Contacts of the helix formed by residues 196 - 216 (chain A) in PDB entry 3U6D
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 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A SER 3.4 3.7 + - - -
195A LEU* 1.3 77.4 - - - +
197A SER* 1.3 65.0 + - - +
198A LYS* 3.4 9.8 + - - +
199A GLU* 2.9 38.3 + - - +
200A ILE* 3.0 22.1 + - - +
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Residues in contact with SER 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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149A ALA* 6.5 0.4 - - - -
196A SER* 1.3 73.6 - - - +
198A LYS* 1.3 62.8 + - - +
200A ILE* 3.3 8.6 + - - +
201A GLU* 3.1 39.7 + - - +
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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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196A SER* 3.1 10.1 + - - +
197A SER* 1.3 80.0 - - - +
199A GLU* 1.3 59.4 + - + +
201A GLU* 3.5 11.3 + - - +
202A ARG* 3.0 41.8 + - + +
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Residues in contact with GLU 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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184A ALA 6.0 0.4 - - - +
185A GLY 5.3 1.7 - - - +
186A ILE* 3.6 24.0 - - + +
190A ARG* 2.9 44.9 + - - -
194A SER 3.9 0.3 - - - +
195A LEU* 3.3 7.6 - - + -
196A SER* 2.9 38.2 + - - +
198A LYS* 1.3 76.3 - - + +
200A ILE* 1.3 60.2 + - - +
202A ARG* 3.4 5.9 + - - +
203A LEU* 2.8 31.4 + - - +
274A ARG* 5.4 1.9 - - - +
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Residues in contact with ILE 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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145A PRO* 3.5 29.8 - - + +
148A LEU* 4.1 17.3 - - + +
149A ALA* 3.9 20.9 - - + +
152A ALA* 4.0 23.1 - - + -
195A LEU* 3.7 33.2 - - + +
196A SER 3.0 20.6 + - - +
197A SER* 3.6 9.4 - - - +
199A GLU* 1.3 76.7 - - - +
201A GLU* 1.3 59.5 + - + +
203A LEU* 3.3 4.5 + - + +
204A HIS* 2.9 29.1 + - - +
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Residues in contact with GLU 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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145A PRO* 4.4 26.0 - - + +
197A SER* 3.1 27.9 + - - +
198A LYS* 3.8 8.6 - - - +
200A ILE* 1.3 76.6 - - + +
202A ARG* 1.3 58.1 + - - +
204A HIS* 3.8 2.3 + - - +
205A GLU* 3.0 31.1 + - - +
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Residues in contact with ARG 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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183A ARG 2.9 24.4 + - - -
184A ALA* 3.7 26.6 + - + +
185A GLY* 5.0 0.6 - - - +
198A LYS* 3.0 34.5 + - + +
199A GLU* 3.7 7.0 - - - +
201A GLU* 1.3 78.3 - - - +
203A LEU* 1.3 57.6 + - - +
205A GLU* 3.3 17.0 + - - +
206A GLU* 3.0 54.4 + - - +
251A ARG* 5.8 2.6 - - - +
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Residues in contact with LEU 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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148A LEU* 4.3 10.3 - - + -
159A VAL* 3.7 30.3 - - + -
162A LEU* 6.5 0.2 - - + -
163A LEU* 4.1 16.4 - - + -
180A SER 4.2 8.1 - - - +
181A LEU* 3.7 22.2 - - + -
184A ALA* 3.8 16.8 - - + +
186A ILE* 4.0 4.7 - - + -
195A LEU* 3.9 13.0 - - + -
199A GLU 2.8 21.3 + - - +
200A ILE* 3.6 4.9 - - - +
202A ARG* 1.3 72.1 - - - +
204A HIS* 1.3 60.9 + - - +
206A GLU 3.2 0.9 + - - -
207A MET* 2.8 52.9 + - + +
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Residues in contact with HIS 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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143A PHE* 2.8 49.5 + + - -
144A SER* 3.5 21.4 - - - -
145A PRO* 3.8 29.6 - - + +
148A LEU* 4.2 10.9 - - + +
200A ILE 2.9 17.3 + - - +
201A GLU 3.8 4.7 + - - +
203A LEU* 1.3 75.8 - - - +
205A GLU* 1.3 68.0 + - - +
207A MET* 3.2 6.7 + - - +
208A VAL* 3.0 40.5 + - + +
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Residues in contact with GLU 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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201A GLU 3.0 19.1 + - - +
202A ARG* 3.4 18.3 + - - +
204A HIS* 1.3 83.3 + - - +
206A GLU* 1.3 70.5 + - - +
208A VAL* 3.5 4.4 + - - +
209A ALA* 3.0 29.4 + - + +
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Residues in contact with GLU 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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180A SER* 3.8 19.1 - - - +
183A ARG* 3.3 56.3 + - + +
184A ALA* 3.7 5.4 - - + +
202A ARG* 3.0 42.1 + - - +
203A LEU 3.9 2.7 - - - +
205A GLU* 1.3 86.7 - - - +
207A MET* 1.3 59.0 + - - +
209A ALA* 3.8 4.3 - - - +
210A THR* 2.7 37.9 + - - -
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Residues in contact with MET 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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138A PRO* 5.9 0.4 - - - -
143A PHE* 3.6 34.8 - - + -
148A LEU* 4.3 4.5 - - - -
163A LEU* 3.8 33.0 - - + -
169A VAL* 4.1 8.3 - - + -
172A PHE* 3.6 41.8 - - + -
180A SER* 3.5 24.2 - - - -
203A LEU* 2.8 32.7 + - + +
204A HIS* 3.6 4.7 - - - +
206A GLU* 1.3 77.2 - - - +
208A VAL* 1.3 62.2 + - - +
211A ILE* 3.1 27.7 + - - +
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Residues in contact with VAL 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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138A PRO 3.6 20.6 - - - +
139A LEU* 4.0 14.8 - - + -
143A PHE* 4.5 3.1 - - + +
204A HIS* 3.0 45.1 + - + +
205A GLU* 3.8 4.9 - - - +
207A MET* 1.3 75.3 - - - +
209A ALA* 1.3 55.2 + - - +
211A ILE* 3.5 6.8 - - - +
212A GLY* 2.8 33.5 + - - -
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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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183A ARG* 3.7 16.6 - - - +
205A GLU* 3.0 19.8 + - + +
206A GLU* 3.8 8.5 - - - +
208A VAL* 1.3 78.0 - - - +
210A THR* 1.3 57.7 + - - +
212A GLY* 5.0 0.4 - - - -
213A GLU* 2.9 43.4 + - - +
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Residues in contact with THR 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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172A PHE* 5.1 0.2 - - - -
176A TYR* 3.6 28.4 - - + -
179A GLU* 4.2 14.8 - - + -
180A SER* 3.4 20.6 + - - +
183A ARG* 3.4 35.7 + - - +
206A GLU 2.7 27.7 + - - -
207A MET 3.9 1.1 - - - -
209A ALA* 1.3 76.3 - - - +
211A ILE* 1.3 61.9 + - - +
213A GLU* 3.9 3.0 - - - +
214A ALA* 3.4 19.2 + - - +
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Residues in contact with ILE 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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4A LEU* 4.2 28.5 - - + -
5A PRO* 4.1 10.3 - - + -
138A PRO* 4.3 15.0 - - + -
139A LEU* 3.3 27.6 - - + -
171A GLY 5.1 2.2 - - - +
172A PHE* 4.0 20.0 - - + -
176A TYR* 3.5 37.0 - - + -
207A MET 3.1 18.6 + - - +
208A VAL* 3.5 2.7 - - - +
210A THR* 1.3 79.3 - - - +
212A GLY* 1.3 61.7 + - - +
214A ALA* 3.3 5.0 + - - +
215A VAL* 3.0 34.0 + - + +
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Residues in contact with GLY 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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139A LEU* 3.8 19.5 - - - -
208A VAL 2.8 20.2 + - - -
209A ALA* 4.0 0.4 - - - -
211A ILE* 1.3 76.5 - - - +
213A GLU* 1.3 63.5 + - - +
215A VAL* 3.3 2.8 + - - +
216A MET* 3.2 28.8 + - - +
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Residues in contact with GLU 213 (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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183A ARG* 2.9 39.9 + - - -
209A ALA* 2.9 32.0 + - - +
210A THR* 3.9 3.4 - - - +
212A GLY* 1.3 75.7 - - - +
214A ALA* 1.3 62.8 + - - +
216A MET* 3.3 22.7 + - - +
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Residues in contact with ALA 214 (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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5A PRO* 3.5 20.4 - - + +
176A TYR* 3.4 30.3 - - + +
210A THR 3.4 10.3 + - - +
211A ILE 3.3 4.9 + - - +
212A GLY 3.2 0.6 - - - -
213A GLU* 1.3 79.7 - - - +
215A VAL* 1.3 62.9 + - - +
216A MET 3.3 7.3 - - - +
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Residues in contact with VAL 215 (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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4A LEU* 4.0 14.8 - - + -
5A PRO* 4.0 25.1 - - + +
8A GLU* 4.4 22.2 - - + +
9A THR* 5.2 5.5 + - - -
12A ARG* 5.4 5.4 + - - -
57A ARG* 6.1 0.4 - - - +
139A LEU* 3.9 25.6 - - + -
211A ILE 3.0 21.7 + - - +
212A GLY 3.7 5.2 - - - +
213A GLU 3.3 0.4 - - - -
214A ALA* 1.3 76.8 - - - +
216A MET* 1.3 70.9 + - - +
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Residues in contact with MET 216 (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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212A GLY 3.2 16.8 + - - +
213A GLU* 3.3 17.4 - - - +
214A ALA 3.3 7.2 - - - +
215A VAL* 1.3 88.7 - - + +
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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