Contacts of the helix formed by residues 204 - 212 (chain E) in PDB entry 1M54
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 204 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E PRO* 3.1 33.0 - - + -
199E SER 4.8 2.2 - - - +
200E PRO 3.2 24.2 - - - +
202E SER* 3.8 10.5 - - - +
203E HIS* 1.3 85.9 - - + +
205E GLY* 1.3 54.6 + - - +
207E ALA* 3.0 21.1 - - + +
208E TRP* 2.7 44.5 + - + +
219E ILE* 5.0 1.6 - - + -
221E ASP* 3.4 16.6 - - - +
223E TYR* 6.2 1.1 - - + -
308E TYR* 6.0 2.0 - - - +
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Residues in contact with GLY 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E THR* 4.8 2.2 - - - +
201E GLU* 2.9 40.6 + - - +
203E HIS 3.6 1.8 - - - -
204E VAL* 1.3 74.7 - - - +
206E VAL* 1.3 56.4 + - - +
207E ALA 2.5 18.1 + - - +
208E TRP* 2.8 20.9 + - - +
209E ARG* 3.6 15.6 + - - -
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Residues in contact with VAL 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E VAL* 5.5 3.1 - - + -
189E VAL* 5.4 11.2 - - + -
190E ARG 5.3 2.9 - - - +
191E THR* 4.3 28.3 - - + +
201E GLU* 4.9 2.9 + - - +
205E GLY* 1.3 71.2 - - - +
207E ALA* 1.3 59.2 + - - +
208E TRP 3.4 0.2 - - - -
209E ARG* 3.4 31.6 - - + +
210E LEU* 3.0 37.4 + - + +
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Residues in contact with ALA 207 (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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143E ILE* 4.4 7.7 - - + +
145E PRO* 5.9 0.2 - - + -
168E VAL* 4.8 14.1 - - + +
204E VAL* 3.0 31.2 - - - +
205E GLY 2.5 4.9 + - - -
206E VAL* 1.3 73.8 - - - +
208E TRP* 1.3 50.7 + - - +
210E LEU* 2.4 32.1 + - - +
211E LYS* 2.6 17.7 + - - +
219E ILE* 3.1 26.2 - - + +
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Residues in contact with TRP 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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200E PRO 3.6 18.7 + - - -
201E GLU* 5.1 1.1 - - + -
204E VAL* 2.7 37.2 + - + -
205E GLY* 2.8 16.2 + - - +
207E ALA* 1.3 67.7 - - - +
209E ARG* 1.3 65.5 + - - +
210E LEU 2.7 10.2 + - - -
211E LYS* 4.1 22.5 - - + +
212E ASN* 3.3 29.0 + - - +
219E ILE* 3.3 45.3 - - + -
221E ASP* 5.2 8.1 - - + -
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Residues in contact with ARG 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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201E GLU* 3.8 29.5 + - - +
205E GLY 3.8 21.0 + - - -
206E VAL* 3.4 32.2 + - + +
207E ALA 3.3 0.6 - - - -
208E TRP* 1.3 80.9 - - - +
210E LEU* 1.3 58.5 + - - +
212E ASN* 5.2 0.2 - - - -
213E GLU* 2.5 44.6 - - - +
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Residues in contact with LEU 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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143E ILE* 3.7 21.3 - - + -
166E ILE* 4.5 16.8 - - + -
168E VAL* 4.9 9.4 - - + -
189E VAL* 5.6 6.7 - - + -
206E VAL* 3.0 30.5 - - + +
207E ALA* 2.4 24.2 - - - +
208E TRP 2.7 2.2 - - - -
209E ARG* 1.3 82.7 - - - +
211E LYS* 1.3 54.4 + - - +
212E ASN 2.8 1.1 - - - -
213E GLU* 2.6 10.3 + - + -
214E ILE* 2.5 59.2 + - + -
217E SER* 4.3 1.1 - - - -
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Residues in contact with LYS 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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143E ILE* 4.1 2.9 - - + +
207E ALA 2.6 15.9 + - - +
208E TRP* 4.1 26.9 - - + +
210E LEU* 1.3 72.0 - - - +
212E ASN* 1.3 65.1 + - - +
214E ILE 3.1 8.5 - - - +
215E PRO* 5.0 0.5 - - - +
216E ASN 5.2 0.2 + - - -
217E SER* 2.8 38.7 + - - +
218E HIS* 3.4 27.4 + - - +
219E ILE* 3.3 36.9 + - + +
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Residues in contact with ASN 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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208E TRP* 3.3 12.3 + - - +
209E ARG* 5.2 0.2 - - - -
210E LEU 2.8 0.8 + - - -
211E LYS* 1.3 88.5 - - - +
213E GLU* 1.3 75.5 + - - +
214E ILE 3.4 3.5 + - - -
215E PRO* 4.3 4.7 - - - +
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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