Contacts of the helix formed by residues 188 - 202 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134C LEU* 4.9 4.7 - - + -
155C GLU* 4.5 3.8 - - - +
186C ASP* 2.9 17.4 + - - +
187C SER* 1.3 85.3 - - - +
189C GLN* 1.3 66.9 + - - +
190C ASP 3.4 1.6 - - - -
191C ILE* 3.8 22.4 - - + -
192C ARG* 3.1 25.8 + - + +
219C ASN* 3.8 22.7 - - - +
251C LYS* 6.1 0.4 - - - -
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Residues in contact with GLN 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C PRO* 4.2 9.2 - - + -
186C ASP* 4.2 4.2 + - - +
187C SER 3.9 1.0 - - - -
188C ALA* 1.3 76.8 - - - +
190C ASP* 1.3 62.7 - - - +
192C ARG* 2.9 14.6 - - - +
193C SER* 2.8 42.1 + - - -
209C HIS* 2.7 21.6 + - - -
30D HIS* 3.3 17.0 + - - +
32D THR* 2.5 35.0 + - - +
80D PHE* 3.5 53.0 - - + -
84D THR* 5.1 2.4 - - - +
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Residues in contact with ASP 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C GLN* 1.3 82.5 - - - +
191C ILE* 1.3 63.4 + - + +
193C SER* 3.6 2.6 + - - -
194C GLU* 3.1 25.6 + - - +
249C PHE* 4.5 9.5 - - + -
79D PHE 4.5 3.1 - - - +
80D PHE* 3.8 12.6 - - - +
81D ALA* 2.9 45.8 + - + +
82D ASP* 3.7 12.4 - - - +
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Residues in contact with ILE 191 (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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134C LEU* 4.4 17.0 - - + -
187C SER 3.7 19.1 - - - +
188C ALA* 3.7 22.7 - - + +
190C ASP* 1.3 74.1 - - + +
192C ARG* 1.3 67.4 + - - +
194C GLU* 2.9 14.9 + - - +
195C MET* 3.1 21.0 + - + +
245C VAL* 4.5 10.3 - - + -
246C ALA* 5.1 3.6 - - - -
249C PHE* 3.8 40.6 - - + -
251C LYS* 4.1 28.3 - - + -
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Residues in contact with ARG 192 (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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132C PHE* 5.5 0.2 - - + -
134C LEU* 5.6 2.0 - - + -
186C ASP* 3.0 35.4 + - - -
188C ALA* 3.1 20.4 + - + +
189C GLN* 2.9 32.3 - - - +
191C ILE* 1.3 78.5 - - + +
193C SER* 1.3 65.9 + - - +
195C MET* 3.0 20.3 + - - +
196C CYS* 2.8 23.7 + - - -
209C HIS* 2.7 36.5 + - + +
210C HIS* 3.5 23.3 - - - +
211C HIS 3.6 10.2 - - - +
219C ASN* 3.0 41.2 - - + +
220C GLU 4.2 5.8 - - - -
221C VAL* 4.8 4.3 - - + -
30D HIS* 3.7 4.4 + - - -
32D THR* 4.3 0.4 + - - -
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Residues in contact with SER 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C GLN* 2.8 25.5 + - - -
190C ASP* 3.8 1.1 - - - -
192C ARG* 1.3 75.5 - - - +
194C GLU* 1.3 56.8 + - - +
196C CYS* 3.3 3.4 + - - +
197C LEU* 2.9 35.2 + - - +
209C HIS* 3.0 22.9 + - - -
16D PHE* 3.6 26.2 - - - -
82D ASP* 3.5 22.7 - - - -
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Residues in contact with GLU 194 (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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190C ASP 3.1 11.2 + - - +
191C ILE 2.9 10.7 + - - +
193C SER* 1.3 70.3 - - - +
195C MET* 1.3 69.6 + - - +
196C CYS 2.9 2.1 + - - -
197C LEU* 2.9 26.3 + - + +
198C VAL* 2.8 42.2 + - - +
201C GLN* 5.7 0.9 + - - -
245C VAL* 4.0 12.8 - - + +
248C ARG* 3.3 24.7 + - - -
249C PHE* 3.7 22.7 - - + -
82D ASP* 4.4 5.7 + - - +
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Residues in contact with MET 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C PHE* 4.0 26.7 - - + -
134C LEU* 4.5 9.4 - - + -
191C ILE* 3.2 17.0 - - + +
192C ARG* 3.0 18.6 + - - +
194C GLU* 1.3 75.3 - - - +
196C CYS* 1.3 57.9 + - - +
198C VAL 3.5 0.2 + - - -
199C MET* 2.8 47.0 + - + +
221C VAL* 4.8 6.5 - - + -
241C VAL* 3.6 16.8 - - + +
242C VAL* 3.3 45.3 - - + +
245C VAL* 3.6 13.2 - - + -
246C ALA* 4.0 18.4 - - + +
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Residues in contact with CYS 196 (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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192C ARG 2.8 17.0 + - - -
193C SER 3.3 8.7 - - - +
194C GLU 2.9 0.4 + - - -
195C MET* 1.3 73.1 - - - +
197C LEU* 1.3 68.7 + - - +
199C MET* 3.0 5.5 + - - +
200C GLU* 3.0 26.8 + - - +
206C VAL* 3.6 37.7 - - + -
209C HIS* 3.6 31.9 - - - -
221C VAL* 3.9 10.1 - - - -
16D PHE* 4.0 15.3 - - + -
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Residues in contact with LEU 197 (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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193C SER 2.9 23.2 + - - +
194C GLU* 2.9 23.1 + - - +
196C CYS* 1.3 72.3 - - - +
198C VAL* 1.3 58.7 + - + +
200C GLU* 3.2 9.3 + - - +
201C GLN* 3.0 42.1 + - - +
15D LYS* 4.8 17.9 - - + -
16D PHE* 3.7 23.5 - - + -
82D ASP* 3.4 26.7 - - + +
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Residues in contact with VAL 198 (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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78C PRO* 3.8 29.2 - - + -
79C PHE* 4.2 7.0 - - + -
194C GLU* 2.8 42.4 + - - +
195C MET 3.7 2.9 - - - +
197C LEU* 1.3 69.2 - - - +
199C MET* 1.3 67.0 + - - +
201C GLN* 2.9 31.5 + - - +
202C MET* 2.9 12.7 + - - +
241C VAL* 3.6 26.5 - - + -
245C VAL* 4.2 9.6 - - + -
248C ARG* 5.5 1.6 - - - +
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Residues in contact with MET 199 (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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195C MET* 2.8 32.3 + - + +
196C CYS* 3.5 4.0 - - - +
198C VAL* 1.3 71.8 - - - +
200C GLU* 1.3 59.9 + - - +
202C MET* 3.1 12.8 + - - +
204C LEU* 3.0 40.2 + - + +
206C VAL* 4.3 5.4 - - + -
221C VAL* 3.9 22.2 - - + -
223C THR* 4.5 5.6 - - - -
237C ILE* 5.6 0.2 - - + -
238C TYR* 3.2 53.6 - - + +
241C VAL* 3.7 24.0 - - + -
242C VAL* 3.6 22.4 - - + -
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Residues in contact with GLU 200 (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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196C CYS* 3.0 12.3 + - - +
197C LEU* 3.5 10.7 - - - +
199C MET* 1.3 70.9 - - - +
201C GLN* 1.3 59.6 + - - +
202C MET 3.0 4.9 - - - -
203C GLY* 2.8 20.8 + - - -
204C LEU 3.2 15.0 - - - +
205C VAL* 3.9 3.4 - - - +
206C VAL* 2.9 42.3 + - + +
34D PRO* 5.3 2.8 - - - +
36D HIS* 2.8 36.4 + - - -
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Residues in contact with GLN 201 (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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75C VAL* 3.9 12.1 - - - +
78C PRO* 4.4 15.8 - - + +
194C GLU* 5.7 0.8 + - - -
197C LEU* 3.0 38.5 + - - +
198C VAL* 2.9 21.7 + - - +
200C GLU* 1.3 76.5 - - - +
202C MET* 1.3 60.0 + - + +
203C GLY 3.2 3.0 + - - -
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Residues in contact with MET 202 (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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20C ARG* 5.2 0.7 - - - +
75C VAL* 4.1 25.5 - - + +
76C ILE 4.1 15.7 - - - +
78C PRO* 3.8 25.8 - - + -
86C ILE* 3.8 29.2 - - + -
198C VAL* 2.9 11.3 + - - +
199C MET 3.4 11.9 - - - +
200C GLU 3.0 0.8 - - - -
201C GLN* 1.3 80.7 - - + +
203C GLY* 1.3 53.1 + - - +
204C LEU* 3.5 11.3 + - - +
237C ILE* 4.0 33.6 - - + +
240C TYR* 4.4 11.2 - - + -
241C 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