Contacts of the helix formed by residues 188 - 202 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J LEU* 4.9 4.9 - - + -
155J GLU* 4.5 4.0 - - - +
186J ASP* 2.9 17.1 + - - +
187J SER* 1.3 84.3 - - - +
189J GLN* 1.3 65.3 + - - +
190J ASP 3.4 1.8 - - - -
191J ILE* 3.8 22.7 - - + -
192J ARG* 3.1 26.6 + - + +
219J ASN* 3.8 22.9 - - - +
251J LYS* 6.1 0.4 - - - -
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Residues in contact with GLN 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I HIS* 3.2 17.1 + - - +
32I THR* 2.7 32.4 + - - +
80I PHE* 3.4 54.3 - - + -
84I THR* 5.1 1.7 - - - +
183J PRO* 4.2 9.2 - - + -
186J ASP* 4.2 4.6 + - - +
187J SER 3.9 1.2 - - - -
188J ALA* 1.3 76.7 - - - +
190J ASP* 1.3 63.1 + - - +
192J ARG* 2.9 14.1 - - - +
193J SER* 2.8 42.5 + - - -
209J HIS* 2.7 22.5 + - - -
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Residues in contact with ASP 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I PHE 4.5 4.7 - - - +
80I PHE* 3.8 10.0 - - - +
81I ALA* 2.8 46.9 + - + +
82I ASP* 3.8 10.8 - - - +
188J ALA 3.4 0.4 - - - -
189J GLN* 1.3 81.8 - - - +
191J ILE* 1.3 63.3 + - + +
193J SER* 3.6 2.5 + - - -
194J GLU* 3.1 25.8 + - - +
249J PHE* 4.5 9.1 - - + -
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Residues in contact with ILE 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J LEU* 4.4 17.3 - - + -
187J SER 3.7 18.4 - - - +
188J ALA* 3.7 23.1 - - + +
189J GLN 3.1 0.2 - - - -
190J ASP* 1.3 73.5 - - + +
192J ARG* 1.3 67.1 + - - +
194J GLU* 2.9 15.2 + - - +
195J MET* 3.1 20.9 + - + +
245J VAL* 4.5 10.3 - - + -
246J ALA* 5.1 3.8 - - - -
249J PHE* 3.8 41.3 - - + -
251J LYS* 4.1 28.7 - - + -
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Residues in contact with ARG 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I HIS* 3.7 4.9 + - - -
32I THR* 4.4 0.4 + - - -
134J LEU* 5.6 1.8 - - + -
186J ASP* 3.0 36.6 + - - -
188J ALA* 3.1 20.5 + - + +
189J GLN* 2.9 31.8 - - - +
191J ILE* 1.3 77.8 - - + +
193J SER* 1.3 65.7 + - - +
195J MET* 3.0 21.2 + - - +
196J CYS* 2.8 23.9 + - - -
209J HIS* 2.7 36.0 + - + +
210J HIS* 3.5 22.3 - - - +
211J HIS 3.6 10.6 - - - +
219J ASN* 3.0 42.3 - - + +
220J GLU 4.2 5.8 - - - -
221J VAL* 4.8 3.6 - - + -
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Residues in contact with SER 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I PHE* 3.6 24.5 - - - -
32I THR* 5.1 0.2 - - - +
82I ASP* 3.4 23.2 + - - -
84I THR* 5.6 2.1 - - - +
189J GLN* 2.8 24.9 + - - -
190J ASP* 3.8 1.3 - - - -
192J ARG* 1.3 76.3 - - - +
194J GLU* 1.3 57.3 + - - +
196J CYS* 3.3 3.4 + - - +
197J LEU* 2.9 34.3 + - - +
209J HIS* 3.0 23.8 + - - -
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Residues in contact with GLU 194 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I ASP* 4.4 5.3 + - - +
190J ASP 3.1 11.0 + - - +
191J ILE 2.9 11.2 + - - +
193J SER* 1.3 69.9 - - - +
195J MET* 1.3 69.4 + - - +
196J CYS 2.9 2.0 + - - -
197J LEU* 2.9 26.3 + - + +
198J VAL* 2.8 41.9 + - - +
201J GLN* 5.7 0.7 + - - -
245J VAL* 4.0 12.4 - - + +
248J ARG* 3.3 24.8 + - - -
249J PHE* 3.7 22.4 - - + -
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Residues in contact with MET 195 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J PHE* 4.0 26.2 - - + -
134J LEU* 4.5 9.0 - - + -
191J ILE* 3.2 17.7 - - + +
192J ARG* 3.3 18.6 - - - +
194J GLU* 1.3 74.1 - - - +
196J CYS* 1.3 57.6 + - - +
199J MET* 2.8 46.5 + - + +
221J VAL* 4.8 6.3 - - + -
241J VAL* 3.6 16.6 - - + +
242J VAL* 3.3 46.0 - - + +
245J VAL* 3.6 13.6 - - + +
246J ALA* 4.0 17.9 - - + +
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Residues in contact with CYS 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16I PHE* 4.0 17.0 - - + -
192J ARG 2.8 17.4 + - - -
193J SER 3.3 8.3 - - - +
194J GLU 2.9 0.4 + - - -
195J MET* 1.3 74.1 - - - +
197J LEU* 1.3 67.2 + - - +
199J MET* 3.0 6.2 + - - +
200J GLU* 3.0 26.0 + - + +
206J VAL* 3.6 36.6 - - + -
209J HIS* 3.6 32.1 - - - -
221J VAL* 3.9 10.1 - - - -
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Residues in contact with LEU 197 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I LYS* 4.7 18.4 - - + -
16I PHE* 3.7 23.8 - - + -
82I ASP* 3.3 27.6 - - + +
193J SER 2.9 21.7 + - - +
194J GLU* 2.9 24.4 + - - +
196J CYS* 1.3 71.6 - - - +
198J VAL* 1.3 58.1 + - - +
200J GLU* 3.2 8.9 + - - +
201J GLN* 3.0 42.3 + - - +
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Residues in contact with VAL 198 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J PRO* 3.8 29.4 - - + -
79J PHE* 4.2 6.7 - - + -
194J GLU* 2.8 42.1 + - - +
195J MET 3.7 2.9 - - - +
197J LEU* 1.3 68.4 - - + +
199J MET* 1.3 66.4 + - - +
201J GLN* 2.9 31.5 + - - +
202J MET* 2.9 12.6 + - + +
241J VAL* 3.6 27.8 - - + -
245J VAL* 4.2 9.0 - - + -
248J ARG* 5.5 1.3 - - - +
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Residues in contact with MET 199 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195J MET* 2.8 33.2 + - + +
196J CYS* 3.5 4.0 - - - +
198J VAL* 1.3 72.0 - - - +
200J GLU* 1.3 61.5 + - - +
202J MET* 3.1 12.3 + - - +
204J LEU* 3.0 41.2 + - + +
206J VAL* 4.3 4.7 - - + -
221J VAL* 3.9 21.1 - - + -
223J THR* 4.5 6.1 - - - -
237J ILE* 5.6 0.2 - - + -
238J TYR* 3.2 54.1 - - + +
241J VAL* 3.7 24.2 - - + -
242J VAL* 3.6 22.7 - - + -
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Residues in contact with GLU 200 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I PRO* 5.3 2.9 - - - +
36I HIS* 2.9 36.6 + - - -
196J CYS* 3.0 12.3 + - - +
197J LEU* 3.5 8.6 - - - +
199J MET* 1.3 69.9 - - - +
201J GLN* 1.3 59.4 + - + +
202J MET 3.0 4.5 - - - -
203J GLY* 2.9 20.6 + - - -
204J LEU 3.2 15.9 - - - +
205J VAL* 3.9 3.1 - - - +
206J VAL* 2.9 42.2 + - + +
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Residues in contact with GLN 201 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75J VAL* 3.9 12.3 - - - +
78J PRO* 4.4 16.2 - - + +
194J GLU* 5.7 0.8 + - - -
197J LEU* 3.0 38.2 + - - +
198J VAL* 2.9 22.8 + - - +
200J GLU* 1.3 74.9 - - + +
202J MET* 1.3 60.6 + - + +
203J GLY 3.2 2.6 + - - -
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Residues in contact with MET 202 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J ARG* 5.2 0.7 - - - +
75J VAL* 4.1 24.6 - - + +
76J ILE 4.1 15.9 - - - +
78J PRO* 3.8 26.2 - - + -
86J ILE* 3.8 28.9 - - + -
198J VAL* 2.9 11.8 + - + +
199J MET 3.4 12.1 - - - +
200J GLU 3.0 0.8 - - - -
201J GLN* 1.3 81.6 - - + +
203J GLY* 1.3 55.2 + - - -
204J LEU* 3.5 10.6 + - - +
237J ILE* 4.0 32.6 - - + +
240J TYR* 4.4 12.8 - - + -
241J 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