Contacts of the helix formed by residues 219 - 229 (chain E) in PDB entry 5FHK
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 219 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D THR* 4.8 10.5 - - + +
99E TYR* 4.9 14.8 - - + +
100E ASN* 6.0 0.2 - - - +
191E GLY* 4.8 0.9 - - - -
192E HIS 4.2 5.2 - - - -
217E ALA* 3.2 3.3 + - - +
218E ASN* 1.3 85.7 + - - +
220E LEU* 1.3 62.5 + - - +
221E ASN* 3.5 19.1 - - - +
222E VAL* 3.0 24.7 - - + +
223E VAL* 3.4 12.3 - - - +
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Residues in contact with LEU 220 (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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100E ASN* 3.9 35.5 + - - +
191E GLY* 3.4 33.2 - - - +
192E HIS 3.8 8.0 + - - +
193E PRO* 4.4 6.7 - - + -
194E LEU* 4.4 10.1 - - + -
219E ALA* 1.3 70.2 - - - +
221E ASN* 1.3 66.4 + - - +
222E VAL 3.2 2.0 - - - -
223E VAL* 2.9 18.8 + - + +
224E ARG* 3.0 13.9 + - - +
234E THR* 5.8 0.2 - - - +
235E LEU 4.5 9.9 - - - +
236E MET* 4.3 20.4 - - - +
237E PRO* 4.0 29.8 - - + -
240E MET* 4.3 9.6 - - + -
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Residues in contact with ASN 221 (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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100D ASN 5.9 1.0 + - - -
103D LYS* 4.0 36.5 - - + +
126D THR* 6.0 0.5 - - - +
100E ASN* 5.3 1.4 + - - -
219E ALA* 3.5 19.5 - - - +
220E LEU* 1.3 77.6 - - - +
222E VAL* 1.3 80.0 + - - +
224E ARG* 3.5 12.9 + - - +
225E SER* 3.4 18.4 + - - -
240E MET* 5.3 8.1 - - + +
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Residues in contact with VAL 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D THR* 4.8 6.1 - - + -
103D LYS* 5.2 3.6 - - - -
107D MET* 3.1 35.9 - - + +
124D LEU* 3.9 11.4 - - + -
126D THR* 5.2 3.6 - - + -
215E PHE* 3.2 22.1 - - + -
217E ALA* 3.6 16.4 - - + -
219E ALA* 3.0 28.5 - - + +
221E ASN* 1.3 90.3 + - - +
223E VAL* 1.3 63.0 + - - +
225E SER* 3.3 8.4 + - - -
226E ALA 3.2 16.6 + - - -
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Residues in contact with VAL 223 (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 LEU* 3.6 23.1 - - + +
190E LYS 3.6 9.6 - - - +
191E GLY* 3.5 22.7 - - - +
215E PHE* 4.1 10.8 - - + -
217E ALA* 4.2 10.3 - - + -
219E ALA 3.4 17.7 - - - +
220E LEU* 2.9 14.1 + - + +
222E VAL* 1.3 78.5 - - - +
224E ARG* 1.3 61.6 + - - +
226E ALA* 3.2 4.2 + - - +
227E CYS* 3.0 20.4 + - - +
234E THR* 3.1 28.3 - - + +
236E MET* 4.5 2.0 - - + -
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Residues in contact with ARG 224 (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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103D LYS* 3.1 36.8 - - - +
220E LEU 3.0 9.3 + - - +
221E ASN* 3.9 10.8 + - - +
222E VAL 3.3 0.2 - - - -
223E VAL* 1.3 76.1 - - - +
225E SER* 1.3 70.2 + - - +
227E CYS* 3.3 4.4 + - - +
228E SER* 2.8 66.5 + - - +
236E MET* 3.5 23.7 - - + +
240E MET 5.3 1.1 - - - -
241E ILE* 4.3 16.4 - - + -
244E TYR* 3.5 47.4 + - - -
250E LEU* 4.3 6.7 - - + -
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Residues in contact with SER 225 (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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103D LYS* 4.9 6.8 + - - +
107D MET* 3.6 18.4 - - - +
111D ASN* 3.0 18.7 + - - -
221E ASN 3.4 10.2 + - - -
222E VAL* 3.3 12.3 + - - -
224E ARG* 1.3 96.7 - - - +
226E ALA* 1.3 62.9 + - - +
228E SER* 3.2 4.4 + - - -
229E GLU* 3.2 27.9 + - - +
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Residues in contact with ALA 226 (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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111D ASN* 3.3 23.5 + - - +
114D MET* 4.5 1.1 - - + -
189E LEU* 3.8 11.9 - - + -
215E PHE* 3.8 27.1 - - + -
222E VAL 3.2 3.6 + - - +
223E VAL 3.2 8.3 + - - +
225E SER* 1.3 78.4 + - - +
227E CYS* 1.3 62.4 + - - +
229E GLU* 3.2 6.4 + - - +
231E LEU* 3.2 35.5 + - + +
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Residues in contact with CYS 227 (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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165E VAL* 3.4 21.1 - - - -
166E ALA* 3.7 9.6 - - - -
167E SER* 3.5 11.8 + - - -
189E LEU* 3.5 14.7 - - + +
223E VAL 3.0 16.1 + - - +
224E ARG* 3.6 5.4 - - - +
226E ALA* 1.3 77.0 - - - +
228E SER* 1.4 56.9 + - - +
230E GLY* 2.9 20.6 + - - -
231E LEU 4.0 0.6 + - - +
232E GLY 3.4 21.1 - - - +
234E THR* 3.7 21.1 - - + -
250E LEU* 3.8 14.1 - - + -
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Residues in contact with SER 228 (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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167E SER* 3.6 12.3 + - - -
224E ARG* 2.8 46.1 + - - +
225E SER* 3.2 5.1 + - - -
227E CYS* 1.4 73.0 - - - +
229E GLU* 1.3 66.7 + - - +
230E GLY 3.2 3.5 + - - -
244E TYR* 5.0 3.8 - - - -
249E SER* 4.8 8.6 + - - +
250E LEU* 3.9 22.7 - - - +
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Residues in contact with GLU 229 (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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111D ASN* 3.5 32.8 - - + +
115D SER* 5.6 1.0 + - - -
169E GLU* 4.0 11.9 - - - +
225E SER* 3.2 16.3 + - - +
226E ALA 3.6 8.1 - - - +
227E CYS 3.1 1.6 - - - -
228E SER* 1.3 84.6 - - - +
230E GLY* 1.3 62.0 + - - +
231E LEU* 3.4 11.0 + - + +
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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