Contacts of the helix formed by residues 188 - 202 (chain F) in PDB entry 1FPY
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 ALA 188 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F LEU* 4.9 4.7 - - + -
155F GLU* 4.5 4.3 - - - +
186F ASP* 2.9 16.3 + - - +
187F SER* 1.3 84.7 - - - +
189F GLN* 1.3 65.7 + - - +
190F ASP 3.4 1.8 - - - -
191F ILE* 3.8 22.7 - - + -
192F ARG* 3.1 26.8 + - + +
219F ASN* 3.8 22.7 - - - +
251F LYS* 6.1 0.4 - - - -
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Residues in contact with GLN 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A HIS* 3.3 17.7 + - - +
32A THR* 2.5 35.0 + - - +
80A PHE* 3.5 51.1 - - + -
84A THR* 5.1 2.4 - - - +
183F PRO* 4.2 9.0 - - + -
186F ASP* 4.2 4.0 + - - +
187F SER 3.9 1.4 - - - -
188F ALA* 1.3 76.7 - - - +
190F ASP* 1.3 62.1 + - - +
192F ARG* 2.9 15.1 - - - +
193F SER* 2.8 42.5 + - - -
209F HIS* 2.7 21.2 - - - -
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Residues in contact with ASP 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE 4.6 3.5 - - - +
80A PHE* 3.9 11.0 - - - +
81A ALA* 2.9 46.8 + - + +
82A ASP* 3.7 12.4 - - - +
188F ALA 3.4 0.4 - - - -
189F GLN* 1.3 82.6 - - - +
191F ILE* 1.3 63.5 + - + +
193F SER* 3.6 2.6 + - - -
194F GLU* 3.1 25.8 + - - +
249F PHE* 4.5 9.5 - - + -
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Residues in contact with ILE 191 (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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134F LEU* 4.4 17.0 - - + -
187F SER 3.7 19.1 - - - +
188F ALA* 3.7 22.2 - - + +
190F ASP* 1.3 73.4 - - + +
192F ARG* 1.3 68.4 + - - +
194F GLU* 2.9 14.6 + - - +
195F MET* 3.1 21.8 + - + +
245F VAL* 4.5 10.1 - - + -
246F ALA* 5.1 3.6 - - - -
249F PHE* 3.8 41.3 - - + -
251F LYS* 4.1 28.3 - - + -
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Residues in contact with ARG 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A HIS* 3.8 4.6 + - - -
32A THR* 4.4 0.6 + - - +
134F LEU* 5.6 1.6 - - + -
186F ASP* 3.0 35.0 + - - -
188F ALA* 3.1 21.5 + - + +
189F GLN* 2.9 32.2 - - - +
191F ILE* 1.3 78.3 - - + +
193F SER* 1.3 64.4 + - - +
195F MET* 3.0 20.8 + - - +
196F CYS* 2.8 24.3 + - - -
209F HIS* 2.7 38.6 + - + +
210F HIS* 3.5 22.8 - - - +
211F HIS 3.6 10.0 - - - +
219F ASN* 3.0 41.7 - - + +
220F GLU 4.2 5.6 - - - -
221F VAL* 4.8 4.5 - - + -
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Residues in contact with SER 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.6 27.8 - - - -
82A ASP* 3.5 23.1 + - - -
189F GLN* 2.8 25.2 + - - -
190F ASP* 3.8 1.6 - - - -
192F ARG* 1.3 75.8 - - - +
194F GLU* 1.3 57.2 + - - +
196F CYS* 3.3 3.0 + - - +
197F LEU* 2.9 33.7 + - - +
209F HIS* 3.0 22.5 + - - -
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Residues in contact with GLU 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASP* 4.5 5.7 + - - +
190F ASP 3.1 10.4 + - - +
191F ILE 2.9 10.9 + - - +
193F SER* 1.3 70.7 - - - +
195F MET* 1.3 68.7 + - - +
196F CYS 2.9 1.8 + - - -
197F LEU* 2.9 27.6 + - + +
198F VAL* 2.8 43.9 + - - +
201F GLN* 5.7 0.7 + - - -
245F VAL* 4.0 12.2 - - + +
248F ARG* 3.3 24.6 + - - -
249F PHE* 3.7 23.3 - - + -
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Residues in contact with MET 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F PHE* 4.0 26.7 - - + -
134F LEU* 4.5 9.2 - - + -
191F ILE* 3.2 17.0 - - + +
192F ARG* 3.0 18.1 + - - +
194F GLU* 1.3 74.3 - - - +
196F CYS* 1.3 56.6 + - - +
199F MET* 2.8 48.0 + - + +
221F VAL* 4.8 6.5 - - + -
241F VAL* 3.6 16.2 - - + +
242F VAL* 3.3 45.8 - - + +
245F VAL* 3.6 13.4 - - + +
246F ALA* 4.0 17.9 - - + +
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Residues in contact with CYS 196 (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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16A PHE* 4.1 14.6 - - + -
34A PRO* 6.0 0.4 - - + -
192F ARG 2.8 16.3 + - - -
193F SER 3.3 9.0 - - - +
194F GLU 2.9 0.6 + - - -
195F MET* 1.3 73.4 - - - +
197F LEU* 1.3 67.6 + - - +
199F MET* 3.0 5.7 + - - +
200F GLU* 3.0 26.4 + - - +
206F VAL* 3.6 37.0 - - + -
209F HIS* 3.6 32.3 - - - -
221F VAL* 3.9 10.1 - - - -
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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
----------------------------------------------------------
15A LYS* 4.8 17.5 - - + -
16A PHE* 3.7 23.6 - - + -
82A ASP* 3.5 26.9 - - + +
193F SER 2.9 23.2 + - - +
194F GLU* 2.9 24.2 + - - +
196F CYS* 1.3 72.4 - - - +
198F VAL* 1.3 58.6 + - + +
200F GLU* 3.2 9.0 + - - +
201F GLN* 3.0 43.0 + - - +
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Residues in contact with VAL 198 (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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78F PRO* 3.8 29.2 - - + -
79F PHE* 4.2 6.7 - - + -
194F GLU* 2.8 43.4 + - - +
195F MET 3.7 2.9 - - - +
197F LEU* 1.3 69.0 - - - +
199F MET* 1.3 67.4 + - - +
201F GLN* 2.9 31.5 + - - +
202F MET* 2.9 12.3 + - + +
241F VAL* 3.6 28.0 - - + -
245F VAL* 4.2 8.3 - - + -
248F ARG* 5.5 1.3 - - - +
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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
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195F MET* 2.8 34.0 + - + +
196F CYS* 3.5 4.7 - - - +
198F VAL* 1.3 71.8 - - - +
200F GLU* 1.3 61.0 + - - +
202F MET* 3.1 11.9 + - - +
204F LEU* 3.0 39.4 + - + +
206F VAL* 4.3 4.7 - - + -
221F VAL* 3.9 21.3 - - + -
223F THR* 4.5 5.8 - - - -
237F ILE* 5.6 0.2 - - + -
238F TYR* 3.2 53.2 - - + +
241F VAL* 3.7 24.2 - - + -
242F VAL* 3.6 22.7 - - + -
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Residues in contact with GLU 200 (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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34A PRO* 5.4 2.5 - - - +
36A HIS* 2.9 36.9 + - - -
196F CYS 3.0 12.9 + - - +
197F LEU* 3.5 10.0 - - - +
199F MET* 1.3 69.9 - - - +
201F GLN* 1.3 58.7 + - - +
202F MET 3.0 4.5 - - - -
203F GLY* 2.9 20.8 + - - -
204F LEU 3.2 15.1 - - - +
205F VAL* 3.9 3.4 - - - +
206F VAL* 2.9 42.2 + - + +
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Residues in contact with GLN 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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75F VAL* 3.9 11.6 - - - +
78F PRO* 4.4 16.7 - - + +
194F GLU* 5.7 0.8 + - - -
197F LEU* 3.0 37.6 + - - +
198F VAL* 2.9 20.7 + - - +
200F GLU* 1.3 75.8 - - + +
202F MET* 1.3 60.6 + - + +
203F GLY 3.2 2.8 + - - -
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Residues in contact with MET 202 (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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20F ARG* 5.2 0.7 - - - +
75F VAL* 4.1 25.7 - - + +
76F ILE 4.1 15.7 - - - +
78F PRO* 3.8 26.5 - - + -
86F ILE* 3.8 28.9 - - + -
198F VAL* 2.9 12.1 + - - +
199F MET 3.4 11.2 - - - +
200F GLU 3.0 0.8 - - - -
201F GLN* 1.3 80.0 - - + +
203F GLY* 1.3 55.9 + - - +
204F LEU* 3.5 11.1 + - - +
237F ILE* 4.0 31.8 - - + +
240F TYR* 4.5 12.3 - - + -
241F VAL* 3.5 27.6 - - - -
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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
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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