Contacts of the helix formed by residues 199 - 209 (chain E) in PDB entry 2P1N
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 SER 199 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173E GLY 4.1 8.0 + - - -
174E HIS* 5.8 1.3 - - - -
176E LEU* 5.4 0.6 - - - +
177E SER* 3.8 20.6 + - - -
197E GLU* 3.9 0.6 + - - -
198E VAL* 1.3 79.4 - - - +
200E PHE* 1.3 64.5 + - - +
201E SER* 3.7 8.5 + - - -
202E ALA* 3.3 18.7 + - - +
203E LEU 2.9 18.9 + - - -
205E ARG* 5.3 0.2 + - - -
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Residues in contact with PHE 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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197E GLU* 5.3 5.9 + - - +
198E VAL* 3.4 6.4 + - - +
199E SER* 1.3 71.8 + - - +
201E SER* 1.3 66.6 + - - +
203E LEU* 3.3 11.2 + - + +
204E GLU* 2.7 45.2 + - - +
222E VAL* 4.2 15.7 - - + -
223E PRO* 5.6 0.4 - - + -
226E LYS* 3.7 57.0 - - + +
229E THR* 3.6 18.6 - - + -
230E LEU* 3.3 40.8 - - + -
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Residues in contact with SER 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E SER* 3.7 6.6 + - - -
200E PHE* 1.3 85.0 - - - +
202E ALA* 1.3 58.0 + - - +
204E GLU* 3.8 7.5 - - - +
205E ARG* 3.0 48.3 + - - +
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Residues in contact with ALA 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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176E LEU* 4.0 14.1 - - + +
177E SER* 3.4 31.4 - - - +
199E SER* 3.3 15.0 + - - +
200E PHE 3.1 1.0 - - - -
201E SER* 1.3 76.9 + - - +
203E LEU* 1.3 60.6 + - - +
205E ARG* 3.2 23.1 + - - +
206E LEU* 2.7 32.2 + - - +
209E ARG* 4.8 0.5 + - - -
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Residues in contact with LEU 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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176E LEU* 3.7 27.4 - - + +
189E LEU* 4.3 15.5 - - + -
191E ILE* 4.9 5.2 - - + -
198E VAL* 3.8 13.0 - - + -
199E SER 2.9 16.7 + - - +
200E PHE* 3.6 10.1 - - + +
202E ALA* 1.3 75.4 - - - +
204E GLU* 1.3 64.9 + - - +
206E LEU* 3.2 4.9 + - + +
207E VAL* 3.0 37.2 + - + +
216E LEU* 4.5 6.3 - - + -
218E LEU* 4.1 11.9 - - + -
222E VAL* 4.2 15.7 - - + -
230E LEU* 3.5 34.1 - - + -
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Residues in contact with GLU 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 PHE* 2.7 31.1 + - + +
201E SER* 3.8 7.2 - - - +
203E LEU* 1.3 75.5 - - - +
205E ARG* 1.3 59.9 + - - +
207E VAL* 3.4 2.8 + - - +
208E THR* 2.9 34.6 + - - +
229E THR* 3.4 27.3 - - + +
230E LEU* 3.9 18.8 - - + -
233E ARG* 2.8 45.7 + - + +
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Residues in contact with ARG 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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181E ASP* 5.5 8.8 + - - -
199E SER* 5.3 0.2 + - - -
201E SER* 3.0 23.8 + - - +
202E ALA* 3.6 34.0 + - - +
204E GLU* 1.3 78.9 - - + +
206E LEU* 1.3 61.6 + - - +
208E THR* 3.3 7.5 + - + +
209E ARG* 3.2 43.5 + - - +
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Residues in contact with LEU 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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176E LEU* 4.0 24.2 - - + -
179E PHE* 3.9 26.2 - - + -
183E TYR* 4.4 8.3 - - + -
186E LEU* 4.2 22.4 - - + -
189E LEU* 4.5 6.1 - - + -
202E ALA 2.7 17.7 + - - +
203E LEU* 3.4 8.5 - - + +
205E ARG* 1.3 74.4 - - - +
207E VAL* 1.3 65.8 + - + +
208E THR 3.0 1.5 + - - -
209E ARG* 3.5 25.9 + - - +
210E CYS* 3.0 38.9 + - - -
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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
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186E LEU* 6.2 2.7 - - + -
189E LEU* 6.0 0.4 - - + -
203E LEU* 3.0 30.9 + - + +
204E GLU* 4.0 4.7 - - - +
206E LEU* 1.3 78.5 - - + +
208E THR* 1.3 65.2 + - - +
210E CYS* 3.3 16.6 + - - +
213E LEU* 3.8 17.8 - - + +
216E LEU* 3.8 31.2 - - + -
230E LEU* 4.2 11.9 - - + +
233E ARG* 3.9 18.0 - - + +
234E ALA* 3.5 29.9 - - + +
236E GLN* 5.7 0.5 + - - -
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Residues in contact with THR 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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204E GLU* 2.9 21.9 + - - -
205E ARG* 3.7 9.0 - - + +
206E LEU 3.0 0.8 - - - -
207E VAL* 1.3 82.9 - - - +
209E ARG* 1.3 60.5 + - + +
210E CYS 3.6 3.5 + - - -
211E PRO* 5.0 2.9 - - - +
233E ARG* 3.1 56.5 + - + +
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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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179E PHE* 3.3 25.9 + - - +
180E PRO 2.9 22.2 + - - -
181E ASP* 3.3 34.7 + - - +
183E TYR* 2.9 21.1 + - - +
184E THR* 3.3 23.3 - - + +
202E ALA 4.8 0.4 + - - -
205E ARG* 3.2 49.3 + - - +
206E LEU* 3.5 20.3 - - - +
208E THR* 1.3 81.5 - - + +
210E CYS* 1.3 56.3 + - - +
211E PRO* 3.4 8.5 - - - +
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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