Contacts of the helix formed by residues 194 - 209 (chain A) in PDB entry 1Q0R
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 ASP 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A PRO 4.2 0.8 + - - -
193A PHE* 1.3 76.4 - - - +
195A ASP* 1.3 65.1 + - - +
196A ALA* 3.3 12.6 + - - +
197A GLU* 3.0 67.1 + - + +
198A TYR* 3.3 9.2 + - - +
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Residues in contact with ASP 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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180A VAL* 3.7 22.6 - - + +
184A ARG* 3.0 45.0 + - - -
193A PHE* 3.6 17.6 - - - +
194A ASP* 1.3 74.3 + - - +
196A ALA* 1.3 58.1 + - - +
198A TYR 3.3 1.6 + - - -
199A ALA* 2.9 30.2 + - - +
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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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194A ASP* 3.3 11.9 + - - +
195A ASP* 1.3 79.4 - - - +
197A GLU* 1.3 62.2 + - - +
199A ALA* 3.4 7.7 + - - +
200A ARG* 3.0 22.3 + - - +
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Residues in contact with GLU 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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192A PRO 5.3 0.3 - - - +
194A ASP* 3.0 40.7 + - + +
196A ALA* 1.3 75.4 - - - +
198A TYR* 1.3 63.1 + - + +
200A ARG* 3.3 7.8 + - - +
201A TRP* 3.0 57.8 + - + +
279A PRO* 3.6 10.9 - - - +
280A SER* 2.6 48.0 + - - -
281A SER 4.7 0.2 + - - -
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Residues in contact with TYR 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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180A VAL* 3.7 9.6 - - + -
183A TRP* 3.4 37.0 - + + -
193A PHE* 3.5 37.7 - + + -
194A ASP 3.3 11.4 + - - +
195A ASP 4.0 3.4 - - - +
196A ALA 3.3 0.2 - - - -
197A GLU* 1.3 78.8 - - + +
199A ALA* 1.3 60.5 + - - +
201A TRP* 3.3 28.8 + + - +
202A GLU* 3.0 33.3 + - + +
277A ALA* 3.7 2.9 - - + +
278A LEU* 2.9 22.4 + - - -
279A PRO* 3.9 17.0 - - + -
2712A 1PE 2.6 48.3 + - - -
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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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176A VAL* 3.8 18.8 - - + +
180A VAL* 3.4 12.9 - - + +
195A ASP 2.9 18.7 + - - +
196A ALA* 3.5 9.2 - - - +
198A TYR* 1.3 76.5 - - - +
200A ARG* 1.3 57.1 + - - +
202A GLU* 3.3 1.6 + - - -
203A GLU* 2.9 40.9 + - - +
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Residues in contact with ARG 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 ALA 3.0 14.1 + - - +
197A GLU* 3.6 10.8 - - - +
199A ALA* 1.3 74.3 - - - +
201A TRP* 1.3 65.5 + - + +
203A GLU* 3.2 21.7 + - - +
204A ARG* 3.0 78.5 + - - +
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Residues in contact with TRP 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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37A LEU* 4.6 6.3 - - - +
40A PRO* 3.5 23.7 - - + +
42A GLU* 3.0 26.6 + - + -
197A GLU* 3.0 51.1 + - + +
198A TYR* 3.6 41.1 - + - +
199A ALA 3.3 0.4 - - - -
200A ARG* 1.3 78.8 - - + +
202A GLU* 1.3 56.5 + - - +
204A ARG* 3.4 30.4 + - - +
205A ALA* 3.0 25.1 + - - +
278A LEU 3.3 27.1 - - - -
280A SER* 3.8 2.9 - - - -
283A HIS* 3.6 24.2 - + - -
2712A 1PE 4.0 17.8 - - - +
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Residues in contact with GLU 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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176A VAL* 4.5 14.4 - - + -
179A ARG* 3.0 49.7 + - + +
180A VAL* 4.8 3.4 - - + -
182A LYS* 4.8 2.1 + - - -
183A TRP* 2.7 33.8 + - + +
198A TYR* 3.0 20.4 + - + +
199A ALA 3.8 3.1 - - - +
201A TRP* 1.3 73.9 - - - +
203A GLU* 1.3 61.0 + - - +
205A ALA* 3.2 2.4 + - - +
206A ILE* 2.9 36.4 + - - +
2712A 1PE 2.7 34.7 + - - -
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Residues in contact with GLU 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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172A ARG* 3.5 26.4 + - - +
176A VAL* 3.9 23.4 - - + +
199A ALA* 2.9 25.8 + - - +
200A ARG* 3.5 26.4 - - + +
202A GLU* 1.3 77.3 - - - +
204A ARG* 1.3 58.0 + - + +
206A ILE* 3.3 1.4 + - - +
207A ASP* 2.9 36.8 + - - +
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Residues in contact with ARG 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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37A LEU* 4.0 16.7 - - + +
41A ASP* 3.7 31.6 + - - +
42A GLU* 2.9 41.0 + - - -
45A ARG* 5.5 1.2 - - - +
200A ARG* 3.0 68.1 + - - +
201A TRP* 3.4 26.9 - - - +
202A GLU 3.2 0.2 - - - -
203A GLU* 1.3 76.4 - - + +
205A ALA* 1.3 56.0 + - - +
207A ASP* 3.4 9.6 + - - +
208A HIS* 2.9 29.5 + - - +
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Residues in contact with ALA 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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35A SER* 4.8 5.6 + - - +
37A LEU* 3.7 23.9 - - + +
179A ARG* 4.5 4.3 - - - +
201A TRP 3.0 14.5 + - - +
202A GLU* 3.2 10.7 + - - +
204A ARG* 1.3 75.8 - - - +
206A ILE* 1.3 60.4 + - - +
208A HIS* 3.4 4.2 + - - +
209A ALA* 3.2 22.0 + - - +
2712A 1PE 3.2 28.5 - - - +
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Residues in contact with ILE 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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172A ARG* 3.4 22.7 - - + +
175A GLU* 4.2 13.9 - - + -
176A VAL* 3.7 26.0 - - + -
179A ARG* 3.4 35.9 - - - +
202A GLU 2.9 20.3 + - - +
203A GLU* 3.8 4.0 - - - +
205A ALA* 1.3 74.8 - - - +
207A ASP* 1.3 62.9 + - - +
209A ALA* 3.0 11.9 + - - +
211A GLY 2.8 42.1 + - - +
212A VAL 3.7 9.6 - - - +
213A LEU* 3.9 12.3 - - + -
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Residues in contact with ASP 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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64A ARG* 4.2 4.2 + - - -
172A ARG* 2.9 33.2 + - - -
203A GLU* 2.9 22.5 + - - +
204A ARG* 3.6 9.0 - - - +
206A ILE* 1.3 73.5 - - - +
208A HIS* 1.3 59.6 + - - +
210A GLY* 3.0 20.4 + - - -
211A GLY* 3.8 5.6 + - - +
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Residues in contact with HIS 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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14A TRP* 3.3 37.3 - + - -
35A SER* 4.2 4.6 + - - -
37A LEU* 3.6 26.1 - - + +
58A ASP* 2.7 41.7 + - - -
63A GLY* 3.8 8.7 - - - -
64A ARG* 2.8 53.3 + - + +
204A ARG 2.9 18.6 + - - +
205A ALA 3.5 6.7 + - - +
206A ILE 3.2 0.2 - - - -
207A ASP* 1.3 76.4 - - - +
209A ALA* 1.3 55.3 + - - +
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Residues in contact with ALA 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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63A GLY* 4.5 23.1 - - - +
64A ARG* 5.9 0.2 - - - -
205A ALA 3.2 12.4 + - - +
206A ILE* 3.0 10.5 + - - +
208A HIS* 1.3 75.6 + - - +
210A GLY* 1.3 61.1 + - - -
211A GLY 3.2 1.5 + - - -
212A VAL* 3.4 33.8 - - + +
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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