Contacts of the helix formed by residues 205 - 215 (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 VAL 205 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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532B PRO* 4.7 10.3 - - + -
533B ASP* 4.6 4.3 - - - +
591B GLY* 6.1 1.3 - - - -
171E PHE* 5.2 0.4 - - + -
173E SER* 3.7 40.8 - - - +
174E LEU 4.4 6.1 - - - +
175E THR* 6.1 0.4 - - - -
176E THR* 4.1 20.2 - - - +
203E ALA* 5.0 0.9 - - + -
204E GLU* 1.3 76.1 - - - +
206E ARG* 1.3 68.7 + - - +
207E VAL* 3.4 13.6 + - + +
208E CYS* 3.6 19.4 + - - +
209E THR* 3.2 21.4 + - - -
219E TYR* 3.3 8.7 + - - +
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Residues in contact with ARG 206 (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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533B ASP* 3.5 26.2 + - - +
588B CYS 4.1 14.6 - - - +
589B GLU* 4.8 15.6 + - - +
612B HIS* 4.9 4.8 - - - -
613B HIS* 3.0 62.8 + - - +
204E GLU* 4.0 1.9 + - - -
205E VAL* 1.3 76.7 - - - +
207E VAL* 1.3 65.0 + - + +
209E THR* 3.0 16.6 + - - +
210E VAL* 2.9 43.7 + - + +
213E ARG* 3.6 34.3 - - - +
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Residues in contact with VAL 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B GLU 3.4 27.4 - - - +
590B ASN* 3.7 25.6 - - - +
591B GLY* 4.8 1.8 - - - +
145E LEU* 4.3 12.6 - - + -
176E THR* 4.1 33.4 - - + +
182E ILE* 4.7 14.1 - - + -
186E ILE* 4.9 4.5 - - + +
205E VAL* 3.2 7.3 - - + +
206E ARG* 1.3 84.5 - - + +
208E CYS* 1.3 59.2 + - - +
210E VAL* 3.3 8.0 + - + +
211E LEU* 2.9 27.8 + - + +
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Residues in contact with CYS 208 (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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145E LEU* 4.2 19.7 - - - -
171E PHE* 4.1 26.0 - - - -
173E SER* 6.1 0.2 - - - -
176E THR* 5.1 0.2 - - - -
198E VAL* 4.0 22.6 - - + +
205E VAL* 3.6 19.4 + - + +
206E ARG 3.3 0.4 - - - -
207E VAL* 1.3 78.6 - - - +
209E THR* 1.3 57.5 - - - +
211E LEU* 3.5 8.0 - - - +
212E ALA* 2.9 30.7 + - - +
219E TYR* 3.5 27.9 - - + +
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Residues in contact with THR 209 (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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204E GLU* 3.5 25.4 + - - +
205E VAL 3.2 13.4 + - - -
206E ARG* 3.0 19.7 + - - +
208E CYS* 1.3 76.0 - - - +
210E VAL* 1.3 61.5 + - - +
212E ALA* 3.4 4.4 + - + +
213E ARG* 2.9 37.6 + - + +
219E TYR* 4.0 14.7 - - + -
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Residues in contact with VAL 210 (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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589B GLU 6.0 0.9 - - - +
183E TYR* 4.2 27.1 - - + +
186E ILE* 4.5 7.7 - - + +
206E ARG* 2.9 45.9 + - + +
207E VAL* 3.8 10.5 - - + +
209E THR* 1.3 73.2 - - - +
211E LEU* 1.3 65.7 + - - +
213E ARG* 3.4 28.7 - - - +
214E GLU* 3.0 35.3 + - + +
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Residues in contact with LEU 211 (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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145E LEU* 3.8 28.3 - - + -
149E LEU* 4.2 16.2 - - + -
169E ILE* 3.9 23.3 - - + -
182E ILE* 5.7 0.2 - - + -
186E ILE* 3.8 33.9 - - + +
189E LEU* 6.1 2.5 - - + -
196E VAL* 4.0 15.7 - - + -
198E VAL* 4.1 7.2 - - + -
207E VAL* 2.9 17.5 + - + +
208E CYS* 3.5 7.6 - - - +
210E VAL* 1.3 75.7 - - - +
212E ALA* 1.3 57.5 + - - +
215E THR* 2.9 48.0 + - - +
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Residues in contact with ALA 212 (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 VAL 4.2 13.0 - - - +
198E VAL* 4.8 7.0 - - + -
208E CYS 2.9 20.9 + - - +
209E THR* 3.6 3.1 - - + +
211E LEU* 1.3 73.9 - - - +
213E ARG* 1.3 57.8 + - - +
216E GLY* 3.8 3.8 + - - -
217E GLY 3.5 23.7 + - - +
218E THR* 4.3 9.9 - - - +
219E TYR* 3.9 31.2 - - + +
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Residues in contact with ARG 213 (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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613B HIS* 5.3 3.2 - - - -
183E TYR* 5.9 0.4 + - - -
206E ARG* 3.6 33.9 - - - +
209E THR* 2.9 29.2 + - + +
210E VAL* 3.4 29.9 - - + +
211E LEU 3.2 0.4 - - - -
212E ALA* 1.3 79.7 - - - +
214E GLU* 1.3 73.1 + - + +
215E THR 3.5 0.4 - - - -
216E GLY* 4.1 6.5 + - - -
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Residues in contact with GLU 214 (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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183E TYR* 4.2 19.6 + - - -
186E ILE* 3.3 35.6 - - + +
187E LYS* 4.8 3.5 + - - +
190E LYS* 3.3 32.6 - - + +
210E VAL* 3.0 24.9 + - + +
213E ARG* 1.3 82.6 - - + +
215E THR* 1.3 66.1 + - - +
216E GLY* 3.4 0.6 - - - -
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Residues in contact with THR 215 (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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186E ILE* 5.0 7.2 + - - +
189E LEU* 5.0 11.6 - - + +
190E LYS* 5.1 9.5 + - - +
194E ILE 3.3 26.5 - - - +
195E ARG* 3.7 9.1 - - - +
196E VAL* 3.3 33.0 - - + +
211E LEU* 2.9 32.1 + - - +
214E GLU* 1.3 80.6 - - - +
216E GLY* 1.3 56.9 + - - +
217E GLY 3.7 0.2 - - - -
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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