Contacts of the helix formed by residues 188 - 202 (chain E) in PDB entry 1F1H
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134E LEU* 4.6 4.9 - - + -
155E GLU* 4.7 3.4 - - - +
186E ASP* 2.9 6.2 + - - +
187E SER* 1.3 82.9 + - - +
189E GLN* 1.3 64.1 + - - +
190E ASP 3.5 1.8 - - - -
191E ILE* 3.8 23.3 - - + -
192E ARG* 2.9 42.1 + - + +
219E ASN* 3.8 18.2 - - - +
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Residues in contact with GLN 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E PRO* 4.3 9.9 - - + -
186E ASP* 4.0 4.0 + - - +
187E SER 3.7 2.6 + - - -
188E ALA* 1.3 74.8 - - - +
190E ASP* 1.3 64.8 + - - +
192E ARG* 2.9 31.0 - - - +
193E SER* 3.1 20.6 + - - -
209E HIS* 3.2 9.9 - - - -
18F ASP* 4.8 0.2 - - - -
30F HIS* 3.0 19.8 + - - -
32F THR* 3.0 19.0 + - - +
80F PHE* 3.5 26.7 - - + -
1488F MPD 2.8 57.6 + - + +
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Residues in contact with ASP 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E SER 5.4 0.4 + - - -
188E ALA 3.5 0.2 - - - -
189E GLN* 1.3 77.7 - - - +
191E ILE* 1.3 65.5 + - + +
194E GLU* 3.1 26.5 + - - +
249E PHE* 4.4 11.4 - - + -
79F PHE 4.8 4.3 - - - +
80F PHE* 3.6 1.7 - - - -
81F ALA* 2.7 29.4 + - + +
82F ASP* 4.4 0.3 - - - +
1488F MPD 2.6 41.7 + - - +
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Residues in contact with ILE 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E LEU* 4.0 10.5 - - + -
187E SER* 3.9 10.3 - - - +
188E ALA* 3.7 31.0 - - + +
189E GLN 3.2 0.4 - - - -
190E ASP* 1.3 76.9 - - + +
192E ARG* 1.3 61.8 + - - +
194E GLU* 3.3 5.0 + - - +
195E MET* 3.1 45.6 + - + +
245E VAL* 4.5 4.5 - - + -
246E ALA* 5.0 3.8 - - - -
249E PHE* 3.7 41.5 - - + -
251E LYS* 4.5 26.0 - - + +
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Residues in contact with ARG 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E PHE* 5.4 0.4 - - + -
134E LEU* 5.7 1.8 - - + -
186E ASP* 2.8 40.6 + - - -
188E ALA* 2.9 25.7 + - + +
189E GLN* 2.9 25.7 - - - +
191E ILE* 1.3 76.9 - - + +
193E SER* 1.3 58.4 + - - +
195E MET* 3.0 16.7 + - - +
196E CYS* 2.9 27.9 + - - -
209E HIS* 2.8 36.5 + - + +
210E HIS* 3.4 20.9 - - - +
211E HIS 3.6 13.0 - - - +
219E ASN* 2.9 43.9 - - + +
220E GLU 4.2 6.1 - - - -
221E VAL* 4.5 6.0 - - + +
30F HIS* 3.8 4.4 + - - -
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Residues in contact with SER 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E GLN 3.1 4.9 + - - -
192E ARG* 1.3 75.6 - - - +
194E GLU* 1.3 62.9 + - - +
196E CYS* 3.1 3.1 + - - +
197E LEU* 2.9 29.5 + - - +
209E HIS* 2.8 23.1 + - - -
16F PHE* 3.6 15.9 - - - -
82F ASP* 3.4 10.1 - - - -
1488F MPD 2.5 45.6 - - - +
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Residues in contact with GLU 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E ASP 3.1 12.8 + - - +
191E ILE 3.5 9.0 - - - +
192E ARG 3.2 0.2 - - - -
193E SER* 1.3 75.6 - - - +
195E MET* 1.3 65.4 + - - +
197E LEU* 3.2 20.7 + - - +
198E VAL* 3.0 40.5 + - - +
245E VAL* 4.1 10.5 - - + +
248E ARG* 2.9 31.2 + - - -
249E PHE* 3.7 23.3 - - + -
82F ASP* 4.5 7.3 + - - +
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Residues in contact with MET 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E PHE* 3.8 22.9 - - + -
134E LEU* 4.1 16.4 - - + -
191E ILE* 3.3 32.8 - - + +
192E ARG* 3.0 17.1 + - - +
194E GLU* 1.3 77.4 - - - +
196E CYS* 1.3 56.3 + - - +
198E VAL 3.5 0.2 + - - -
199E MET* 2.9 44.4 + - + +
221E VAL* 4.6 5.4 - - + -
241E VAL* 3.6 13.7 - - + +
242E VAL* 3.7 42.2 - - + +
245E VAL* 3.7 15.5 - - + -
246E ALA 4.2 5.6 - - - +
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Residues in contact with CYS 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E ARG 2.9 16.6 + - - -
193E SER 3.1 7.2 + - - +
195E MET* 1.3 74.5 - - - +
197E LEU* 1.3 66.5 + - - +
199E MET* 3.2 3.4 + - - +
200E GLU* 3.0 29.5 + - - +
206E VAL* 3.7 35.2 - - + -
209E HIS* 3.7 24.9 - - - -
221E VAL* 3.7 17.0 - - - -
16F PHE* 3.9 16.8 - - + -
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Residues in contact with LEU 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E SER 2.9 18.7 + - - +
194E GLU* 3.2 17.9 + - - +
196E CYS* 1.3 75.3 - - - +
198E VAL* 1.3 59.6 + - + +
200E GLU* 3.3 10.9 + - - +
201E GLN* 3.0 41.1 + - - +
15F LYS* 4.5 22.4 - - + +
16F PHE* 3.6 25.6 - - + -
82F ASP* 3.2 30.1 - - + +
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Residues in contact with VAL 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E PRO* 3.5 34.5 - - + -
79E PHE* 4.2 4.5 - - + -
194E GLU* 3.0 34.1 + - - +
197E LEU* 1.3 74.8 - - + +
199E MET* 1.3 65.0 + - - +
201E GLN* 3.0 19.8 + - - +
202E MET* 3.0 21.2 + - + +
241E VAL* 3.8 24.9 - - + -
245E VAL* 4.4 8.7 - - + -
248E ARG* 4.5 9.0 - - - +
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Residues in contact with MET 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E MET* 2.9 30.8 + - + +
196E CYS 3.6 4.9 - - - +
198E VAL* 1.3 74.8 - - - +
200E GLU* 1.3 59.3 + - - +
202E MET* 2.9 19.3 + - - +
203E GLY 3.4 0.3 + - - -
204E LEU* 3.1 36.0 + - + +
206E VAL* 4.3 4.9 - - + -
221E VAL* 3.7 26.0 - - + -
223E THR* 4.2 7.0 - - - -
238E TYR* 3.5 45.5 - - + +
241E VAL* 3.8 21.8 - - + -
242E VAL* 3.6 26.7 - - + -
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Residues in contact with GLU 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E CYS* 3.0 19.5 + - - +
197E LEU* 3.6 11.2 - - - +
199E MET* 1.3 72.9 - - - +
201E GLN* 1.3 61.6 + - - +
202E MET 2.9 6.1 + - - -
203E GLY* 3.0 13.2 + - - -
204E LEU 3.3 19.3 - - - +
205E VAL* 4.0 2.7 - - - +
206E VAL* 3.0 31.0 + - + +
34F PRO* 5.4 2.7 - - - +
36F HIS* 2.8 37.3 + - - -
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Residues in contact with GLN 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E VAL* 4.0 9.2 - - - +
76E ILE 5.4 0.5 - - - +
78E PRO* 4.3 17.5 - - + +
197E LEU* 3.0 34.1 + - - +
198E VAL* 3.0 20.9 + - - +
200E GLU* 1.3 75.2 - - - +
202E MET* 1.3 61.7 + - + +
203E GLY 3.4 1.3 + - - -
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Residues in contact with MET 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ARG* 5.1 0.7 - - - +
75E VAL* 3.8 29.0 - - + +
76E ILE 4.1 7.9 - - - +
78E PRO* 3.7 28.3 - - + -
86E ILE* 3.6 30.5 - - + -
198E VAL 3.0 10.1 + - - +
199E MET 2.9 11.5 + - - +
200E GLU 2.9 1.2 - - - -
201E GLN* 1.3 83.2 - - + +
203E GLY* 1.3 56.2 + - - +
204E LEU* 3.5 8.4 + - - +
237E ILE* 3.8 34.4 - - + +
240E TYR* 4.3 12.8 - - + -
241E VAL* 3.6 26.9 - - - -
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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