Contacts of the helix formed by residues 195 - 206 (chain E) in PDB entry 3P05
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 ASN 195 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155E GLN* 2.9 39.3 + - - +
156E GLY 3.2 27.5 + - - +
157E PRO* 3.5 22.7 + - + -
158E LYS 5.2 0.2 - - - -
159E GLU 4.2 2.2 + - - -
194E ALA* 1.3 74.1 - - - +
196E PRO* 1.3 65.8 - - + +
197E ASP* 3.4 11.1 + - - +
198E CYS* 2.9 23.5 + - - +
199E LYS* 2.8 30.7 + - - +
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Residues in contact with PRO 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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157E PRO* 5.9 1.3 - - + -
194E ALA 3.8 0.6 - - - +
195E ASN* 1.3 85.5 - - + +
197E ASP* 1.3 70.4 + - - +
199E LYS* 3.7 9.9 - - + +
200E THR* 3.0 29.9 + - - +
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Residues in contact with ASP 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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157E PRO 5.3 4.2 - - - +
195E ASN* 3.4 10.2 + - - +
196E PRO* 1.3 79.5 - - - +
198E CYS* 1.3 66.3 + - - +
200E THR* 3.3 6.2 + - - +
201E ILE* 3.1 30.1 + - + +
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Residues in contact with CYS 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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155E GLN* 3.5 35.0 - - - +
161E PHE* 4.2 7.4 - - + -
194E ALA* 4.3 4.7 - - + -
195E ASN* 2.9 16.5 + - - +
197E ASP* 1.3 79.7 - - - +
199E LYS* 1.3 58.6 + - - +
201E ILE* 3.1 7.8 + - - +
202E LEU* 2.8 35.6 + - + +
218E CYS* 3.7 38.6 - - - -
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Residues in contact with LYS 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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191E VAL* 3.7 14.6 - - + +
192E GLN* 3.0 43.0 + - - +
194E ALA* 3.9 17.6 + - + +
195E ASN 2.8 17.1 + - - +
196E PRO* 3.7 9.2 - - + +
198E CYS* 1.3 76.1 - - - +
200E THR* 1.3 57.4 + - - +
202E LEU* 3.4 6.3 + - - +
203E LYS* 3.0 49.2 + - + +
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Residues in contact with THR 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 PRO* 3.0 19.2 + - - +
197E ASP* 3.5 6.7 - - - +
199E LYS* 1.3 74.3 - - - +
201E ILE* 1.3 66.8 + - + +
203E LYS* 3.3 7.8 + - - +
204E ALA* 3.2 21.7 + - + +
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Residues in contact with ILE 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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197E ASP* 3.1 17.0 + - + +
198E CYS* 3.1 14.5 + - - +
200E THR* 1.3 79.8 - - + +
202E LEU* 1.3 61.7 + - - +
204E ALA* 3.6 8.6 + - - +
205E LEU* 3.5 18.9 + - - +
217E ALA* 3.6 44.6 - - + +
218E CYS* 4.3 9.0 - - + -
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Residues in contact with LEU 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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161E PHE* 3.8 29.8 - - + -
191E VAL* 4.0 26.1 - - + +
194E ALA* 4.2 11.4 - - + -
198E CYS 2.8 26.9 + - - +
199E LYS 3.8 4.3 - - - +
201E ILE* 1.3 71.9 - - - +
203E LYS* 1.3 64.3 + - - +
205E LEU* 3.3 23.9 + - + +
206E GLY 3.9 4.0 + - - +
214E MET* 3.8 44.0 - - + +
217E ALA* 4.9 0.7 - - + -
218E CYS* 3.5 21.3 - - - -
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Residues in contact with LYS 203 (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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191E VAL* 4.4 19.2 - - + +
192E GLN* 6.4 0.4 - - - +
199E LYS* 3.0 34.7 + - + +
200E THR* 3.3 7.6 + - - +
202E LEU* 1.3 75.0 - - - +
204E ALA* 1.3 63.7 + - - +
206E GLY* 3.1 15.6 + - - -
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Residues in contact with ALA 204 (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 THR* 3.2 10.6 + - + +
201E ILE* 3.6 13.2 - - - +
203E LYS* 1.3 79.1 - - - +
205E LEU* 1.3 61.2 + - - +
206E GLY* 3.3 1.0 + - - -
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Residues in contact with LEU 205 (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 ILE 3.5 9.8 + - - +
202E LEU* 3.3 17.4 + - + +
203E LYS 3.2 1.0 - - - -
204E ALA* 1.3 77.8 - - - +
206E GLY* 1.3 66.1 + - - +
207E PRO 4.6 2.1 - - - +
209E ALA* 4.3 11.3 - - + +
213E GLU* 4.0 11.7 - - + +
214E MET* 3.9 31.4 - - + +
217E ALA* 3.9 28.3 - - + -
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Residues in contact with GLY 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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202E LEU 3.9 3.4 + - - +
203E LYS 3.1 15.9 + - - -
204E ALA 3.2 1.9 - - - -
205E LEU* 1.3 81.4 - - - +
207E PRO* 1.3 79.3 - - - +
209E ALA* 3.7 14.9 - - - +
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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