Contacts of the helix formed by residues 185 - 203 (chain F) 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 SER 185 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178F TRP* 3.7 29.0 - - - -
186F TYR* 1.3 66.8 + - - +
187F GLU* 3.3 6.5 - - - +
188F ALA* 3.1 25.9 - - - +
189F ARG* 4.0 1.9 + - - +
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Residues in contact with TYR 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ARG* 5.4 1.3 - - - -
58F HIS* 4.7 10.2 + - - -
175F LEU* 3.4 48.9 + - + +
176F GLU* 4.3 6.1 - - - +
177F ALA 5.4 0.7 - - - -
178F TRP* 4.2 33.8 - + + -
185F SER* 1.3 75.4 - - - +
187F GLU* 1.3 60.1 + - + +
188F ALA 3.0 6.2 + - - -
189F ARG* 3.1 6.7 + - + +
190F GLU* 2.9 58.8 + - + +
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Residues in contact with GLU 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ARG* 5.3 5.2 - - - +
185F SER 3.3 3.7 - - - +
186F TYR* 1.3 77.2 - - + +
188F ALA* 1.3 64.4 + - - +
190F GLU* 3.8 24.0 - - - +
191F ARG* 3.0 59.4 + - + +
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Residues in contact with ALA 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F SER* 3.1 22.4 + - - +
186F TYR 3.0 0.4 - - - -
187F GLU* 1.3 79.8 - - - +
189F ARG* 1.3 57.9 + - - +
191F ARG* 3.5 14.1 + - - +
192F HIS* 3.2 23.6 + - - +
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Residues in contact with ARG 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174F GLN* 5.9 1.8 + - - +
175F LEU* 3.5 27.3 - - + +
178F TRP* 2.8 58.1 - - + +
185F SER 4.0 1.5 + - - +
186F TYR* 3.1 7.6 + - + +
188F ALA* 1.3 78.8 - - + +
190F GLU* 1.3 56.9 + - - +
191F ARG 3.1 1.6 - - - -
192F HIS* 2.7 16.6 + - + +
193F VAL* 2.6 48.2 + - + +
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Residues in contact with GLU 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ARG* 2.7 47.9 + - + +
56F PRO* 3.3 33.2 - - + +
57F ALA* 3.8 11.1 - - + +
58F HIS* 4.7 4.3 - - + -
175F LEU* 3.7 16.5 - - + +
186F TYR* 2.9 43.3 + - + +
187F GLU* 3.8 21.1 - - - +
189F ARG* 1.3 78.9 - - - +
191F ARG* 1.3 60.3 + - - +
193F VAL 3.9 0.2 + - - -
194F ALA* 3.5 13.5 + - - +
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Residues in contact with ARG 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F PRO* 3.9 20.2 - - + -
187F GLU* 3.0 64.9 + - + +
188F ALA* 3.5 10.6 + - - +
190F GLU* 1.3 75.9 - - + +
192F HIS* 1.3 66.5 + - - +
194F ALA* 3.5 5.0 - - - +
195F GLU* 3.5 18.6 + - - +
229F LEU 3.4 26.5 - - - +
230F GLY* 4.6 12.6 + - - +
231F VAL* 4.1 12.2 - - + +
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Residues in contact with HIS 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F ALA 3.2 18.6 + - - +
189F ARG* 2.7 20.3 + - - +
191F ARG* 1.3 74.8 - - - +
193F VAL* 1.3 66.4 + - - +
194F ALA 3.1 1.6 - - - -
195F GLU* 2.9 47.0 - - + +
196F ARG* 3.4 8.1 + - + +
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Residues in contact with VAL 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F ALA* 4.4 4.0 - - + -
171F GLU* 4.3 24.7 - - + +
172F LEU* 5.8 0.7 - - - -
175F LEU* 3.6 31.9 - - + -
189F ARG* 2.6 37.8 + - + +
190F GLU 4.3 1.1 - - - +
192F HIS* 1.3 75.3 - - + +
194F ALA* 1.3 60.9 + - - +
196F ARG* 3.3 12.5 + - - +
197F LEU* 3.0 38.9 + - + +
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Residues in contact with ALA 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F PRO* 3.5 32.3 - - + -
57F ALA* 4.2 8.2 - - - +
60F MET* 3.9 5.4 - - - +
190F GLU 3.5 17.5 + - - +
191F ARG 3.5 7.4 - - - +
193F VAL* 1.3 79.5 - - - +
195F GLU* 1.3 51.9 + - - +
197F LEU* 3.0 4.4 + - - +
198F LEU* 2.7 36.3 + - - +
226F MET* 3.8 3.8 - - + -
231F VAL* 3.7 11.7 - - + -
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Residues in contact with GLU 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191F ARG 3.5 5.0 + - - +
192F HIS* 2.9 46.4 + - + +
194F ALA* 1.3 78.8 - - - +
196F ARG* 1.3 61.2 - - + +
198F LEU* 3.9 4.4 - - - +
199F MET* 3.0 48.7 + - + +
231F VAL* 3.6 16.7 - - + +
232F ARG 3.6 26.7 - - - +
233F THR* 5.1 1.8 + - - +
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Residues in contact with ARG 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F TRP* 5.1 2.4 - - - -
171F GLU* 3.1 45.8 + - - +
192F HIS* 3.4 11.0 + - + +
193F VAL* 3.3 15.2 + - - +
194F ALA 3.1 0.4 - - - -
195F GLU* 1.3 82.9 - - + +
197F LEU* 1.3 69.1 + - - +
199F MET* 3.2 19.6 + - - +
200F HIS* 3.0 49.0 + - + -
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Residues in contact with LEU 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F ALA* 3.9 25.6 - - + +
60F MET* 3.9 13.9 - - + +
61F ALA* 4.9 0.7 - - - +
168F TRP* 3.7 56.6 + - + +
171F GLU* 4.3 21.3 - - + -
172F LEU* 5.3 5.6 - - + +
193F VAL* 3.0 29.5 + - + +
194F ALA 3.5 4.7 - - - +
196F ARG* 1.3 85.5 - - - +
198F LEU* 1.3 62.1 + - - +
200F HIS* 3.0 19.7 + - + +
201F LEU* 3.1 12.1 + - - +
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Residues in contact with LEU 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F MET* 3.5 28.6 - - + +
194F ALA 2.7 21.2 + - - +
195F GLU* 3.9 6.3 - - - +
197F LEU* 1.3 73.1 - - - +
199F MET* 1.3 61.2 + - - +
201F LEU* 3.6 7.4 - - + +
202F GLU* 3.3 27.1 + - + +
219F VAL* 5.8 2.9 - - + +
222F ILE* 4.1 20.2 - - + +
223F GLY* 5.2 7.0 - - - +
226F MET* 3.8 26.9 - - + -
231F VAL* 3.8 18.8 - - + +
233F THR* 3.8 20.6 - - - +
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Residues in contact with MET 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F GLU* 3.0 49.6 + - + +
196F ARG* 3.5 11.7 - - - +
197F LEU 3.1 1.0 - - - -
198F LEU* 1.3 72.7 - - - +
200F HIS* 1.3 60.3 - - - +
201F LEU 2.9 4.9 - - - -
202F GLU* 2.9 7.5 + - - +
203F GLU* 2.7 49.6 + - - +
233F THR* 3.5 39.3 - - + +
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Residues in contact with HIS 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F GLN* 5.7 0.2 - - - +
168F TRP* 3.4 40.8 - + + -
196F ARG* 3.0 57.7 + - + +
197F LEU* 3.0 12.0 + - - +
199F MET* 1.3 78.1 - - - +
201F LEU* 1.3 57.9 + - - +
203F GLU* 4.3 6.8 - - - +
204F MET* 3.2 33.6 + - - +
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Residues in contact with LEU 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F MET* 3.2 26.2 - - + -
63F LEU* 4.8 1.3 - - + -
64F GLN* 4.2 40.2 - - + +
67F ALA* 5.8 6.5 - - + -
168F TRP* 5.5 0.2 - - - -
197F LEU 3.1 9.9 + - - +
198F LEU* 3.6 15.0 - - + +
199F MET 2.9 0.6 - - - -
200F HIS* 1.3 77.9 - - - +
202F GLU* 1.3 67.3 + - + +
204F MET* 3.6 4.2 + - - +
205F GLN* 3.3 17.2 + - - -
208F ILE* 4.6 17.9 - - + +
219F VAL* 4.9 8.5 - - + -
222F ILE* 4.3 27.6 - - + -
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Residues in contact with GLU 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F LEU* 3.3 22.7 - - + +
199F MET* 2.9 6.1 + - - +
201F LEU* 1.3 75.7 - - + +
203F GLU* 1.3 69.3 + - - +
204F MET 2.8 11.4 + - - -
205F GLN* 2.8 40.6 + - - +
206F HIS* 5.4 0.7 - - - -
219F VAL* 3.8 26.1 - - + +
233F THR* 3.1 38.6 + - - +
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Residues in contact with GLU 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199F MET* 2.7 48.4 + - - +
200F HIS* 4.0 8.4 + - - +
202F GLU* 1.3 86.0 - - - +
204F MET* 1.3 77.5 + - + +
205F GLN* 3.6 0.4 - - - -
206F HIS* 4.9 9.3 - - - -
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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