Contacts of the helix formed by residues 203 - 218 (chain P) in PDB entry 3HOU
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 203 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200P ASN 5.2 0.6 + - - -
202P ILE* 1.3 82.1 - - - +
204P ASP* 1.3 59.4 + - - +
205P ASP* 3.8 3.3 + - - +
206P GLU* 3.0 31.9 + - - +
207P LEU* 3.0 24.6 + - - +
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Residues in contact with ASP 204 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 3.4 29.5 + - - +
83A HIS* 5.7 1.6 - - - -
85A ASP* 3.8 31.9 - - + +
188P ALA* 2.6 41.3 - - - +
189P ASP* 4.2 2.8 + - - +
192P LYS* 3.4 24.0 + - - +
202P ILE 3.7 0.2 + - - -
203P SER* 1.3 74.7 - - - +
205P ASP* 1.3 58.7 + - - +
208P GLU* 2.8 29.5 + - - +
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Residues in contact with ASP 205 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASP* 3.5 34.3 - - + +
86A LEU 4.1 8.1 - - - +
87A ALA* 5.2 1.9 - - - -
273A ASN* 4.8 3.5 + - - -
277A GLU* 3.6 28.1 - - + +
203P SER* 3.4 3.8 + - - +
204P ASP* 1.3 78.4 - - - +
206P GLU* 1.3 55.2 + - - +
208P GLU* 2.9 19.3 + - - +
209P ARG* 2.6 40.1 + - - +
212P LYS* 4.7 1.9 + - - -
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Residues in contact with GLU 206 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A HIS* 4.1 11.1 + - - -
202P ILE* 4.2 9.1 - - + +
203P SER* 3.0 22.7 + - - +
205P ASP* 1.3 76.2 - - - +
207P LEU* 1.3 63.5 + - - +
209P ARG* 3.0 40.2 + - - +
210P ILE* 3.1 34.8 + - - +
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Residues in contact with LEU 207 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180P LEU* 4.3 21.5 - - + -
188P ALA* 3.6 14.4 - - + +
191P ALA* 3.8 10.1 - - + -
192P LYS* 3.5 38.1 - - + -
198P LEU* 4.5 3.8 - - + -
202P ILE* 3.2 30.6 - - + +
203P SER 3.0 20.3 + - - +
204P ASP 4.0 0.9 - - - +
206P GLU* 1.3 76.7 - - - +
208P GLU* 1.3 61.2 + - - +
210P ILE* 3.6 6.9 + - + +
211P LEU* 2.8 48.0 + - + +
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Residues in contact with GLU 208 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 2.6 47.8 + - - +
85A ASP* 5.7 0.7 - - - +
186P ASP 3.7 18.4 - - - +
187P THR* 4.0 5.2 - - - +
188P ALA* 4.1 7.7 + - + +
204P ASP 2.8 21.2 + - - +
205P ASP* 2.9 19.6 + - - +
207P LEU* 1.3 78.8 - - - +
209P ARG* 1.3 53.2 + - - +
211P LEU* 3.2 10.5 - - - +
212P LYS* 2.7 49.1 + - + +
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Residues in contact with ARG 209 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A GLU* 3.1 49.0 + - - +
278A THR* 4.1 9.7 + - - +
281A HIS* 3.5 53.2 + - + +
205P ASP* 2.6 26.2 + - - +
206P GLU* 3.0 33.6 + - - +
208P GLU* 1.3 69.2 - - - +
210P ILE* 1.3 58.0 + - + +
211P LEU 2.9 0.9 - - - -
212P LYS* 2.6 62.4 + - - +
213P GLU* 3.0 5.4 + - - +
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Residues in contact with ILE 210 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166P LEU* 4.2 19.0 - - + +
167P LEU* 3.8 29.2 - - + -
169P SER* 5.2 2.2 - - - +
170P THR* 3.5 31.2 - - + -
180P LEU* 6.5 0.7 - - + -
202P ILE* 4.1 13.7 - - + -
206P GLU* 3.1 30.0 + - - +
207P LEU* 4.0 8.3 - - + +
209P ARG* 1.3 78.8 - - + +
211P LEU* 1.3 57.8 + - - +
213P GLU* 3.3 8.9 + - - +
214P LEU* 2.9 29.1 + - + +
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Residues in contact with LEU 211 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180P LEU* 4.9 7.6 - - + -
183P LEU 5.8 0.2 - - - +
185P CYS* 2.8 53.0 - - + +
186P ASP 4.0 9.6 - - - +
188P ALA* 4.0 14.4 - - - -
191P ALA* 4.4 3.1 - - + -
207P LEU* 2.8 54.4 + - + +
208P GLU* 3.2 15.5 - - - +
210P ILE* 1.3 78.2 - - + +
212P LYS* 1.3 52.8 + - + +
214P LEU* 3.4 8.6 + - + +
215P SER* 2.4 32.0 + - - -
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Residues in contact with LYS 212 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A GLU* 4.2 10.1 + - - -
205P ASP* 4.7 1.8 + - - -
208P GLU* 2.7 43.9 + - + +
209P ARG* 2.6 56.9 + - + +
211P LEU* 1.3 67.5 - - - +
213P GLU* 1.3 54.9 + - - +
215P SER* 2.3 27.5 + - - -
216P ASN* 2.7 26.4 - - - +
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Residues in contact with GLU 213 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166P LEU* 3.7 27.6 - - + +
209P ARG 3.0 6.8 + - - +
210P ILE* 3.3 8.7 + - - +
212P LYS* 1.3 78.7 - - - +
214P LEU* 1.3 62.3 + - - +
216P ASN* 3.0 27.5 + - - +
217P LEU* 3.1 37.4 + - - +
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Residues in contact with LEU 214 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153P ARG* 3.3 31.6 - - - +
154P PHE* 3.2 22.2 - - + -
163P VAL* 3.5 32.8 - - + -
166P LEU* 4.1 14.3 - - + +
167P LEU* 4.3 11.2 - - + -
180P LEU 4.5 9.0 - - - +
181P GLY* 4.6 3.1 - - - +
210P ILE* 2.9 18.4 + - + +
211P LEU* 3.5 10.5 - - + +
212P LYS 3.1 0.2 - - - -
213P GLU* 1.3 76.8 - - - +
215P SER* 1.3 57.0 + - - +
217P LEU* 4.9 2.0 - - + +
218P GLU* 3.0 21.8 + - - +
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Residues in contact with SER 215 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153P ARG* 5.1 3.6 - - - +
185P CYS 5.5 1.7 + - - -
211P LEU 2.4 20.6 + - - -
212P LYS* 2.3 29.2 + - - -
214P LEU* 1.3 72.7 - - - +
216P ASN* 1.3 60.7 + - - +
218P GLU* 2.4 35.6 - - - +
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Residues in contact with ASN 216 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212P LYS* 2.7 23.7 + - - +
213P GLU* 3.0 25.6 + - - +
215P SER* 1.3 82.4 - - - +
217P LEU* 1.3 57.9 + - + +
218P GLU 2.5 26.3 + - - +
219P THR* 4.8 0.2 - - - -
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Residues in contact with LEU 217 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154P PHE* 4.2 4.9 - - + -
159P THR* 4.0 18.4 - - - +
162P ALA* 3.2 39.9 - - + +
163P VAL* 3.7 7.4 - - + +
166P LEU* 3.5 27.1 - - + -
213P GLU* 3.1 36.5 + - - +
214P LEU* 4.6 3.4 - - - +
216P ASN* 1.3 78.1 - - + +
218P GLU* 1.3 49.7 + - - +
219P THR* 2.4 26.3 + - - -
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Residues in contact with GLU 218 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153P ARG* 3.3 32.9 + - + +
154P PHE* 3.4 20.6 - - + -
184P ALA* 5.2 1.9 - - - +
214P LEU 3.0 13.8 + - - +
215P SER* 2.4 47.9 - - - +
216P ASN 2.5 10.8 + - - +
217P LEU* 1.3 68.5 - - - +
219P THR* 1.3 75.1 + - - +
220P LEU* 3.4 1.9 + - - +
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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