.1 + - - +
202A LYS 3.5 0.2 - - - -
203A LYS* 1.3 80.2 - - + +
205A ASN* 1.3 67.2 + - - +
206A ILE* 3.5 21.1 + - + +
218A ASN* 5.5 1.9 + - - -
221A GLU* 5.5 2.4 - - - +
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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