Contacts of the helix formed by residues 210 - 230 (chain D) in PDB entry 3SPD
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 HIS 210 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198D LEU* 3.9 2.7 - - - -
207D PHE* 2.8 29.1 + - + +
208D GLY* 3.4 2.2 + - - -
209D ARG* 1.3 78.8 - - - +
211D PHE* 1.3 64.5 + - - +
212D THR 3.3 2.5 - - - -
213D LYS* 3.3 40.1 + - + +
214D LEU* 3.1 19.8 + - - +
7G G 5.6 1.6 + - - -
8G A 3.6 14.8 + - - +
11H G 6.4 2.5 - - - -
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Residues in contact with PHE 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D LEU* 3.4 29.8 - - + -
161D LYS* 3.3 23.1 - - - -
162D ASN* 3.3 38.4 - - - -
163D SER* 3.6 22.4 - - - +
166D TYR* 4.6 4.9 - - + -
198D LEU* 3.6 8.1 - - - -
209D ARG 3.0 8.1 + - - +
210D HIS* 1.3 69.0 - - - +
212D THR* 1.3 65.1 + - - +
214D LEU* 3.1 14.5 + - + +
215D LYS* 2.8 56.9 + - + +
8G A 2.8 22.5 + - - +
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Residues in contact with THR 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D PHE* 1.3 78.8 - - - +
213D LYS* 1.3 64.6 + - + +
215D LYS* 3.4 9.0 + - + +
216D ALA* 3.1 21.8 + - + +
7G G 3.6 33.1 + - - +
8G A 2.7 32.4 + - - -
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Residues in contact with LYS 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D PHE* 3.8 18.9 - - + -
210D HIS* 3.3 43.8 + - + +
211D PHE 3.2 0.4 - - - -
212D THR* 1.3 77.1 - - + +
214D LEU* 1.3 65.8 + - - +
216D ALA* 3.3 7.5 + - - +
217D HIS* 3.1 22.9 + - - +
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Residues in contact with LEU 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D TYR* 3.6 53.4 - - + +
198D LEU* 3.9 21.5 - - + -
199D LYS 4.5 0.9 - - - -
200D CYS* 4.2 11.4 - - + +
207D PHE* 3.8 36.7 - - + -
210D HIS 3.1 12.9 + - - +
211D PHE* 3.4 14.6 - - + +
213D LYS* 1.3 77.1 - - - +
215D LYS* 1.3 65.0 + - - +
217D HIS* 3.0 5.0 + - + +
218D LEU* 2.8 42.4 + - + +
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Residues in contact with LYS 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D HIS 5.4 0.6 + - - -
156D VAL* 5.9 0.2 - - - +
157D SER 2.9 27.1 + - - +
158D PRO* 4.5 4.6 + - - +
160D LEU* 2.8 31.3 + - + +
161D LYS* 5.3 0.2 - - - -
211D PHE* 2.8 52.5 + - + +
212D THR* 3.5 11.7 - - + +
213D LYS 3.3 0.2 - - - -
214D LEU* 1.3 73.1 - - - +
216D ALA* 1.3 63.2 + - - +
218D LEU* 3.2 18.8 + - + +
219D GLN* 3.2 12.3 + - - +
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Residues in contact with ALA 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D THR* 3.1 10.6 + - + +
213D LYS* 3.7 10.5 - - - +
214D LEU 3.2 0.4 - - - -
215D LYS* 1.3 78.8 - - - +
217D HIS* 1.3 61.9 + - - +
219D GLN* 3.2 10.9 + - - +
220D GLU* 3.2 24.5 + - - +
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Residues in contact with HIS 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D CYS* 3.6 14.3 - - + +
203D CYS* 3.7 3.0 - - - -
205D GLU* 3.2 25.6 + - - -
207D PHE* 3.4 29.2 - + + -
213D LYS 3.1 7.4 + - - +
214D LEU* 3.0 10.0 + - + +
216D ALA* 1.3 75.9 - - - +
218D LEU* 1.3 59.2 + - - +
220D GLU* 3.2 19.9 + - + +
221D GLU* 2.8 34.5 + - + +
601D ZN 2.1 37.7 - - - -
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Residues in contact with LEU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ASP 3.8 20.9 - - - +
155D HIS* 3.7 18.4 - - + +
156D VAL* 3.4 14.7 - - + +
160D LEU* 4.1 10.3 - - + -
166D TYR* 3.9 23.3 - - + +
200D CYS* 4.7 10.1 - - - -
201D TRP* 3.8 25.4 - - + +
214D LEU* 2.8 40.6 + - + +
215D LYS* 3.2 11.6 + - - +
217D HIS* 1.3 75.5 - - - +
219D GLN* 1.3 62.6 + - - +
221D GLU* 3.2 6.1 + - + +
222D TYR* 2.9 18.9 + - - +
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Residues in contact with GLN 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LYS* 5.2 2.5 + - - +
156D VAL* 3.2 29.1 - - + +
215D LYS 3.2 10.9 + - - +
216D ALA* 3.3 12.8 - - - +
218D LEU* 1.3 75.4 - - - +
220D GLU* 1.3 66.2 + - + +
222D TYR* 3.1 14.1 + - - +
223D ASP* 3.0 51.5 + - - +
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Residues in contact with GLU 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D ALA* 3.2 13.0 + - - +
217D HIS* 3.2 21.2 + - + +
219D GLN* 1.3 77.7 - - + +
221D GLU* 1.3 57.9 + - + +
223D ASP* 3.3 10.5 + - - +
224D ASP* 2.9 39.8 + - - +
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Residues in contact with GLU 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D TYR* 5.4 0.7 - - - -
200D CYS* 3.5 6.9 - - - -
201D TRP* 5.7 4.5 - - + +
202D ARG* 2.9 48.0 + - + +
203D CYS* 3.2 16.3 + - - +
217D HIS* 2.8 33.0 + - + +
218D LEU* 3.6 9.6 - - + +
219D GLN 3.2 0.2 - - - -
220D GLU* 1.3 73.3 - - - +
222D TYR* 1.3 57.3 + - - +
224D ASP* 3.5 7.8 + - - +
225D TRP* 2.9 29.3 + - - +
601D ZN 2.0 39.7 - - - -
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Residues in contact with TYR 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LYS* 3.5 35.9 + - + +
120D LEU* 3.6 49.8 + - + +
132D TYR* 3.6 24.0 - + - +
154D ASP* 3.9 9.9 - - + -
156D VAL* 3.8 13.5 - - + -
218D LEU 2.9 12.9 + - - +
219D GLN* 3.5 11.0 - - - +
221D GLU* 1.3 74.3 - - - +
223D ASP* 1.3 72.8 + - - +
225D TRP* 3.1 12.8 + + - -
226D LEU* 2.8 60.8 + - + +
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Residues in contact with ASP 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D GLN* 3.0 45.0 + - - +
220D GLU* 3.6 11.8 - - - +
222D TYR* 1.3 80.6 - - - +
224D ASP* 1.3 65.3 + - - +
226D LEU* 3.5 6.5 + - - +
227D ASP* 3.0 25.5 + - - +
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Residues in contact with ASP 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ARG* 3.8 12.5 + - - +
220D GLU* 2.9 25.6 + - - +
221D GLU* 3.6 11.1 - - - +
223D ASP* 1.3 78.9 - - - +
225D TRP* 1.3 62.4 + - - +
227D ASP* 3.4 5.4 + - - +
228D LYS* 3.0 24.3 + - - +
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Residues in contact with TRP 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU* 3.9 12.8 - - + -
124D LEU* 3.6 43.1 - - + -
128D ALA* 4.0 12.7 + - + -
129D LEU* 4.7 3.8 - - + -
131D ASN 5.7 0.6 + - - -
132D TYR* 3.3 65.0 - + + +
202D ARG* 3.8 23.9 - - - +
221D GLU 2.9 17.1 + - - +
222D TYR* 3.7 13.7 - + - +
224D ASP* 1.3 75.8 - - - +
226D LEU* 1.3 80.4 + - + +
228D LYS* 3.3 6.1 + - + +
229D SER* 2.8 46.4 + - - -
701D SO4 3.6 26.2 + - - -
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Residues in contact with LEU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU 5.5 0.9 - - - +
121D SER* 3.9 23.8 - - - -
124D LEU* 4.2 12.3 - - + -
222D TYR* 2.8 50.7 + - + +
223D ASP* 3.8 7.2 - - - +
225D TRP* 1.3 83.1 - - + +
227D ASP* 1.3 65.0 + - - +
229D SER* 3.0 2.0 + - - -
230D VAL* 2.9 49.0 + - + +
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Residues in contact with ASP 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D ASP 3.0 18.1 + - - +
224D ASP* 3.7 6.3 - - - +
226D LEU* 1.3 76.1 - - - +
228D LYS* 1.3 60.7 + - - +
230D VAL* 3.8 8.8 + - - +
231D SER* 2.6 41.5 + - - -
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Residues in contact with LYS 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D ARG* 4.0 10.9 - - - +
224D ASP 3.0 17.3 + - - +
225D TRP* 3.6 6.3 - - + +
227D ASP* 1.3 78.4 - - - +
229D SER* 1.3 64.1 + - - +
231D SER* 3.6 13.2 + - - -
232D MET* 4.1 9.9 - - - +
701D SO4 2.9 33.0 + - - +
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Residues in contact with SER 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D GLN 5.5 0.6 - - - +
124D LEU* 3.6 24.7 - - - -
128D ALA* 4.7 10.7 - - - +
225D TRP* 2.8 46.0 + - - -
226D LEU 3.0 3.8 + - - -
228D LYS* 1.3 77.6 - - - +
230D VAL* 1.3 59.2 + - - +
231D SER 3.0 8.8 + - - -
232D MET* 3.3 19.6 + - - +
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Residues in contact with VAL 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D SER* 4.6 1.6 - - - +
123D GLN* 3.7 46.4 - - + +
124D LEU* 4.1 9.6 - - + -
226D LEU* 2.9 41.4 + - + +
227D ASP* 3.8 13.2 - - - +
229D SER* 1.3 73.9 - - - +
231D SER* 1.3 57.6 + - - +
232D MET* 3.2 8.1 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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