Contacts of the helix formed by residues 210 - 231 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C LEU* 4.0 2.9 - - - -
207C PHE* 2.8 30.0 + - + +
208C GLY* 3.4 2.6 + - - -
209C ARG* 1.3 79.7 - - - +
211C PHE* 1.3 62.9 + - - +
212C THR 3.3 0.9 - - - -
213C LYS* 3.3 38.7 + - + +
214C LEU* 3.2 19.6 + - - +
11G G 6.2 4.5 - - - -
7H A 5.7 0.6 + - - -
8H T 3.3 14.5 + - - +
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Residues in contact with PHE 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160C LEU* 3.5 26.2 - - + -
161C LYS* 3.4 22.4 - - - -
162C ASN* 3.4 37.2 - - - -
163C SER* 3.7 22.9 - - - +
166C TYR* 4.6 5.2 - - + -
198C LEU* 3.6 8.5 - - - -
209C ARG 3.0 8.6 + - - +
210C HIS* 1.3 68.5 - - - +
212C THR* 1.3 64.6 + - - +
214C LEU* 3.2 15.3 + - + +
215C LYS* 2.8 60.8 + - + +
8H T 2.8 21.7 + - - +
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Residues in contact with THR 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C PHE* 1.3 79.5 - - - +
213C LYS* 1.3 66.3 + - + +
215C LYS* 3.4 9.4 + - + +
216C ALA* 3.1 21.6 + - + +
7H A 3.8 32.4 + - - +
8H T 2.8 29.9 + - - -
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Residues in contact with LYS 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C PHE* 3.8 18.5 - - + -
210C HIS* 3.3 39.4 + - + +
211C PHE 3.2 0.4 - - - -
212C THR* 1.3 79.9 - - + +
214C LEU* 1.3 66.0 + - - +
216C ALA* 3.3 7.5 + - - +
217C HIS* 3.0 22.5 + - - +
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Residues in contact with LEU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C TYR* 3.6 44.0 - - + +
198C LEU* 4.0 21.1 - - + -
199C LYS 4.4 1.6 - - - -
200C CYS* 4.2 20.9 - - + +
207C PHE* 3.8 36.0 - - + -
210C HIS 3.2 11.9 + - - +
211C PHE* 3.2 17.1 + - + +
213C LYS* 1.3 76.1 - - - +
215C LYS* 1.3 57.5 + - - +
217C HIS* 3.0 4.7 + - + +
218C LEU* 2.8 47.9 + - + +
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Residues in contact with LYS 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C HIS 5.3 0.8 + - - +
156C VAL* 5.6 0.5 - - - +
157C SER 2.9 34.1 + - - +
158C PRO* 4.5 4.8 + - - +
160C LEU* 2.9 24.4 + - + +
161C LYS* 5.4 0.2 - - - -
211C PHE* 2.8 49.4 + - + +
212C THR* 3.5 11.7 - - + +
214C LEU* 1.3 77.1 - - - +
216C ALA* 1.3 61.6 + - - +
218C LEU* 3.2 18.2 + - + +
219C GLN* 3.2 12.8 + - - +
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Residues in contact with ALA 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C THR* 3.1 11.2 + - + +
213C LYS* 3.7 9.9 - - - +
214C LEU 3.2 0.4 - - - -
215C LYS* 1.3 77.1 - - - +
217C HIS* 1.3 62.2 + - - +
219C GLN* 3.3 10.2 + - - +
220C GLU* 3.2 28.5 + - - +
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Residues in contact with HIS 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C CYS* 3.6 15.4 - - + +
203C CYS* 3.7 3.5 - - - -
205C GLU* 3.2 26.2 + - - -
207C PHE* 3.4 27.6 - + + -
213C LYS 3.0 7.4 + - - +
214C LEU* 3.0 10.2 + - + +
216C ALA* 1.3 75.8 - - - +
218C LEU* 1.3 60.6 + - + +
220C GLU* 3.1 22.1 + - + +
221C GLU* 2.8 35.0 + - + +
601C ZN 2.1 36.2 - - - -
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Residues in contact with LEU 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ASP 3.9 11.6 - - - +
155C HIS* 3.6 19.5 - - + +
156C VAL* 3.3 15.5 - - + +
160C LEU* 4.1 9.6 - - + -
166C TYR* 3.9 29.2 - - + +
200C CYS* 4.7 10.3 - - - -
201C TRP* 3.8 34.1 - - + +
214C LEU* 2.8 38.2 + - + +
215C LYS* 3.2 12.3 + - + +
217C HIS* 1.3 68.7 - - - +
219C GLN* 1.3 60.5 + - - +
221C GLU* 3.3 7.0 + - + +
222C TYR* 2.9 23.6 + - - +
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Residues in contact with GLN 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LYS* 5.2 2.5 + - - +
156C VAL* 3.3 28.5 - - + +
215C LYS 3.2 10.6 + - - +
216C ALA* 3.3 12.6 - - - +
217C HIS 3.2 0.2 - - - -
218C LEU* 1.3 76.5 - - - +
220C GLU* 1.3 64.8 + - + +
222C TYR* 3.1 14.3 + - - -
223C ASP* 3.0 56.9 + - - +
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Residues in contact with GLU 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ALA* 3.2 16.4 + - - +
217C HIS* 3.1 27.2 + - + +
219C GLN* 1.3 78.3 - - + +
221C GLU* 1.3 56.5 + - - +
223C ASP* 3.3 11.1 + - - +
224C ASP* 2.9 39.6 + - - +
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Residues in contact with GLU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C TYR* 5.4 0.4 - - - -
200C CYS* 3.6 6.4 - - - -
201C TRP* 5.6 4.3 - - + +
202C ARG* 2.9 48.2 + - + +
203C CYS* 3.2 14.6 + - - +
217C HIS* 2.8 30.3 + - + +
218C LEU* 3.6 12.3 - - + +
219C GLN 3.3 0.2 - - - -
220C GLU* 1.3 73.5 - - - +
222C TYR* 1.3 57.8 + - - +
224C ASP* 3.4 10.2 + - - +
225C TRP* 2.9 30.0 + - - +
601C ZN 2.0 39.6 - - - -
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Residues in contact with TYR 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C LYS* 3.6 36.1 + - + +
120C LEU* 3.6 44.7 + - + +
132C TYR* 3.6 21.3 - - - -
154C ASP* 3.9 11.7 - - + -
156C VAL* 3.8 12.8 - - + -
218C LEU 2.9 14.1 + - - +
219C GLN* 3.1 11.6 + - - +
221C GLU* 1.3 74.2 - - - +
223C ASP* 1.3 79.1 + - - +
225C TRP* 3.1 19.3 + + - -
226C LEU* 2.8 54.5 + - + +
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Residues in contact with ASP 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C GLN* 3.0 46.5 + - - +
220C GLU* 3.6 11.6 - - - +
222C TYR* 1.3 82.9 - - - +
224C ASP* 1.3 65.9 + - - +
226C LEU* 3.5 6.9 + - - +
227C ASP* 3.0 24.3 + - - +
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Residues in contact with ASP 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ARG* 3.9 11.7 - - - +
220C GLU* 2.9 27.0 + - - +
221C GLU* 3.5 11.3 - - - +
222C TYR 3.1 0.2 - - - -
223C ASP* 1.3 78.7 - - - +
225C TRP* 1.3 63.7 + - - +
227C ASP* 3.3 7.2 + - - +
228C LYS* 3.1 22.9 + - - +
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Residues in contact with TRP 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LEU* 4.0 6.5 - - + -
124C LEU* 3.7 42.6 - - + -
128C ALA* 4.1 12.3 + - + -
129C LEU* 4.7 3.8 - - + -
131C ASN 5.7 0.4 + - - -
132C TYR* 3.3 70.3 - + + +
202C ARG* 3.8 20.8 - - - +
221C GLU 2.9 17.8 + - - +
222C TYR* 3.1 14.3 + + - +
224C ASP* 1.3 75.6 - - - +
226C LEU* 1.3 73.2 + - + +
228C LYS* 3.3 5.3 + - + +
229C SER* 2.7 54.5 + - - -
701C SO4 3.2 27.6 + - - -
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Residues in contact with LEU 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C LEU 5.5 0.7 - - - +
121C SER* 3.9 28.9 - - - -
124C LEU* 4.2 13.7 - - + -
222C TYR* 2.8 46.2 + - + +
223C ASP* 3.7 7.2 - - - +
225C TRP* 1.3 86.4 - - + +
227C ASP* 1.3 62.9 + - - +
229C SER* 3.1 1.1 + - - -
230C VAL* 3.0 44.1 + - + +
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Residues in contact with ASP 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C ASP 3.0 17.7 + - - +
224C ASP* 3.6 6.1 - - - +
225C TRP 3.3 0.2 - - - -
226C LEU* 1.3 77.5 - - - +
228C LYS* 1.3 55.9 + - - +
230C VAL* 3.6 8.7 + - - +
231C SER* 2.6 46.1 + - - -
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Residues in contact with LYS 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B PRO 5.9 1.2 + - - -
83B HIS* 4.7 10.5 - - - -
202C ARG* 4.1 10.2 - - - +
224C ASP 3.1 16.7 + - - +
225C TRP* 3.6 5.8 - - + +
227C ASP* 1.3 76.4 + - - +
229C SER* 1.3 65.0 + - - +
231C SER* 3.5 16.3 + - - -
232C MET 3.8 11.8 + - - +
701C SO4 3.2 26.4 + - - +
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Residues in contact with SER 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C GLN 5.1 2.1 - - - +
124C LEU* 3.7 25.9 - - - +
128C ALA* 4.7 12.4 - - - +
225C TRP* 2.7 48.6 + - - -
226C LEU 3.1 1.8 + - - -
228C LYS* 1.3 80.1 - - - +
230C VAL* 1.3 62.0 + - - +
231C SER 3.3 0.2 - - - -
232C MET* 3.7 16.3 + - - +
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Residues in contact with VAL 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C SER* 4.7 1.1 - - - +
123C GLN* 3.7 44.2 - - + +
124C LEU* 4.1 9.2 - - + -
226C LEU* 3.0 39.3 + - + +
227C ASP* 3.7 12.6 - - - +
229C SER* 1.3 77.4 - - - +
231C SER* 1.3 61.4 + - - +
232C MET* 3.0 12.8 + - - +
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Residues in contact with SER 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C ASP* 2.6 33.7 + - - -
228C LYS* 3.6 11.4 - - - -
229C SER 3.3 0.8 - - - -
230C VAL* 1.3 77.3 - - - +
232C MET* 1.3 73.0 + - - +
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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
------------------------------------------------------------
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