Contacts of the helix formed by residues 224 - 237 (chain E) in PDB entry 5OF4
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 ASP 224 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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726B GLN* 4.9 0.4 - - - +
222E ILE* 3.3 8.0 - - - +
223E LEU* 1.3 100.2 - - - +
225E GLU* 1.3 61.2 + - - +
226E SER* 3.4 21.5 + - - +
227E HIS* 3.0 16.0 + - + +
228E TYR 2.9 21.8 + - - -
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Residues in contact with GLU 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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75E ASP 4.9 0.6 - - - +
76E LEU* 3.5 30.3 - - + -
77E LYS* 3.4 46.8 + - - +
83E CYS* 4.1 12.8 - - - -
87E LEU* 4.2 4.5 - - + +
223E LEU 5.1 0.7 - - - +
224E ASP* 1.3 73.1 - - - +
226E SER* 1.3 63.4 + - - +
228E TYR* 3.2 11.0 + - - +
229E LYS* 3.0 27.6 + - - +
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Residues in contact with SER 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224E ASP* 3.4 16.3 + - - +
225E GLU* 1.3 78.8 - - - +
227E HIS* 1.3 57.9 + - - +
229E LYS* 3.2 11.6 + - - +
230E GLU* 2.9 36.4 + - - +
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Residues in contact with HIS 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B GLN* 2.9 37.2 + - + +
221E VAL 3.8 4.6 + - - -
222E ILE* 3.4 28.0 - - + -
224E ASP* 3.0 24.5 + - + +
226E SER* 1.3 78.4 + - - +
228E TYR* 1.3 59.8 + - - +
230E GLU* 2.5 35.1 + - + +
231E LEU* 3.0 49.3 + - + +
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Residues in contact with TYR 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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76E LEU* 5.8 0.7 - - + -
83E CYS* 4.2 10.3 - - - -
84E THR* 3.3 45.5 + - - +
87E LEU* 3.5 33.2 - - + -
170E ILE* 3.8 18.9 - - + +
199E ILE* 4.5 11.0 - - + -
201E LEU* 4.6 14.8 - - + -
222E ILE* 3.6 40.9 - - + +
224E ASP 2.9 6.9 + - - +
225E GLU* 3.2 15.3 - - - +
227E HIS* 1.3 74.9 - - - +
229E LYS* 1.3 59.0 - - - +
231E LEU* 3.3 2.3 + - - +
232E LEU* 3.0 59.7 + - + +
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Residues in contact with LYS 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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87E LEU* 3.5 41.0 - - + +
90E TYR* 3.6 40.9 - - + -
225E GLU 3.0 14.8 + - - +
226E SER* 3.3 11.7 - - - +
228E TYR* 1.3 73.2 - - - +
230E GLU* 1.3 58.9 + - - +
232E LEU* 3.9 3.8 - - + +
233E THR* 2.6 39.5 + - - +
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Residues in contact with GLU 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E SER* 2.9 20.8 + - - +
227E HIS* 2.5 50.5 + - + +
229E LYS* 1.3 76.6 - - - +
231E LEU* 1.3 61.6 + - + +
233E THR* 3.4 6.8 + - - +
234E HIS* 2.9 25.6 + - - +
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Residues in contact with LEU 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E ILE* 4.1 11.2 - - + -
220E HIS* 3.5 56.3 - - + +
221E VAL 4.5 0.2 - - - +
222E ILE* 3.7 24.0 - - + -
227E HIS* 3.0 41.3 + - + +
228E TYR 4.1 0.2 - - - +
229E LYS 3.3 0.4 - - - -
230E GLU* 1.3 75.6 - - + +
232E LEU* 1.3 62.0 + - - +
234E HIS* 3.1 17.7 + - + +
235E HIS* 2.9 36.7 + - - -
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Residues in contact with LEU 232 (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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87E LEU* 3.6 28.3 - - + +
88E LEU* 4.6 3.6 - - + +
90E TYR* 5.4 8.3 - - + -
91E PHE* 3.4 23.0 - - + -
168E LEU* 4.3 19.5 - - + -
170E ILE* 4.6 9.0 - - + -
199E ILE* 4.1 21.5 - - + -
228E TYR* 3.0 48.0 + - + +
229E LYS* 4.2 4.9 - - + +
231E LEU* 1.3 74.8 - - - +
233E THR* 1.3 57.8 + - - +
235E HIS* 3.2 4.3 + - + +
236E VAL* 3.0 32.3 + - - +
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Residues in contact with THR 233 (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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90E TYR* 4.2 19.3 + - - +
94E GLU* 4.3 8.5 + - - +
229E LYS* 2.6 25.5 + - - +
230E GLU* 3.5 7.0 - - - +
232E LEU* 1.3 74.9 - - - +
234E HIS* 1.3 65.9 + - - +
236E VAL* 3.3 22.6 + - + +
237E SER* 3.9 4.0 + - - -
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Residues in contact with HIS 234 (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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218E THR* 4.8 14.7 + - + +
220E HIS* 4.9 11.0 + - - -
230E GLU 2.9 15.2 + - - +
231E LEU* 3.1 19.0 + - + +
233E THR* 1.3 78.3 - - - +
235E HIS* 1.3 80.5 + + - +
236E VAL 3.2 0.9 + - - -
237E SER* 3.4 18.1 + - - +
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Residues in contact with HIS 235 (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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59E ARG* 3.1 25.0 + - - +
91E PHE* 4.1 16.5 - - + -
166E GLU* 4.3 11.1 + - - -
168E LEU* 3.8 19.5 - - + +
197E SER* 3.5 33.4 - - - -
199E ILE* 3.6 31.1 - - + +
218E THR* 4.5 11.7 + - - -
220E HIS* 4.6 10.1 - + - -
231E LEU* 2.9 27.9 + - + +
232E LEU* 3.2 9.1 + - - +
234E HIS* 1.3 84.9 - + - +
236E VAL* 1.3 64.2 + - - +
237E SER 3.4 2.4 - - - +
239E PRO* 6.2 0.4 - - - -
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Residues in contact with VAL 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E ARG* 3.0 12.6 + - - -
90E TYR* 5.7 0.9 - - + -
91E PHE* 3.5 23.1 - - + -
94E GLU* 4.0 37.2 - - + +
95E TYR* 5.0 3.1 - - - +
98E GLN* 3.7 34.0 - - + +
99E ASN* 3.2 18.9 + - - +
232E LEU 3.0 19.7 + - - +
233E THR* 3.4 13.0 - - + +
234E HIS 3.1 0.8 - - - -
235E HIS* 1.3 77.9 - - - +
237E SER* 1.3 67.1 + - - +
238E PRO* 3.9 0.3 - - - +
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Residues in contact with SER 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E ARG* 3.4 1.6 + - - -
98E GLN* 5.9 2.9 - - - +
233E THR 3.9 3.7 + - - -
234E HIS* 3.4 14.5 + - - +
235E HIS* 3.4 3.7 - - - +
236E VAL* 1.3 83.1 - - - +
238E PRO* 1.3 78.5 + - - +
239E PRO* 3.3 9.9 - - - +
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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