Contacts of the helix formed by residues 196 - 212 (chain A) in PDB entry 2H0A
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 THR 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A ARG* 1.3 81.7 - - - +
197A VAL* 1.3 58.0 + - - +
198A PHE* 3.0 3.4 - - - +
199A ALA* 2.8 23.3 + - + +
200A GLU* 2.7 45.3 + - - +
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ASP* 4.6 14.6 - - - +
162A ASN* 3.2 30.0 - - - +
195A ARG* 3.5 39.4 - - + +
196A THR* 1.3 75.8 - - - +
198A PHE* 1.3 61.8 + - + +
200A GLU* 3.5 4.6 + - - +
201A ARG* 3.0 66.7 + - - +
295A GLN* 5.9 0.2 - - - +
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Residues in contact with PHE 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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184A ALA* 5.4 4.9 - - + -
185A VAL* 3.4 67.3 - - + +
187A GLU* 6.1 2.5 - - + -
195A ARG* 4.8 20.2 - - + -
196A THR* 3.0 0.8 - - - -
197A VAL* 1.3 78.8 - - + +
199A ALA* 1.3 66.5 + - - +
200A GLU 3.2 0.2 - - - -
201A ARG* 3.4 37.1 - - - +
202A MET* 3.0 26.2 + - - +
226A HIS* 5.1 4.9 - + + -
251A GLY* 3.8 9.9 - - - -
252A ALA* 4.7 4.7 - - + -
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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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196A THR* 2.8 31.5 + - + +
198A PHE* 1.3 80.0 - - - +
200A GLU* 1.3 62.7 + - + +
202A MET* 3.6 4.3 + - - +
203A ALA* 3.1 23.6 + - - +
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Residues in contact with GLU 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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162A ASN* 3.9 15.7 - - + -
163A ARG* 2.9 52.1 + - - +
196A THR* 2.7 27.6 + - - +
197A VAL* 3.7 6.1 - - - +
199A ALA* 1.3 76.0 - - + +
201A ARG* 1.3 65.5 + - - +
203A ALA* 3.1 12.4 + - - +
204A GLY 3.1 11.1 + - - -
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Residues in contact with ARG 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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162A ASN* 2.9 33.8 + - - +
166A GLY* 3.3 14.4 - - - -
195A ARG* 5.9 0.8 - - - +
197A VAL* 3.0 43.0 + - - +
198A PHE* 3.4 30.5 + - - +
200A GLU* 1.3 75.5 - - - +
202A MET* 1.3 56.8 - - - +
205A PHE* 3.0 26.2 + - - +
249A PHE* 4.7 9.8 - - + -
251A GLY* 2.7 33.2 + - - -
252A ALA* 4.8 2.0 - - - +
279A PHE* 3.1 34.1 - - + +
280A ASP* 4.0 5.3 + - - -
295A GLN* 3.3 28.9 + - - +
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Residues in contact with MET 202 (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 ALA* 4.0 12.8 - - + -
183A ILE 4.5 3.6 - - - +
184A ALA* 4.0 20.4 - - + -
198A PHE 3.0 18.9 + - - +
199A ALA* 3.9 5.6 - - - +
201A ARG* 1.3 75.8 - - - +
203A ALA* 1.3 58.4 + - - +
205A PHE* 3.4 22.0 - - - +
206A GLN* 3.0 50.8 + - - +
216A PHE* 4.7 7.4 - - - -
221A LEU* 3.4 35.0 - - + -
249A PHE* 5.5 5.8 - - + -
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Residues in contact with ALA 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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163A ARG* 3.8 29.8 - - - +
199A ALA 3.1 17.1 + - - +
200A GLU* 3.1 7.0 + - - +
202A MET* 1.3 73.6 - - - +
204A GLY* 1.3 60.4 + - - +
206A GLN* 3.4 11.6 + - - +
207A GLU* 3.0 33.9 + - - +
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Residues in contact with GLY 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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163A ARG* 3.6 19.6 - - - +
166A GLY 3.7 2.5 - - - -
167A ARG* 3.2 30.4 - - - +
200A GLU 3.1 9.7 + - - -
203A ALA* 1.3 74.6 - - - +
205A PHE* 1.3 65.3 + - - +
207A GLU* 3.3 5.5 + - - +
208A ALA* 2.9 22.3 + - - +
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Residues in contact with PHE 205 (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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166A GLY 3.1 16.1 + - - +
169A ALA 4.0 4.5 - - - -
170A GLY* 3.5 32.8 - - - -
173A LEU* 4.2 3.8 - - + -
180A ILE* 3.7 24.7 - - + -
182A ALA* 3.8 13.0 - - + -
201A ARG 3.0 18.9 + - - +
202A MET* 3.4 25.1 - - - +
204A GLY* 1.3 77.8 - - - +
206A GLN* 1.3 62.7 + - + +
208A ALA* 3.9 1.4 - - - +
209A LEU* 3.1 48.3 + - + +
216A PHE* 3.8 17.3 - + - -
249A PHE* 3.6 37.2 - + + -
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Residues in contact with GLN 206 (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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202A MET* 3.0 39.2 + - + +
203A ALA* 3.8 8.2 - - - +
204A GLY 3.2 0.2 - - - -
205A PHE* 1.3 75.9 - - + +
207A GLU* 1.3 60.8 + - + +
209A LEU* 3.5 7.8 + - - +
210A LYS* 2.9 31.1 + - - +
216A PHE* 4.6 30.5 + - + +
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Residues in contact with GLU 207 (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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163A ARG* 4.3 19.5 + - - +
167A ARG* 4.7 9.0 - - - -
203A ALA 3.0 24.7 + - - +
204A GLY* 3.3 7.6 + - - +
206A GLN* 1.3 77.4 - - + +
208A ALA* 1.3 61.1 + - - +
210A LYS* 3.4 18.0 + - - +
211A GLU* 2.8 40.6 + - - +
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Residues in contact with ALA 208 (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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167A ARG* 3.4 34.5 - - + +
170A GLY* 4.0 0.4 - - - -
171A ALA* 3.5 21.0 + - + +
204A GLY 2.9 16.6 + - - +
205A PHE 3.9 2.7 - - - +
207A GLU* 1.3 75.7 - - - +
209A LEU* 1.3 64.2 + - - +
211A GLU* 3.3 13.2 + - - +
212A ALA* 3.1 24.3 + - - +
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Residues in contact with LEU 209 (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 GLY* 3.6 26.0 - - - +
173A LEU* 5.4 0.2 - - + -
174A ALA* 4.2 4.9 - - + -
180A ILE* 3.8 28.0 - - + -
205A PHE* 3.1 45.6 + - + +
206A GLN 3.8 3.8 - - - +
208A ALA* 1.3 76.2 - - - +
210A LYS* 1.3 63.6 + - - +
212A ALA* 3.1 9.5 + - - +
214A ARG* 3.1 40.9 + - + +
216A PHE* 3.3 40.6 - - + +
220A ARG* 5.5 0.2 - - - +
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Residues in contact with LYS 210 (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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206A GLN 2.9 18.0 + - - +
207A GLU* 3.5 19.8 + - - +
209A LEU* 1.3 76.9 - - - +
211A GLU* 1.3 60.3 + - + +
212A ALA 3.0 5.5 + - - -
213A GLY* 3.0 16.1 + - - -
215A PRO* 4.1 21.5 - - + +
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Residues in contact with GLU 211 (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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167A ARG* 5.0 7.6 - - - -
207A GLU* 2.8 35.1 + - + +
208A ALA* 3.3 9.9 + - - +
210A LYS* 1.3 79.0 - - + +
212A ALA* 1.3 57.1 + - - +
213A GLY 3.4 0.6 + - - -
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Residues in contact with ALA 212 (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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171A ALA* 5.4 4.0 - - + -
174A ALA* 3.8 27.3 - - + +
208A ALA 3.1 14.6 + - - +
209A LEU 3.7 5.2 - - - +
210A LYS 3.0 1.8 + - - -
211A GLU* 1.3 78.0 - - - +
213A GLY* 1.3 58.1 + - - +
214A ARG* 3.3 11.6 + - + +
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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