Contacts of the helix formed by residues 188 - 202 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 4.9 4.9 - - + -
155A GLU* 4.5 4.3 - - - +
186A ASP* 2.9 16.6 + - - +
187A SER* 1.3 85.1 - - - +
189A GLN* 1.3 65.5 + - - +
190A ASP 3.4 2.0 - - - -
191A ILE* 3.8 22.2 - - + -
192A ARG* 3.1 26.9 + - + +
219A ASN* 3.8 22.0 - - - +
251A LYS* 6.1 0.7 - - - -
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Residues in contact with GLN 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A PRO* 4.2 9.6 - - + -
186A ASP* 4.2 4.2 + - - +
187A SER 3.9 1.6 + - - -
188A ALA* 1.3 76.9 - - - +
190A ASP* 1.3 61.5 + - - +
192A ARG* 2.9 15.5 - - - +
193A SER* 2.8 42.6 + - - -
209A HIS* 2.7 22.0 - - - -
30B HIS* 3.3 17.8 + - - +
32B THR* 2.6 32.7 + - - +
80B PHE* 3.4 52.9 - - + -
84B THR* 5.1 2.1 - - - +
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Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ALA 3.4 0.2 - - - -
189A GLN* 1.3 82.2 - - - +
191A ILE* 1.3 64.0 + - + +
193A SER* 3.6 3.0 + - - -
194A GLU* 3.1 25.6 + - - +
249A PHE* 4.5 9.3 - - + -
79B PHE 4.5 4.9 - - - +
80B PHE* 3.8 11.3 - - - +
81B ALA* 2.8 46.8 + - + +
82B ASP* 3.8 10.3 - - - +
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Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU* 4.4 16.4 - - + -
187A SER 3.7 18.8 - - - +
188A ALA* 3.7 22.9 - - + +
189A GLN 3.1 0.2 - - - -
190A ASP* 1.3 74.0 - - + +
192A ARG* 1.3 67.2 + - - +
194A GLU* 2.9 14.7 + - - +
195A MET* 3.1 21.5 + - + +
245A VAL* 4.5 10.3 - - + -
246A ALA* 5.1 3.8 - - - -
249A PHE* 3.8 39.9 - - + -
251A LYS* 4.1 28.9 - - + -
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Residues in contact with ARG 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PHE* 5.5 0.2 - - + -
134A LEU* 5.6 2.0 - - + -
186A ASP* 3.0 35.0 + - - -
188A ALA* 3.1 22.0 + - + +
189A GLN* 2.9 32.3 - - - +
191A ILE* 1.3 78.5 - - + +
193A SER* 1.3 64.8 + - - +
195A MET* 3.0 20.4 + - - +
196A CYS* 2.8 24.3 + - - -
209A HIS* 2.7 36.7 + - + +
210A HIS* 3.5 22.9 - - - +
211A HIS 3.6 9.7 - - - +
219A ASN* 3.0 41.9 - - + +
220A GLU 4.2 5.6 - - - -
221A VAL* 4.8 4.7 - - + -
30B HIS* 3.8 4.8 + - - -
32B THR* 4.4 0.4 + - - -
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Residues in contact with SER 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A GLN* 2.8 25.4 + - - -
190A ASP 3.8 1.3 - - - -
192A ARG* 1.3 75.7 - - - +
194A GLU* 1.3 57.0 + - - +
196A CYS* 3.3 3.2 + - - +
197A LEU* 2.9 34.5 + - - +
209A HIS* 3.0 23.0 + - - -
16B PHE* 3.6 26.5 - - - +
82B ASP* 3.4 23.1 + - - -
84B THR* 5.6 1.7 - - - +
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Residues in contact with GLU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A ASP 3.1 11.0 + - - +
191A ILE 2.9 10.3 + - - +
193A SER* 1.3 70.7 - - - +
195A MET* 1.3 68.7 + - - +
196A CYS 2.9 1.6 + - - -
197A LEU* 2.9 27.4 + - + +
198A VAL* 2.8 42.3 + - - +
201A GLN* 5.7 0.7 + - - -
245A VAL* 4.0 12.5 - - + +
248A ARG* 3.3 25.0 + - - -
249A PHE* 3.7 23.1 - - + -
82B ASP* 4.4 5.5 + - - +
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Residues in contact with MET 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PHE* 4.0 26.7 - - + -
134A LEU* 4.5 9.4 - - + -
191A ILE* 3.2 16.8 - - + +
192A ARG* 3.3 18.6 - - - +
194A GLU* 1.3 74.0 - - - +
196A CYS* 1.3 57.7 + - - +
199A MET* 2.8 47.0 + - + +
221A VAL* 4.8 6.1 - - + -
241A VAL* 3.6 16.6 - - + +
242A VAL* 3.3 45.8 - - + +
245A VAL* 3.6 13.2 - - + -
246A ALA* 4.0 18.4 - - + +
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Residues in contact with CYS 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ARG 2.8 17.2 + - - -
193A SER 3.3 9.4 - - - +
194A GLU 2.9 0.4 + - - -
195A MET* 1.3 73.3 - - - +
197A LEU* 1.3 68.4 + - - +
199A MET* 3.0 5.7 + - - +
200A GLU* 3.0 26.0 + - + +
206A VAL* 3.6 37.2 - - + -
209A HIS* 3.6 32.3 - - - -
221A VAL* 3.9 9.9 - - - -
16B PHE* 4.0 15.3 - - + -
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Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A SER 2.9 22.3 + - - +
194A GLU* 2.9 23.1 + - - +
196A CYS* 1.3 71.7 - - - +
198A VAL* 1.3 59.4 + - + +
200A GLU* 3.2 9.6 + - - +
201A GLN* 3.0 42.1 + - - +
15B LYS* 4.7 18.4 - - + -
16B PHE* 3.7 23.8 - - + -
82B ASP* 3.3 27.4 - - + +
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Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PRO* 3.8 29.2 - - + -
79A PHE* 4.2 6.5 - - + -
194A GLU* 2.8 42.0 + - - +
195A MET 3.7 2.9 - - - +
197A LEU* 1.3 68.8 - - - +
199A MET* 1.3 67.0 + - - +
201A GLN* 2.9 30.2 + - - +
202A MET* 2.9 12.7 + - + +
241A VAL* 3.6 27.8 - - + -
245A VAL* 4.2 9.4 - - + -
248A ARG* 5.5 1.8 - - - +
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Residues in contact with MET 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A MET* 2.8 32.6 + - + +
196A CYS* 3.0 5.1 + - - +
198A VAL* 1.3 72.4 - - - +
200A GLU* 1.3 60.6 + - - +
202A MET* 3.1 12.6 + - - +
204A LEU* 3.0 39.8 + - + +
206A VAL* 4.3 4.9 - - + -
221A VAL* 3.9 20.9 - - + -
223A THR* 4.5 6.1 - - - -
237A ILE* 5.6 0.2 - - + -
238A TYR* 3.2 53.8 - - + +
241A VAL* 3.7 23.1 - - + -
242A VAL* 3.6 22.9 - - + -
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Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A CYS* 3.0 12.7 + - - +
197A LEU* 3.5 10.3 - - - +
199A MET* 1.3 70.5 - - - +
201A GLN* 1.3 58.8 + - - +
202A MET 3.0 4.7 - - - -
203A GLY* 2.9 21.0 + - - -
204A LEU 3.2 14.6 - - - +
205A VAL* 3.9 3.7 - - - +
206A VAL* 2.9 41.7 + - + +
34B PRO* 4.8 2.9 - - - +
36B HIS* 2.9 35.9 + - - -
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Residues in contact with GLN 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL* 3.9 12.1 - - - +
78A PRO* 4.4 17.0 - - + +
194A GLU* 5.7 1.0 + - - -
197A LEU* 3.0 38.6 + - - +
198A VAL* 2.9 21.0 + - - +
200A GLU* 1.3 74.9 - - - +
202A MET* 1.3 59.9 + - + +
203A GLY 3.2 2.6 + - - -
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Residues in contact with MET 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ARG* 5.2 0.9 - - - +
75A VAL* 4.1 25.1 - - + +
76A ILE 4.1 16.2 - - - +
78A PRO* 3.8 25.8 - - + -
86A ILE* 3.8 28.9 - - + -
198A VAL* 2.9 11.6 + - + +
199A MET 3.4 12.1 - - - +
200A GLU 3.0 0.6 - - - -
201A GLN* 1.3 79.9 - - + +
203A GLY* 1.3 53.8 + - - -
204A LEU* 3.5 10.9 + - - +
237A ILE* 4.0 32.2 - - + +
240A TYR* 4.5 11.7 - - + -
241A 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
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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