Contacts of the helix formed by residues 188 - 202 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G LEU* 4.9 5.2 - - + -
155G GLU* 4.5 4.3 - - - +
186G ASP* 2.9 16.9 + - - +
187G SER* 1.3 84.5 - - - +
189G GLN* 1.3 65.5 + - - +
190G ASP 3.4 1.6 - - - -
191G ILE* 3.8 22.7 - - + -
192G ARG* 3.1 26.5 + - + +
219G ASN* 3.8 22.4 - - - +
251G LYS* 6.1 0.7 - - - -
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Residues in contact with GLN 189 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183G PRO* 4.2 9.2 - - + -
186G ASP* 4.2 4.2 + - - +
187G SER 3.9 1.6 - - - -
188G ALA* 1.3 76.2 - - - +
190G ASP* 1.3 61.5 + - - +
192G ARG* 2.9 14.4 + - - +
193G SER* 2.8 42.0 + - - -
209G HIS* 2.7 21.2 + - - -
30L HIS* 3.3 17.4 + - - +
32L THR* 2.5 33.5 + - - +
80L PHE* 3.4 53.4 - - + -
84L THR* 5.0 1.9 - - - +
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Residues in contact with ASP 190 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G GLN* 1.3 81.5 - - - +
191G ILE* 1.3 63.3 + - + +
193G SER* 3.6 2.3 + - - -
194G GLU* 3.1 25.6 + - - +
249G PHE* 4.5 9.3 - - + -
79L PHE 4.4 5.4 - - - +
80L PHE* 3.7 11.8 - - - +
81L ALA* 2.7 49.0 + - + +
82L ASP* 3.7 11.2 - - - +
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Residues in contact with ILE 191 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G LEU* 4.4 17.3 - - + -
187G SER 3.7 18.6 - - - +
188G ALA* 3.7 23.6 - - + +
189G GLN 3.1 0.2 - - - -
190G ASP* 1.3 74.5 - - + +
192G ARG* 1.3 67.8 + - - +
194G GLU* 2.9 14.9 + - - +
195G MET* 3.1 20.9 + - + +
245G VAL* 4.2 10.3 - - + +
246G ALA* 5.1 4.0 - - - -
249G PHE* 3.8 40.6 - - + -
251G LYS* 4.1 28.5 - - + -
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Residues in contact with ARG 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G LEU* 5.6 1.6 - - + -
186G ASP* 3.0 35.0 + - - -
188G ALA* 3.1 21.4 + - + +
189G GLN* 2.9 32.6 - - - +
191G ILE* 1.3 76.9 - - + +
193G SER* 1.3 65.5 + - - +
195G MET* 3.0 21.8 + - - +
196G CYS* 2.8 24.3 + - - -
209G HIS* 2.7 37.5 + - + +
210G HIS* 3.5 23.7 - - - +
211G HIS 3.6 11.0 - - - +
219G ASN* 3.0 43.2 - - + +
220G GLU 4.2 6.1 - - - -
221G VAL* 4.8 4.4 - - + +
30L HIS* 3.7 4.4 + - - -
32L THR* 4.3 0.2 + - - -
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Residues in contact with SER 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G GLN* 2.8 24.4 + - - -
190G ASP* 3.8 1.1 - - - -
192G ARG* 1.3 76.1 - - - +
194G GLU* 1.3 56.6 + - - +
196G CYS* 3.3 3.2 + - - +
197G LEU* 2.9 34.8 + - - +
209G HIS* 3.0 23.0 + - - -
16L PHE* 3.5 26.5 - - - -
82L ASP* 3.3 23.7 + - - -
84L THR* 5.5 1.9 - - - +
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Residues in contact with GLU 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190G ASP 3.1 10.2 + - - +
191G ILE 2.9 11.2 + - - +
193G SER* 1.3 70.7 - - - +
195G MET* 1.3 69.7 + - - +
196G CYS 2.9 2.5 + - - -
197G LEU* 2.9 25.7 + - + +
198G VAL* 2.8 42.7 + - - +
201G GLN* 5.7 0.9 + - - -
245G VAL* 4.0 11.7 - - + +
248G ARG* 3.3 24.3 + - - -
249G PHE* 3.7 22.9 - - + -
82L ASP* 4.3 5.5 + - - +
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Residues in contact with MET 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G PHE* 4.0 27.1 - - + -
134G LEU* 4.5 9.0 - - + -
191G ILE* 3.2 17.0 - - + +
192G ARG* 3.3 19.3 - - - +
194G GLU* 1.3 74.7 - - - +
196G CYS* 1.3 57.1 + - - +
198G VAL 3.5 0.2 + - - -
199G MET* 2.8 48.0 + - + +
221G VAL* 4.8 5.8 - - + -
241G VAL* 3.6 17.4 - - + +
242G VAL* 3.3 46.4 - - + +
245G VAL* 3.6 13.6 - - + +
246G ALA* 4.0 17.9 - - + +
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Residues in contact with CYS 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G ARG 2.8 16.5 + - - -
193G SER 3.3 9.0 - - - +
194G GLU 2.9 0.8 + - - -
195G MET* 1.3 72.4 - - - +
197G LEU* 1.3 66.9 + - - +
199G MET* 3.0 5.4 + - - +
200G GLU* 3.0 26.8 + - + +
206G VAL* 3.6 36.6 - - + -
209G HIS* 3.6 33.0 - - - -
221G VAL* 3.9 10.1 - - - -
16L PHE* 3.9 15.9 - - + -
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Residues in contact with LEU 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193G SER 2.9 22.1 + - - +
194G GLU* 2.9 24.0 + - - +
196G CYS* 1.3 72.9 - - - +
198G VAL* 1.3 58.3 + - + +
200G GLU* 3.2 8.6 + - - +
201G GLN* 3.0 42.7 + - - +
15L LYS* 4.6 19.3 - - + -
16L PHE* 3.7 23.8 - - + -
82L ASP* 3.3 28.3 - - + +
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Residues in contact with VAL 198 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G PRO* 3.8 28.9 - - + -
79G PHE* 4.2 7.0 - - + -
194G GLU* 2.8 43.2 + - - +
195G MET 3.7 2.9 - - - +
197G LEU* 1.3 69.5 - - - +
199G MET* 1.3 67.8 + - - +
201G GLN* 2.9 31.0 + - - +
202G MET* 2.9 13.0 + - + +
241G VAL* 3.6 28.0 - - + -
245G VAL* 4.2 9.4 - - + -
248G ARG* 5.5 1.3 - - - +
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Residues in contact with MET 199 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195G MET* 2.8 32.5 + - + +
196G CYS* 3.5 4.3 - - - +
198G VAL* 1.3 72.7 - - - +
200G GLU* 1.3 59.6 + - - +
202G MET* 3.1 12.2 + - - +
204G LEU* 3.0 41.6 + - + +
206G VAL* 4.3 4.9 - - + -
221G VAL* 3.9 20.9 - - + -
223G THR* 4.5 6.1 - - - -
237G ILE* 5.6 0.2 - - + -
238G TYR* 3.2 53.4 - - + +
241G VAL* 3.7 23.8 - - + -
242G VAL* 3.6 22.9 - - + -
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Residues in contact with GLU 200 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G CYS* 3.0 12.4 + - - +
197G LEU* 3.5 10.4 - - - +
199G MET* 1.3 70.9 - - - +
201G GLN* 1.3 58.1 + - + +
202G MET 3.0 4.7 - - - -
203G GLY* 2.8 21.0 + - - -
204G LEU 3.2 14.1 - - - +
205G VAL* 3.9 3.2 - - - +
206G VAL* 2.9 41.0 + - + +
34L PRO* 5.3 2.4 - - - +
36L HIS* 2.8 37.8 + - - -
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Residues in contact with GLN 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G VAL* 3.9 12.6 - - - +
78G PRO* 4.4 16.1 - - - +
194G GLU* 5.7 1.0 + - - -
197G LEU* 3.0 39.7 + - - +
198G VAL* 2.9 21.3 + - - +
200G GLU* 1.3 74.9 - - - +
202G MET* 1.3 59.9 + - + +
203G GLY 3.2 2.8 + - - -
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Residues in contact with MET 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ARG* 5.2 0.7 - - - +
75G VAL* 4.1 24.8 - - + +
76G ILE 4.1 15.3 - - - +
78G PRO* 3.8 25.8 - - + -
86G ILE* 3.8 28.9 - - + -
198G VAL* 2.9 11.6 + - - +
199G MET* 3.4 12.3 - - - +
200G GLU 3.0 0.8 - - - -
201G GLN* 1.3 80.5 - - + +
203G GLY* 1.3 54.2 + - - -
204G LEU* 3.5 11.4 + - - +
237G ILE* 4.0 34.1 - - + +
240G TYR* 4.5 12.3 - - + -
241G 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
------------------------------------------------------------
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