Contacts of the helix formed by residues 188 - 202 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H LEU* 4.9 4.9 - - + -
155H GLU* 4.5 4.3 - - - +
186H ASP* 2.9 16.1 + - - +
187H SER* 1.3 83.6 - - - +
189H GLN* 1.3 65.2 + - - +
190H ASP 3.4 1.8 - - - -
191H ILE* 3.8 22.9 - - + -
192H ARG* 3.1 25.6 + - + +
217H GLY* 6.5 0.2 - - - -
219H ASN* 3.8 22.7 - - - +
251H LYS* 6.1 0.4 - - - -
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Residues in contact with GLN 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G PHE* 5.9 0.2 - - - +
30G HIS* 3.3 17.6 + - - +
32G THR* 2.6 33.6 + - - +
80G PHE* 3.5 52.0 - - + -
84G THR* 5.1 2.1 - - - +
183H PRO* 4.2 9.4 - - + -
186H ASP* 4.2 4.6 + - - +
187H SER 3.9 1.2 - - - -
188H ALA* 1.3 76.6 - - - +
190H ASP* 1.3 62.1 + - - +
192H ARG* 2.9 15.1 - - - +
193H SER* 2.8 42.1 + - - -
209H HIS* 2.7 22.3 + - - -
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Residues in contact with ASP 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G PHE 4.6 4.3 - - - +
80G PHE* 3.8 9.9 - - - +
81G ALA* 2.8 46.7 + - + +
82G ASP* 3.8 10.9 + - - +
188H ALA 3.4 0.2 - - - -
189H GLN* 1.3 82.8 - - - +
191H ILE* 1.3 64.0 + - + +
193H SER* 3.6 2.4 + - - -
194H GLU* 3.1 25.3 + - - +
249H PHE* 4.5 9.3 - - + -
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Residues in contact with ILE 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H LEU* 4.4 17.3 - - + -
187H SER 3.7 18.6 - - - +
188H ALA* 3.7 23.6 - - + +
189H GLN 3.1 0.2 - - - -
190H ASP* 1.3 73.9 - - + +
192H ARG* 1.3 67.5 + - - +
194H GLU* 2.9 14.6 + - - +
195H MET* 3.1 20.8 + - + +
245H VAL* 4.2 10.5 - - + +
246H ALA* 5.1 3.6 - - - -
249H PHE* 3.8 41.1 - - + -
251H LYS* 4.1 28.9 - - + -
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Residues in contact with ARG 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G HIS* 3.8 4.4 + - - -
32G THR* 4.4 0.4 + - - -
134H LEU* 5.6 2.2 - - + -
186H ASP* 3.0 34.8 + - - -
188H ALA* 3.1 21.7 + - + +
189H GLN* 2.9 32.5 - - - +
191H ILE* 1.3 79.1 - - + +
193H SER* 1.3 65.0 + - - +
195H MET* 3.0 20.1 + - - +
196H CYS* 2.8 24.1 + - - -
209H HIS* 2.7 36.7 + - + +
210H HIS* 3.5 23.1 - - - +
211H HIS 3.6 11.4 - - - +
219H ASN* 3.0 42.6 - - + +
220H GLU 4.2 5.6 - - - -
221H VAL* 4.8 4.2 - - + +
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Residues in contact with SER 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G PHE* 3.6 24.8 - - - -
82G ASP* 3.4 23.1 + - - -
189H GLN* 2.8 24.5 + - - -
190H ASP 3.8 1.6 - - - -
192H ARG* 1.3 76.8 - - - +
194H GLU* 1.3 56.9 + - - +
196H CYS* 3.3 3.6 + - - +
197H LEU* 2.9 33.6 + - - +
209H HIS* 3.0 24.4 + - - -
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Residues in contact with GLU 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G ASP* 4.5 5.8 + - - +
190H ASP 3.1 10.6 + - - +
191H ILE 2.9 10.3 + - - +
193H SER* 1.3 70.7 - - - +
195H MET* 1.3 69.3 + - - +
196H CYS 2.9 1.9 + - - -
197H LEU* 2.9 26.7 + - + +
198H VAL* 2.8 42.9 + - - +
201H GLN* 5.7 0.7 + - - -
245H VAL* 4.0 12.0 - - + +
248H ARG* 3.3 24.2 + - - -
249H PHE* 3.7 22.7 - - + -
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Residues in contact with MET 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H PHE* 4.0 26.9 - - + -
134H LEU* 4.5 9.0 - - + -
191H ILE* 3.2 17.0 - - + +
192H ARG* 3.3 18.8 - - - +
194H GLU* 1.3 75.4 - - - +
196H CYS* 1.3 56.7 + - - +
199H MET* 2.8 46.7 + - + +
221H VAL* 4.8 6.7 - - + -
241H VAL* 3.6 15.9 - - + +
242H VAL* 3.3 45.8 - - + +
245H VAL* 3.6 14.1 - - + +
246H ALA* 4.0 17.5 - - + +
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Residues in contact with CYS 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G PHE* 4.1 14.8 - - + -
34G PRO* 6.0 0.2 - - + -
192H ARG 2.8 16.5 + - - -
193H SER 3.3 9.2 - - - +
194H GLU 2.9 0.2 + - - -
195H MET* 1.3 73.5 - - - +
197H LEU* 1.3 66.7 + - - +
199H MET* 3.0 5.9 + - - +
200H GLU* 3.0 26.6 + - + +
206H VAL* 3.6 37.0 - - + -
209H HIS* 3.6 33.0 - - - -
221H VAL* 3.9 9.6 - - - -
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Residues in contact with LEU 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G LYS* 4.8 17.0 - - + -
16G PHE* 3.7 24.4 - - + -
82G ASP* 3.4 26.9 - - + +
193H SER 2.9 22.5 + - - +
194H GLU* 2.9 24.0 + - - +
196H CYS* 1.3 71.5 - - - +
198H VAL* 1.3 57.9 + - + +
200H GLU* 3.2 9.3 + - - +
201H GLN* 3.0 42.7 + - - +
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Residues in contact with VAL 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H PRO* 3.8 29.2 - - + -
79H PHE* 4.2 7.0 - - + -
194H GLU* 2.8 42.3 + - - +
195H MET 3.7 2.9 - - - +
197H LEU* 1.3 68.6 - - - +
199H MET* 1.3 66.5 + - - +
201H GLN* 2.9 31.1 + - - +
202H MET* 2.9 13.4 + - - +
241H VAL* 3.6 28.3 - - + -
245H VAL* 4.2 9.9 - - + -
248H ARG* 5.5 1.6 - - - +
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Residues in contact with MET 199 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195H MET* 2.8 34.5 + - + +
196H CYS* 3.5 4.5 - - - +
198H VAL* 1.3 73.1 - - - +
200H GLU* 1.3 60.8 + - - +
202H MET* 3.1 12.8 + - - +
204H LEU* 3.0 40.2 + - + +
206H VAL* 4.3 5.2 - - + -
221H VAL* 3.9 21.1 - - + -
223H THR* 4.5 5.6 - - - -
237H ILE* 5.6 0.2 - - + -
238H TYR* 3.2 53.4 - - + +
241H VAL* 3.7 23.8 - - + -
242H VAL* 3.6 22.7 - - + -
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Residues in contact with GLU 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G PRO* 5.4 2.5 - - - +
36G HIS* 2.9 35.4 + - - -
196H CYS* 3.0 13.3 + - - +
197H LEU* 3.5 8.8 - - - +
199H MET* 1.3 70.3 - - - +
201H GLN* 1.3 58.9 + - - +
202H MET 3.0 4.5 - - - -
203H GLY* 2.9 21.0 + - - -
204H LEU 3.2 15.6 - - - +
205H VAL* 3.9 2.8 - - - +
206H VAL* 2.9 42.1 + - + +
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Residues in contact with GLN 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H VAL* 3.9 12.6 - - - +
78H PRO* 4.4 16.0 - - + +
194H GLU* 5.7 0.6 + - - -
197H LEU* 3.0 39.2 + - - +
198H VAL* 2.9 21.1 + - - +
200H GLU* 1.3 75.4 - - - +
202H MET* 1.3 61.3 + - + +
203H GLY 3.2 2.2 + - - -
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Residues in contact with MET 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H ARG* 5.2 1.1 - - - +
75H VAL* 4.1 24.9 - - + +
76H ILE 4.1 14.8 - - - +
78H PRO* 3.8 25.8 - - + -
86H ILE* 3.8 29.2 - - + -
198H VAL* 2.9 13.5 + - + +
199H MET* 3.4 12.8 - - - +
200H GLU 3.0 0.6 - - - -
201H GLN* 1.3 80.3 - - + +
203H GLY* 1.3 54.6 + - - -
204H LEU* 3.5 11.4 + - - +
237H ILE* 4.0 32.3 - - + +
240H TYR* 4.5 11.7 - - + -
241H VAL* 3.5 27.4 - - - -
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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
------------------------------------------------------------
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