Contacts of the helix formed by residues 188 - 202 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU* 4.9 4.9 - - + -
155B GLU* 4.5 4.0 - - - +
186B ASP* 2.9 16.8 + - - +
187B SER* 1.3 84.7 - - - +
189B GLN* 1.3 65.5 + - - +
190B ASP 3.4 1.8 - - - -
191B ILE* 3.8 22.4 - - + -
192B ARG* 3.1 25.8 + - + +
219B ASN* 3.8 22.7 - - - +
251B LYS* 6.1 0.4 - - - -
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Residues in contact with GLN 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B PRO* 4.2 9.0 - - + -
186B ASP* 4.2 4.2 + - - +
187B SER 3.9 1.0 - - - -
188B ALA* 1.3 77.3 - - - +
190B ASP* 1.3 62.3 - - - +
192B ARG* 2.9 14.8 - - - +
193B SER* 2.8 42.4 + - - -
209B HIS* 2.7 21.8 + - - -
30C HIS* 3.3 17.2 + - - +
32C THR* 2.7 31.6 + - - +
80C PHE* 3.3 56.0 - - + +
84C THR* 5.0 1.7 - - - +
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Residues in contact with ASP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ALA 3.4 0.2 - - - -
189B GLN* 1.3 82.8 - - - +
191B ILE* 1.3 63.4 + - + +
193B SER* 3.6 2.3 + - - -
194B GLU* 3.1 25.6 + - - +
249B PHE* 4.5 9.9 - - + -
79C PHE 4.4 6.2 - - - +
80C PHE* 3.7 9.9 - - - +
81C ALA* 2.7 48.0 + - + +
82C ASP* 3.9 10.2 - - - +
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Residues in contact with ILE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU* 4.4 16.2 - - + -
187B SER 3.7 19.1 - - - +
188B ALA* 3.7 22.7 - - + +
189B GLN 3.1 0.2 - - - -
190B ASP* 1.3 73.6 - - + +
192B ARG* 1.3 67.4 + - - +
194B GLU* 2.9 14.6 + - - +
195B MET* 3.1 21.2 + - + +
245B VAL* 4.5 9.9 - - + -
246B ALA* 5.1 3.8 - - - -
249B PHE* 3.8 40.8 - - + -
251B LYS* 4.1 28.3 - - + -
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Residues in contact with ARG 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 5.6 1.1 - - + -
186B ASP* 3.0 35.0 + - - -
188B ALA* 3.1 21.3 + - + +
189B GLN* 2.9 32.4 - - - +
191B ILE* 1.3 77.9 - - + +
193B SER* 1.3 65.2 + - - +
195B MET* 3.0 20.5 + - - +
196B CYS* 2.8 24.3 + - - -
209B HIS* 2.7 38.0 + - + +
210B HIS* 3.5 22.3 - - - +
211B HIS 3.6 10.0 - - - +
219B ASN* 3.0 43.6 - - + +
220B GLU 4.2 5.4 - - - -
221B VAL* 4.8 4.9 - - + +
30C HIS* 3.7 5.3 + - - -
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B GLN* 2.8 25.5 + - - -
190B ASP* 3.8 0.9 - - - -
192B ARG* 1.3 76.3 - - - +
194B GLU* 1.3 56.7 + - - +
196B CYS* 3.3 2.9 + - - +
197B LEU* 2.9 34.2 + - - +
209B HIS* 3.0 22.2 + - - -
16C PHE* 3.6 25.5 - - - -
82C ASP* 3.2 25.0 + - - +
84C THR* 5.5 1.9 - - - +
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Residues in contact with GLU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ASP 3.1 10.8 + - - +
191B ILE 2.9 10.7 + - - +
193B SER* 1.3 70.3 - - - +
195B MET* 1.3 69.8 + - - +
196B CYS 2.9 1.8 + - - -
197B LEU* 2.9 26.3 + - + +
198B VAL* 2.8 42.1 + - - +
201B GLN* 5.7 0.7 + - - -
245B VAL* 4.0 12.2 - - + +
248B ARG* 3.3 24.3 + - - -
249B PHE* 3.7 22.9 - - + -
82C ASP* 4.3 5.9 + - - +
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Residues in contact with MET 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE* 4.0 26.5 - - + -
134B LEU* 4.5 8.5 - - + -
191B ILE* 3.2 16.8 - - + +
192B ARG* 3.3 18.4 - - - +
194B GLU* 1.3 73.7 - - - +
196B CYS* 1.3 57.3 + - - +
198B VAL 3.5 0.2 + - - -
199B MET* 2.8 47.7 + - + +
221B VAL* 4.8 6.1 - - + -
241B VAL* 3.6 16.8 - - + +
242B VAL* 3.3 46.4 - - + +
245B VAL* 3.6 13.5 - - + -
246B ALA* 4.0 18.8 - - + +
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Residues in contact with CYS 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ARG 2.8 16.6 + - - -
193B SER 3.3 8.3 - - - +
194B GLU 2.9 0.8 + - - -
195B MET* 1.3 72.7 - - - +
197B LEU* 1.3 67.5 + - - +
199B MET* 3.0 5.7 + - - +
200B GLU* 3.0 26.0 + - + +
206B VAL* 3.6 36.1 - - + -
209B HIS* 3.6 32.5 - - - -
221B VAL* 3.9 9.6 - - - -
16C PHE* 3.9 17.0 - - + -
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B SER 2.9 21.5 + - - +
194B GLU* 2.9 22.9 + - - +
196B CYS* 1.3 72.2 - - - +
198B VAL* 1.3 59.4 + - + +
200B GLU* 3.2 9.2 + - - +
201B GLN* 3.0 42.4 + - - +
15C LYS* 4.6 20.0 - - + -
16C PHE* 3.8 22.4 - - + -
82C ASP* 3.2 28.0 - - + +
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Residues in contact with VAL 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PRO* 3.8 29.2 - - + -
79B PHE* 4.2 7.4 - - + -
194B GLU* 2.8 42.8 + - - +
195B MET 3.7 2.7 - - - +
197B LEU* 1.3 69.4 - - - +
199B MET* 1.3 67.6 + - - +
201B GLN* 2.9 31.0 + - - +
202B MET* 2.9 12.7 + - + +
241B VAL* 3.6 27.1 - - + -
245B VAL* 4.2 9.2 - - + -
248B ARG* 5.5 1.3 - - - +
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Residues in contact with MET 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B MET* 2.8 33.5 + - + +
196B CYS* 3.5 4.3 - - - +
198B VAL* 1.3 71.6 - - - +
200B GLU* 1.3 62.0 + - - +
202B MET* 3.1 11.9 + - - +
204B LEU* 3.0 41.1 + - + +
206B VAL* 4.3 5.2 - - + -
221B VAL* 3.9 22.0 - - + -
223B THR* 4.5 6.3 - - - -
237B ILE* 5.6 0.2 - - + -
238B TYR* 3.2 52.9 - - + +
241B VAL* 3.7 24.9 - - + -
242B VAL* 3.6 22.2 - - + -
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Residues in contact with GLU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B CYS* 3.0 12.0 + - - +
197B LEU* 3.5 10.8 - - - +
199B MET* 1.3 71.2 - - - +
201B GLN* 1.3 58.8 + - - +
202B MET 3.0 4.7 - - - -
203B GLY* 2.8 20.6 + - - -
204B LEU 3.2 14.3 - - - +
205B VAL* 3.9 2.8 - - - +
206B VAL* 2.9 41.2 + - + +
34C PRO* 5.4 2.8 - - - +
36C HIS* 2.8 36.4 + - - -
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Residues in contact with GLN 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 3.9 12.5 - - - +
78B PRO* 4.4 16.3 - - + +
194B GLU* 5.7 1.0 + - - -
197B LEU* 3.0 39.7 + - - +
198B VAL* 2.9 21.1 + - - +
200B GLU* 1.3 74.6 - - + +
202B MET* 1.3 60.9 + - + +
203B GLY 3.2 2.6 + - - -
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Residues in contact with MET 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG* 5.2 0.2 - - - +
75B VAL* 4.1 25.3 - - + +
76B ILE 4.1 16.2 - - - +
78B PRO* 3.8 24.7 - - + -
86B ILE* 3.8 29.4 - - + -
198B VAL* 2.9 11.4 + - - +
199B MET* 3.4 11.4 - - - +
200B GLU 3.0 0.6 - - - -
201B GLN* 1.3 80.1 - - + +
203B GLY* 1.3 54.4 + - - +
204B LEU* 3.5 10.9 + - - +
237B ILE* 4.0 33.7 - - + +
240B TYR* 4.5 12.1 - - + -
241B VAL* 3.5 27.8 - - - -
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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