Contacts of the helix formed by residues 213 - 230 (chain C) in PDB entry 1SHZ
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 GLU 213 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL* 5.0 11.7 - - + +
211C ASP* 2.7 11.9 + - - +
212C GLU* 1.3 81.9 - - - +
214C LYS* 1.3 64.7 + - - +
215C SER 3.0 2.7 - - - -
216C ALA* 2.9 35.5 + - - +
217C ALA* 3.2 11.8 + - - +
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Residues in contact with LYS 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C GLU* 4.1 28.0 + - - +
72C PRO* 5.3 6.3 - - + -
109C VAL* 4.1 27.6 - - + +
110C LEU* 4.6 11.2 - - + -
208C ILE* 5.0 7.0 - - + -
209C SER* 3.1 38.3 + - - -
211C ASP* 3.3 28.3 + - + +
213C GLU* 1.3 78.4 - - - +
215C SER* 1.3 59.2 + - - +
217C ALA* 3.4 2.8 + - - +
218C VAL* 3.0 34.3 + - + +
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Residues in contact with SER 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C GLN* 3.3 28.0 + - - -
208C ILE* 3.9 27.5 - - - +
209C SER 5.6 0.4 - - - -
211C ASP 3.8 8.1 + - - -
212C GLU* 3.4 19.9 + - - -
214C LYS* 1.3 78.2 - - - +
216C ALA* 1.3 66.3 + - - +
218C VAL* 3.5 1.1 + - - +
219C VAL* 3.0 32.5 + - - +
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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 GLU 4.7 2.0 - - - +
213C GLU* 2.9 33.0 + - - +
215C SER* 1.3 80.3 + - - +
217C ALA* 1.3 63.5 + - - +
219C VAL* 4.1 4.1 - - - +
220C ASN* 2.7 41.5 + - - +
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Residues in contact with ALA 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C VAL* 4.0 28.9 - - + -
110C LEU* 4.0 17.9 - - + +
213C GLU* 3.2 7.7 + - - +
214C LYS 3.6 9.2 - - - +
215C SER 3.2 0.2 - - - -
216C ALA* 1.3 79.8 - - - +
218C VAL* 1.3 52.6 + - - +
220C ASN* 3.3 7.3 + - - +
221C ALA* 2.7 37.2 + - - +
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Residues in contact with VAL 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ALA* 4.2 18.6 - - + -
72C PRO* 3.7 25.8 - - + -
76C LEU* 4.0 17.7 - - + -
110C LEU* 4.0 8.5 - - + -
201C LEU* 6.1 0.9 - - + -
208C ILE* 4.7 13.9 - - + -
214C LYS* 3.0 21.7 + - + +
215C SER* 3.8 6.5 - - - +
216C ALA 3.3 0.2 - - - -
217C ALA* 1.3 72.3 - - - +
219C VAL* 1.3 68.4 + - + +
221C ALA* 2.9 2.6 + - - +
222C ILE* 2.7 49.6 + - + +
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Residues in contact with VAL 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C LEU* 5.1 7.0 - - + +
201C LEU* 5.2 8.7 - - + +
202C GLU* 3.7 44.4 - - + +
205C GLN* 4.9 13.2 - - + -
208C ILE* 4.9 11.2 - - + -
215C SER 3.0 19.0 + - - +
216C ALA* 4.2 4.5 - - - +
218C VAL* 1.3 77.0 - - + +
220C ASN* 1.3 54.6 + - - +
222C ILE* 3.6 8.5 + - - +
223C GLY* 2.7 31.9 + - - -
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Residues in contact with ASN 220 (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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216C ALA* 2.7 34.4 + - - +
217C ALA* 3.4 6.4 - - - +
218C VAL 3.0 0.6 - - - -
219C VAL* 1.3 75.8 - - - +
221C ALA* 1.3 60.2 + - - +
223C GLY* 3.1 2.1 + - - -
224C LEU* 2.8 31.4 + - - +
227C ARG* 4.4 7.2 + - - +
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Residues in contact with ALA 221 (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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76C LEU* 4.0 26.0 - - + -
80C HIS* 2.8 43.7 + - + +
110C LEU* 4.1 9.9 - - + -
217C ALA 2.7 20.6 + - - +
218C VAL 3.4 3.6 - - - +
220C ASN* 1.3 71.3 - - - +
222C ILE* 1.3 66.1 + - - +
224C LEU* 3.2 0.8 + - - -
225C TYR* 3.2 12.0 + - - +
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Residues in contact with ILE 222 (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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60C MET* 4.2 18.2 - - + -
63C LEU* 3.5 42.8 - - + +
67C ALA* 4.8 2.5 - - + -
76C LEU* 3.6 11.4 - - + -
198C LEU* 4.2 10.5 - - + -
201C LEU* 4.8 15.5 - - + -
218C VAL* 2.7 42.3 + - + +
219C VAL* 3.8 7.0 - - - +
221C ALA* 1.3 70.9 - - - +
223C GLY* 1.3 64.3 + - - +
225C TYR* 3.2 6.2 + - - +
226C MET* 3.0 39.6 + - + +
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Residues in contact with GLY 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C LEU* 5.0 7.6 - - - -
219C VAL 2.7 23.0 + - - -
220C ASN* 3.1 2.9 + - - -
222C ILE* 1.3 77.2 - - - +
224C LEU* 1.3 61.8 + - - +
226C MET* 3.2 6.8 + - - +
227C ARG* 3.0 40.5 + - - +
233C THR* 4.7 5.7 + - - -
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Residues in contact with LEU 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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80C HIS* 3.9 22.4 - - + +
83C MET* 4.3 26.6 - - + +
98C ASP* 6.3 3.4 - - + -
220C ASN 2.8 15.0 + - - +
221C ALA 3.2 7.4 + - - +
223C GLY* 1.3 71.3 - - - +
225C TYR* 1.3 63.2 + - - +
227C ARG* 3.2 34.4 + - + +
228C HIS* 3.3 9.7 + - - +
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Residues in contact with TYR 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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53C LYS* 2.7 37.6 + - - +
59C LEU* 3.4 33.2 - - + -
76C LEU* 6.4 0.9 - - + -
79C LEU* 3.6 47.0 - - + +
80C HIS* 4.2 10.5 - - + -
82C ASP* 5.7 0.3 + - - -
83C MET* 4.6 14.6 - - + -
221C ALA 3.2 10.1 + - - +
222C ILE* 3.8 7.4 - - - +
224C LEU* 1.3 78.0 - - - +
226C MET* 1.3 67.5 + - + +
228C HIS* 2.8 47.1 + + + +
229C LEU* 3.4 18.0 + - + +
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Residues in contact with MET 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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56C PRO* 4.2 8.3 - - - +
59C LEU* 3.6 25.6 - - + -
60C MET* 3.9 27.4 - - - +
63C LEU* 5.9 1.1 - - + -
194C ALA* 4.7 1.3 - - - -
198C LEU* 4.2 15.5 - - + -
222C ILE* 3.0 33.0 + - + +
223C GLY 3.5 4.9 - - - +
225C TYR* 1.3 83.8 - - + +
227C ARG* 1.3 58.6 + - - +
229C LEU* 2.9 43.8 + - + +
230C GLY 3.0 10.0 + - - -
231C VAL* 3.2 37.0 + - + +
233C THR* 5.6 0.2 - - - +
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Residues in contact with ARG 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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220C ASN* 4.4 7.7 + - - +
223C GLY* 3.0 19.0 + - - +
224C LEU* 3.4 40.8 - - + +
225C TYR 3.1 0.2 - - - -
226C MET* 1.3 76.6 - - - +
228C HIS* 1.3 61.8 + - - +
229C LEU 3.3 0.5 + - - -
230C GLY* 3.5 9.4 + - - -
231C VAL 3.7 21.1 - - - +
233C THR* 3.1 44.4 + - - +
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Residues in contact with HIS 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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83C MET* 3.8 42.3 + - + -
224C LEU 3.3 6.2 + - - +
225C TYR* 2.8 32.9 + + + +
227C ARG* 1.3 77.6 - - - +
229C LEU* 1.3 67.5 + - + +
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Residues in contact with LEU 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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53C LYS 4.0 17.9 - - - +
54C ARG* 4.0 15.9 - - + +
56C PRO* 3.8 31.2 - - + -
59C LEU* 4.8 1.3 - - + -
191C ARG* 4.7 7.2 - - - +
225C TYR* 4.0 22.9 - - + +
226C MET* 2.9 37.8 + - + +
227C ARG 4.2 0.2 - - - -
228C HIS* 1.3 90.2 - - + +
230C GLY* 1.3 56.5 + - - +
231C VAL* 4.8 1.8 - - + -
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Residues in contact with GLY 230 (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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191C ARG* 4.0 23.3 + - - +
226C MET 3.0 1.0 + - - -
227C ARG 3.5 8.4 + - - -
229C LEU* 1.3 81.0 - - - +
231C VAL* 1.3 65.9 + - - +
232C ARG* 3.5 15.9 + - - +
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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
------------------------------------------------------------
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