Contacts of the helix formed by residues 210 - 231 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B LEU* 3.9 3.1 - - - -
207B PHE* 2.8 29.1 + - + +
208B GLY* 3.4 1.9 + - - -
209B ARG* 1.3 78.8 - - - +
211B PHE* 1.3 63.6 + - - +
212B THR 3.3 0.7 - - - -
213B LYS* 3.3 38.7 + - + +
214B LEU* 3.2 19.2 + - - +
7E G 5.6 1.0 + - - -
8E A 3.3 16.9 + - - +
11F G 6.4 1.6 - - - -
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Residues in contact with PHE 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LEU* 3.5 29.2 - - + -
161B LYS* 3.4 24.7 - - - -
162B ASN* 3.3 36.3 - - - -
163B SER* 3.6 21.3 - - - +
166B TYR* 4.6 6.3 - - + -
198B LEU* 3.6 12.3 - - + -
209B ARG 3.0 8.6 + - - +
210B HIS* 1.3 70.0 - - - +
212B THR* 1.3 64.8 + - - +
214B LEU* 3.2 9.9 + - + +
215B LYS* 2.8 54.2 + - + +
8E A 2.8 21.6 + - + +
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Residues in contact with THR 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B PHE* 1.3 79.2 - - - +
213B LYS* 1.3 65.5 + - + +
215B LYS* 3.3 8.7 + - + +
216B ALA* 3.1 22.0 + - + +
7E G 3.6 33.6 + - - +
8E A 2.8 31.7 + - - -
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Residues in contact with LYS 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PHE* 3.8 19.0 - - + -
210B HIS* 3.3 40.7 + - + +
211B PHE 3.2 0.4 - - - -
212B THR* 1.3 78.3 - - + +
214B LEU* 1.3 64.8 + - - +
216B ALA* 3.3 7.7 + - - +
217B HIS* 3.1 22.3 + - - +
8E A 4.6 0.2 + - - -
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B TYR* 3.6 44.9 - - + +
198B LEU* 4.1 20.6 - - + -
199B LYS 4.5 0.9 - - - -
200B CYS* 4.2 20.9 - - + +
207B PHE* 3.7 36.6 - - + -
210B HIS 3.2 12.4 + - - +
211B PHE* 3.5 14.8 - - + +
213B LYS* 1.3 76.3 - - - +
215B LYS* 1.3 57.7 + - - +
217B HIS* 3.0 5.1 + - + +
218B LEU* 2.8 49.1 + - + +
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Residues in contact with LYS 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B HIS 5.3 1.0 + - - +
156B VAL* 5.6 0.6 - - - +
157B SER 2.9 26.9 + - - +
158B PRO* 4.5 4.8 + - - +
160B LEU* 2.8 31.1 + - + +
161B LYS* 5.3 0.2 - - - -
211B PHE* 2.8 48.0 + - + +
212B THR* 3.5 13.0 - - + +
213B LYS 3.2 0.2 - - - -
214B LEU* 1.3 77.3 - - - +
216B ALA* 1.3 61.9 + - - +
218B LEU* 3.2 19.0 + - + +
219B GLN* 3.2 12.3 + - - +
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B THR* 3.1 11.2 + - + +
213B LYS* 3.7 9.2 - - - +
214B LEU 3.2 0.2 - - - -
215B LYS* 1.3 78.4 - - - +
217B HIS* 1.3 62.4 + - - +
219B GLN* 3.3 10.1 + - - +
220B GLU* 3.2 28.3 + - - +
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Residues in contact with HIS 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B CYS* 3.6 14.8 - - + +
203B CYS* 3.7 3.7 - - - -
205B GLU* 3.4 24.3 + - - -
207B PHE* 3.4 29.6 - + + -
213B LYS 3.1 7.4 + - - +
214B LEU* 3.0 10.9 + - + +
216B ALA* 1.3 75.7 - - - +
218B LEU* 1.3 60.3 + - - +
220B GLU* 3.2 23.7 + - + +
221B GLU* 2.8 36.3 + - + +
601B ZN 2.1 36.8 - - - -
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASP 3.8 21.1 - - - +
155B HIS* 3.8 17.3 - - + +
156B VAL* 3.3 15.0 - - + +
160B LEU* 4.2 6.5 - - + -
166B TYR* 3.9 24.0 - - + +
200B CYS* 4.7 9.9 - - - -
201B TRP* 3.8 25.8 - - + +
214B LEU* 2.8 43.8 + - + +
215B LYS* 3.2 14.1 + - - +
217B HIS* 1.3 69.3 - - - +
219B GLN* 1.3 60.2 + - - +
221B GLU* 3.3 6.6 + - + +
222B TYR* 2.9 24.4 + - - +
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Residues in contact with GLN 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 5.2 3.1 + - - +
156B VAL* 3.2 28.7 - - + +
215B LYS 3.2 10.9 + - - +
216B ALA* 3.3 13.0 - - - +
217B HIS 3.2 0.4 - - - -
218B LEU* 1.3 76.3 - - - +
220B GLU* 1.3 65.3 + - + +
222B TYR* 3.1 14.9 + - - +
223B ASP* 2.9 52.1 + - - +
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Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B ALA* 3.2 17.2 + - - +
217B HIS* 3.2 26.7 + - + +
219B GLN* 1.3 79.5 - - + +
221B GLU* 1.3 56.1 + - + +
223B ASP* 3.3 9.6 + - - +
224B ASP* 2.9 40.1 + - - +
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B TYR* 5.4 0.7 - - - -
200B CYS* 3.5 6.0 - - - -
201B TRP* 5.7 4.3 - - + +
202B ARG* 2.8 50.2 + - + +
203B CYS* 3.2 15.1 + - - +
217B HIS* 2.8 29.5 + - + +
218B LEU* 3.6 9.4 - - + +
219B GLN 3.2 0.4 - - - -
220B GLU* 1.3 76.5 - - - +
222B TYR* 1.3 58.1 + - - +
224B ASP* 3.4 7.7 + - - +
225B TRP* 2.9 29.5 + - - +
601B ZN 2.0 40.8 - - - -
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Residues in contact with TYR 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LYS* 3.5 35.7 + - + +
120B LEU* 3.5 43.5 + - + +
132B TYR* 3.6 21.8 - - - -
154B ASP* 3.9 11.2 - - + -
156B VAL* 3.8 13.0 - - + -
218B LEU 2.9 14.1 + - - +
219B GLN* 3.1 11.6 + - - +
221B GLU* 1.3 74.4 - - - +
223B ASP* 1.3 78.3 + - - +
225B TRP* 3.1 18.8 + + - -
226B LEU* 2.8 55.0 + - + +
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Residues in contact with ASP 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B GLN* 2.9 44.2 + - - +
220B GLU* 3.5 11.7 - - - +
222B TYR* 1.3 82.5 - - - +
224B ASP* 1.3 65.9 + - - +
226B LEU* 3.7 6.6 - - - +
227B ASP* 3.0 25.5 + - - +
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Residues in contact with ASP 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ARG* 3.9 12.7 + - - +
220B GLU* 2.9 24.5 + - - +
221B GLU* 3.6 11.1 - - - +
223B ASP* 1.3 79.5 - - - +
225B TRP* 1.3 63.0 + - - +
227B ASP* 3.4 5.8 + - - +
228B LYS* 3.1 24.1 + - - +
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Residues in contact with TRP 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU* 4.0 13.0 - - + -
124B LEU* 3.7 42.4 - - + -
128B ALA* 4.0 12.1 - - + -
129B LEU* 4.7 3.8 - - + -
131B ASN 5.6 1.0 + - - -
132B TYR* 3.3 65.5 - + + +
202B ARG* 3.8 18.5 - - - +
221B GLU 2.9 18.9 + - - +
222B TYR* 3.6 13.0 - + - +
224B ASP* 1.3 75.0 - - - +
226B LEU* 1.3 78.6 + - + +
228B LYS* 3.3 4.1 + - + +
229B SER* 2.8 51.7 + - - -
701B SO4 3.4 30.0 + - - -
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Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU 5.5 0.9 - - - +
121B SER* 3.9 24.0 - - - -
124B LEU* 4.2 12.3 - - + -
222B TYR* 2.8 52.5 + - + +
223B ASP* 3.7 7.2 - - - +
225B TRP* 1.3 78.4 - - + +
227B ASP* 1.3 65.7 + - - +
229B SER* 3.1 1.5 + - - -
230B VAL* 3.1 45.8 + - + +
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Residues in contact with ASP 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ASP 3.0 17.8 + - - +
224B ASP* 3.7 6.1 - - - +
226B LEU* 1.3 76.4 - - - +
228B LYS* 1.3 59.9 + - - +
230B VAL* 3.7 7.6 - - - +
231B SER* 2.7 41.7 + - - -
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Residues in contact with LYS 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ARG* 4.0 10.2 - - - +
224B ASP 3.1 16.5 + - - +
225B TRP 3.6 4.5 - - - +
227B ASP* 1.3 78.6 - - - +
229B SER* 1.3 63.9 + - - +
231B SER* 3.8 12.5 + - - -
232B MET* 4.2 10.9 - - - +
701B SO4 3.4 37.9 + - - +
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Residues in contact with SER 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLN 5.2 1.2 - - - +
124B LEU* 3.7 25.9 - - - +
128B ALA* 4.7 12.9 - - - +
225B TRP* 2.8 49.2 + - - -
226B LEU 3.1 2.4 + - - -
228B LYS* 1.3 80.0 - - - +
230B VAL* 1.3 62.9 + - - +
231B SER 3.3 0.2 - - - -
232B MET* 3.7 14.4 + - - +
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Residues in contact with VAL 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B SER* 4.6 1.1 - - - +
123B GLN* 3.7 44.9 - - + +
124B LEU* 4.0 9.9 - - + -
226B LEU* 3.1 37.2 + - + +
227B ASP* 3.7 11.4 - - - +
229B SER* 1.3 74.6 - - - +
231B SER* 1.3 62.8 + - - +
232B MET* 2.8 20.4 + - - +
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Residues in contact with SER 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B ASP* 2.7 30.3 + - - -
228B LYS* 4.0 8.5 - - - -
229B SER 3.3 0.8 - - - -
230B VAL* 1.3 79.0 - - - +
232B MET* 1.3 72.0 + - - +
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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
------------------------------------------------------------
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