Contacts of the helix formed by residues 194 - 208 (chain A) in PDB entry 5DO7
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 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188A TYR* 5.1 2.2 - - - -
192A GLY 3.7 3.6 + - - -
193A ILE* 1.3 75.1 - - - +
195A THR* 1.3 57.2 + - - +
196A GLY* 3.0 4.5 - - - -
197A GLU* 2.8 45.7 + - - -
198A ARG* 2.8 31.7 + - - +
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Residues in contact with THR 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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188A TYR* 2.9 62.6 + - + -
193A ILE 3.3 3.8 + - - -
194A SER* 1.3 69.4 - - - +
196A GLY* 1.3 60.1 + - - +
198A ARG* 4.0 19.4 + - - +
199A ARG* 4.3 8.0 + - - +
223A LEU* 3.9 17.6 - - - +
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Residues in contact with GLY 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 SER* 3.0 3.6 - - - -
195A THR* 1.3 78.3 + - - +
197A GLU* 1.3 65.2 + - - +
199A ARG* 3.0 23.2 + - - +
200A ARG* 3.4 6.6 + - - -
223A LEU* 4.5 1.6 - - - -
227A THR* 3.5 33.1 + - - +
231A ILE* 4.0 8.9 - - - +
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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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177A LEU* 5.0 7.5 - - + +
179A HIS* 3.9 16.4 - - + -
180A VAL* 3.0 32.3 - - - +
193A ILE* 4.0 9.8 - - + +
194A SER* 2.8 45.0 + - - +
196A GLY* 1.3 68.8 - - - +
198A ARG* 1.3 67.0 + - - +
200A ARG* 2.8 50.4 - - + +
201A VAL* 3.0 5.9 + - - +
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Residues in contact with ARG 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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136A ASP* 3.5 25.4 + - - +
138A LEU* 3.9 28.0 - - + +
185A ILE* 4.9 4.0 - - + -
186A GLY 3.3 25.6 + - - -
187A ASN* 3.8 5.1 + - - +
188A TYR* 3.5 23.0 - - - +
193A ILE* 3.5 29.2 + - + +
194A SER 2.8 17.2 + - - +
195A THR* 4.0 27.6 + - - +
196A GLY 3.3 0.2 - - - -
197A GLU* 1.3 70.2 - - - +
199A ARG* 1.3 66.7 + - - +
201A VAL* 2.8 30.4 + - + +
202A SER 3.1 1.9 + - - -
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Residues in contact with ARG 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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132A VAL* 3.8 16.1 - - - +
133A LEU 2.8 26.2 + - - -
134A GLN 3.2 21.7 + - - -
135A SER* 3.4 20.2 + - - +
136A ASP* 2.9 24.7 + - - +
195A THR 4.3 6.3 + - - +
196A GLY* 3.0 14.0 + - - +
198A ARG* 1.3 74.8 - - - +
200A ARG* 1.3 67.3 + - - +
202A SER* 2.9 21.1 + - - -
203A ILE* 3.3 14.0 + - + +
217A ASP 3.7 2.8 + - - -
219A PRO* 3.5 44.8 + - - +
221A THR 5.9 2.0 + - - -
223A LEU* 5.3 9.0 - - + -
231A ILE* 4.4 24.7 - - + -
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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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175A LEU* 3.0 41.3 + - + +
176A SER* 3.8 15.6 + - - -
177A LEU* 3.7 17.0 - - + +
179A HIS* 5.4 2.4 + - - -
196A GLY* 3.4 3.0 + - - +
197A GLU* 2.8 53.5 + - - +
199A ARG* 1.3 78.2 - - - +
201A VAL* 1.3 62.7 + - - +
203A ILE* 2.8 26.1 + - - +
204A ALA 3.2 6.9 + - - -
227A THR* 6.0 0.8 - - - +
230A GLN* 3.1 38.9 - - - +
231A ILE* 4.1 15.2 - - + +
234A LEU* 3.2 21.5 - - + +
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Residues in contact with VAL 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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138A LEU* 3.3 25.4 - - + -
144A VAL* 3.7 19.5 - - + +
147A THR* 5.6 5.8 - - + -
148A LEU* 3.6 33.0 - - + -
177A LEU* 3.7 16.7 - - + +
185A ILE* 4.4 9.4 - - + -
193A ILE* 5.9 0.7 - - + -
197A GLU 3.0 6.8 + - - +
198A ARG* 2.8 38.7 + - + +
200A ARG* 1.3 71.1 - - - +
202A SER* 1.3 65.6 + - - +
204A ALA* 2.6 22.0 + - - +
205A ALA* 3.2 3.4 + - + +
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Residues in contact with SER 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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132A VAL* 5.0 12.4 - - - +
133A LEU* 5.8 3.3 + - - +
135A SER 4.8 1.2 + - - -
136A ASP* 3.3 35.4 - - - +
138A LEU* 4.6 14.6 - - - +
198A ARG 3.1 5.0 + - - -
199A ARG* 2.9 13.2 + - - -
201A VAL* 1.3 79.4 - - - +
203A ILE* 1.3 64.8 + - - +
205A ALA* 3.3 18.5 + - - +
206A GLN* 3.8 7.3 + - - +
451A GLN* 5.5 1.7 + - - -
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Residues in contact with ILE 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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132A VAL* 4.6 15.0 - - + -
175A LEU* 4.0 14.1 - - + -
199A ARG* 3.5 15.7 - - + +
200A ARG* 2.8 20.7 + - + +
202A SER* 1.3 77.0 - - - +
204A ALA* 1.3 64.3 + - - +
206A GLN* 2.8 15.9 + - - +
207A LEU* 2.8 29.3 - - + +
214A MET* 4.8 0.7 - - + -
216A PHE* 3.9 38.1 - - + -
231A ILE* 5.1 15.9 - - + -
234A LEU* 5.5 8.1 - - + -
235A LEU* 5.4 4.0 - - + -
238A LEU* 4.5 13.7 - - + -
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Residues in contact with ALA 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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148A LEU* 3.5 26.2 - - + -
171A VAL* 3.4 23.9 - - + +
175A LEU* 3.3 20.0 - - + +
177A LEU* 4.6 4.5 - - + -
200A ARG 3.2 2.6 + - - -
201A VAL* 2.6 23.7 + - - +
203A ILE* 1.3 74.2 - - - +
205A ALA* 1.3 52.6 + - - +
207A LEU* 2.8 21.5 + - - -
208A LEU* 3.2 10.7 + - - +
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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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138A LEU* 6.1 4.3 - - + -
147A THR* 6.4 0.9 - - + -
148A LEU* 3.5 15.4 - - + +
151A THR* 3.9 28.1 - - + +
201A VAL* 3.2 4.9 + - + +
202A SER* 3.5 12.8 - - - +
203A ILE 3.1 1.0 + - - -
204A ALA* 1.3 78.3 - - - +
206A GLN* 1.3 69.3 + - - +
208A LEU* 3.7 18.5 + - - +
209A GLN* 3.9 8.7 + - - +
457A LEU* 6.5 0.2 - - + -
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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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130A SER* 2.8 31.8 + - - +
131A TYR 3.4 25.5 - - - +
132A VAL* 4.1 16.6 - - + -
202A SER 4.5 5.2 - - - +
203A ILE* 2.8 15.2 + - + +
205A ALA* 1.3 79.9 - - - +
207A LEU* 1.3 59.8 + - + +
209A GLN* 2.8 46.8 + - - +
211A PRO* 3.4 8.6 - - - +
214A MET* 5.0 4.5 - - - -
357A LYS* 4.9 2.2 - - - +
455A ASP* 3.0 35.0 + - - +
457A LEU* 4.7 6.8 - - - +
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Residues in contact with LEU 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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171A VAL* 4.0 17.2 - - + +
174A GLU* 4.2 15.7 - - + +
175A LEU* 4.5 9.0 - - + -
203A ILE* 2.8 48.7 - - + +
204A ALA* 2.8 9.2 + - - +
206A GLN* 1.3 73.7 - - - +
208A LEU* 1.3 59.2 + - - +
209A GLN 2.9 4.9 - - - -
210A ASP* 2.8 23.6 + - - +
211A PRO* 4.1 5.4 - - - -
214A MET* 4.5 13.5 - - + -
238A LEU* 3.5 28.7 - - + -
243A ARG* 3.7 25.9 + - - +
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Residues in contact with LEU 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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148A LEU* 3.7 23.3 - - + +
151A THR* 4.0 11.2 - - + +
152A ALA* 3.4 45.1 - - + +
155A ALA* 5.7 1.8 - - + -
156A ILE* 3.4 23.8 - - + +
167A LYS* 5.5 1.6 - - + -
168A VAL* 4.6 11.4 - - + +
171A VAL* 3.4 33.9 - - + -
204A ALA 3.2 12.2 + - - +
205A ALA 3.7 12.1 - - - +
206A GLN 3.1 0.4 + - - -
207A LEU* 1.3 76.4 - - - +
209A GLN* 1.3 62.5 + - + +
210A ASP* 3.5 3.2 + - - +
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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