Contacts of the helix formed by residues 203 - 216 (chain X) in PDB entry 1SHU
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 PHE 203 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68X GLN* 4.3 14.8 - - - -
201X GLY 3.1 2.8 + - - -
202X GLY* 1.3 81.7 - - - +
204X GLN* 1.3 64.3 + - - +
205X ALA 3.4 2.2 - - - -
206X LEU* 4.1 20.6 - - + +
207X LYS* 3.0 39.8 + - + +
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Residues in contact with GLN 204 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197X PHE* 3.5 10.8 - - + -
198X PRO* 3.4 39.1 - - + +
200X LYS 3.4 5.5 + - - -
201X GLY* 2.7 28.0 + - - +
202X GLY* 3.0 9.8 - - - +
203X PHE* 1.3 77.9 - - - +
205X ALA* 1.3 59.0 + - - +
207X LYS* 4.3 1.7 - - - +
208X GLY* 2.8 28.2 + - - -
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Residues in contact with ALA 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65X PHE* 3.7 22.0 - - + -
176X VAL* 4.0 11.2 - - + -
197X PHE* 3.6 21.5 - - + -
198X PRO 3.4 23.3 + - - +
199X VAL* 4.5 3.8 - - - +
203X PHE 3.4 0.4 - - - -
204X GLN* 1.3 77.1 - - - +
206X LEU* 1.3 65.5 + - - +
209X ILE* 3.0 29.3 + - - +
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Residues in contact with LEU 206 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65X PHE* 3.8 35.9 - - + +
68X GLN* 2.9 50.5 - - + +
69X LEU* 4.1 21.1 - - + +
203X PHE* 3.6 24.9 + - + +
204X GLN 3.4 0.6 - - - -
205X ALA* 1.3 79.1 - - - +
207X LYS* 1.3 57.5 + - + +
209X ILE* 4.2 0.8 - - - +
210X ILE* 2.9 46.3 + - + +
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Residues in contact with LYS 207 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202X GLY 5.0 3.1 - - - +
203X PHE* 3.0 32.7 + - + +
204X GLN* 4.3 1.8 - - - +
206X LEU* 1.3 76.6 - - + +
208X GLY* 1.3 57.3 + - - +
210X ILE* 4.7 4.9 - - - -
211X ASN* 2.8 54.0 + - - +
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Residues in contact with GLY 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197X PHE* 3.7 23.4 - - - -
204X GLN 2.8 19.8 + - - -
207X LYS* 1.3 77.7 - - - +
209X ILE* 1.3 57.2 + - - +
211X ASN* 3.9 3.3 - - - +
212X SER* 3.0 28.4 + - - -
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Residues in contact with ILE 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65X PHE* 3.8 12.1 - - + -
69X LEU* 4.2 10.3 - - + -
144X ILE* 4.1 24.7 - - + -
174X TYR* 3.8 22.2 - - + -
176X VAL* 3.6 31.4 - - + -
197X PHE* 3.8 21.3 - - + -
205X ALA 3.0 19.5 + - - +
206X LEU* 4.2 1.3 - - - +
208X GLY* 1.3 74.6 - - - +
210X ILE* 1.3 66.5 + - - +
212X SER* 3.2 6.2 + - - -
213X ILE* 3.0 40.6 + - + +
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Residues in contact with ILE 210 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X GLN 5.7 0.2 - - - +
69X LEU* 3.5 25.4 - - + -
72X ARG* 3.7 40.8 - - + +
73X PHE* 4.0 14.1 - - + -
206X LEU* 2.9 36.3 + - + +
207X LYS* 4.0 4.3 - - - +
209X ILE* 1.3 73.2 - - - +
211X ASN* 1.3 64.0 + - - +
213X ILE* 3.2 4.5 + - - +
214X LEU* 2.9 45.6 + - + +
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Residues in contact with ASN 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207X LYS* 2.8 42.0 + - - +
208X GLY* 4.1 3.3 - - - +
210X ILE* 1.3 82.1 - - - +
212X SER* 1.3 55.4 + - - +
214X LEU* 3.5 18.1 + - - +
215X ALA* 3.0 29.3 + - - +
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Residues in contact with SER 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174X TYR* 2.5 37.7 + - - -
195X GLN* 5.4 3.5 + - - -
197X PHE* 6.1 0.7 - - - -
208X GLY 3.0 18.7 + - - -
209X ILE 3.2 4.7 + - - -
211X ASN* 1.3 76.8 - - - +
213X ILE* 1.3 60.4 + - - +
215X ALA* 3.4 14.1 + - - +
216X GLN* 3.0 23.8 + - - +
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Residues in contact with ILE 213 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43X PHE* 4.0 21.0 - - + -
45X LEU* 4.2 18.4 - - + -
69X LEU* 5.2 1.1 - - + -
73X PHE* 3.9 36.8 - - + -
78X MET* 4.4 4.0 - - + -
142X ILE* 3.7 28.7 - - + -
144X ILE* 5.4 0.4 - - + -
174X TYR* 4.7 3.6 - - + +
209X ILE* 3.0 32.0 + - + +
210X ILE 3.7 5.6 - - - +
212X SER* 1.3 75.4 - - - +
214X LEU* 1.3 64.0 + - - +
216X GLN* 3.0 19.6 + - - +
217X SER* 2.8 24.5 + - - +
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Residues in contact with LEU 214 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72X ARG* 3.8 28.3 - - - +
73X PHE* 4.5 13.2 - - + -
210X ILE* 2.9 31.1 + - + +
211X ASN* 3.8 15.3 - - - +
213X ILE* 1.3 75.2 - - - +
215X ALA* 1.3 58.0 + - - +
217X SER* 2.9 35.6 + - - +
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Residues in contact with ALA 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211X ASN 3.0 18.3 + - - +
212X SER* 3.6 9.2 - - - +
213X ILE 3.2 0.4 - - - -
214X LEU* 1.3 76.7 - - - +
216X GLN* 1.3 59.8 + - + +
217X SER 3.3 3.8 + - - +
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Residues in contact with GLN 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X SER 4.6 0.7 - - - +
39X CYS* 3.6 6.9 - - - -
40X ARG* 2.6 62.6 + - - +
43X PHE* 3.7 16.9 - - + -
142X ILE* 4.5 10.0 - - - +
172X SER* 5.7 5.2 + - - -
174X TYR* 3.4 21.0 + - - -
212X SER* 3.0 23.0 + - - +
213X ILE* 3.0 11.9 + - - +
215X ALA* 1.3 76.8 - - + +
217X SER* 1.3 57.9 + - - +
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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