Contacts of the helix formed by residues 201 - 213 (chain E) in PDB entry 3HYW
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 ALA 201 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208C ASP* 4.3 21.8 - - + +
211C ALA* 4.2 9.7 - - + +
212C GLU* 5.1 9.3 - - + +
199E ILE 3.3 0.8 + - - -
200E GLY* 1.3 68.6 - - - -
202E SER* 1.3 56.2 + - - +
203E LYS* 3.3 3.7 + - - -
204E ARG* 3.4 13.3 + - + -
205E LEU* 3.0 28.8 + - + +
372E THR* 4.3 15.1 + - - +
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Residues in contact with SER 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E GLY* 2.7 27.8 + - - -
194E PHE* 3.8 18.2 - - - -
198E GLY* 3.5 2.6 - - - -
199E ILE* 2.8 33.4 + - - -
200E GLY 3.1 2.9 + - - -
201E ALA* 1.3 76.2 - - - +
203E LYS* 1.3 57.9 + - - +
205E LEU* 4.1 6.1 - - - -
206E VAL* 2.9 35.3 + - - +
358E PHE* 3.8 13.7 - - - -
372E THR* 4.7 0.6 - - - +
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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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204A ARG* 6.3 0.2 - - - +
190E TYR* 3.5 49.9 - - + -
191E LEU 3.2 18.8 + - - +
200E GLY 4.9 0.6 + - - -
201E ALA 3.3 1.0 - - - -
202E SER* 1.3 80.1 + - - +
204E ARG* 1.3 62.5 + - - +
206E VAL 3.9 0.3 - - - -
207E GLU* 3.0 54.8 + - - +
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Residues in contact with ARG 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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204A ARG* 3.2 48.8 + - - +
203C LYS* 6.1 0.6 - - - +
204C ARG* 3.2 50.5 + - - +
207C GLU* 3.2 28.5 + - - +
208C ASP* 2.6 46.9 + - - +
201E ALA* 3.4 17.1 + - + +
203E LYS* 1.3 77.8 - - - +
205E LEU* 1.3 57.0 + - - +
208E ASP* 3.0 33.2 + - - +
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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 ALA* 3.0 18.4 + - + +
202E SER* 3.7 4.3 - - - +
203E LYS 3.3 0.2 - - - -
204E ARG* 1.3 77.0 - - - +
206E VAL* 1.3 74.6 + - + +
208E ASP* 3.5 5.7 + - - +
209E LEU* 3.1 42.3 + - + +
351E PHE* 5.5 2.7 - - + -
356E GLY* 5.7 1.1 - - - -
358E PHE* 4.0 27.4 - - + -
372E THR* 4.5 19.5 - - - +
373E LYS 4.7 15.5 - - - +
374E MET* 4.9 15.9 - - + -
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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
----------------------------------------------------------
161E TYR* 3.5 34.3 - - + -
165E LEU* 6.0 0.4 - - + -
191E LEU* 4.0 17.5 - - + -
192E GLY* 4.2 3.4 - - - +
194E PHE* 4.1 24.7 - - + -
202E SER 2.9 23.5 + - - +
203E LYS 4.2 0.9 - - - +
205E LEU* 1.3 84.7 - - + +
207E GLU* 1.3 62.2 + - - +
209E LEU* 3.3 8.8 + - + +
210E PHE* 2.9 38.5 + - + +
351E PHE* 6.3 1.1 - - + -
358E PHE* 4.6 2.9 - - + -
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Residues in contact with GLU 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG* 2.7 36.9 + - - +
190E TYR* 5.1 1.7 - - - +
191E LEU* 4.1 26.3 + - + +
203E LYS* 3.0 51.0 + - - +
204E ARG* 3.6 4.0 - - - +
206E VAL* 1.3 76.4 - - - +
208E ASP* 1.3 56.5 + - - +
210E PHE* 3.4 2.6 + - - +
211E ALA* 2.9 30.7 + - - +
217E TRP* 4.2 27.9 + - + +
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Residues in contact with ASP 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ALA* 3.7 19.4 - - + +
204A ARG* 2.5 45.9 + - - +
204E ARG* 3.0 19.2 + - - +
205E LEU* 3.8 5.9 - - - +
206E VAL 3.3 0.2 - - - -
207E GLU* 1.3 73.6 - - - +
209E LEU* 1.3 60.1 + - - +
211E ALA* 3.3 6.0 + - - +
212E GLU* 2.8 44.4 + - - +
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Residues in contact with LEU 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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165E LEU* 4.4 12.1 - - + -
205E LEU* 3.1 23.4 + - + +
206E VAL* 3.4 16.2 - - + +
208E ASP* 1.3 77.6 - - - +
210E PHE* 1.3 63.5 + - + +
212E GLU* 3.3 10.3 + - - +
213E ARG* 3.1 66.3 + - - +
351E PHE* 3.4 37.2 - - + -
374E MET* 3.6 28.0 - - + -
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Residues in contact with PHE 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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161E TYR* 3.6 26.2 - + - -
164E ALA* 4.8 3.4 - - + -
165E LEU* 3.7 31.9 - - + -
184E PHE* 3.5 42.4 - + + -
191E LEU* 3.7 21.3 - - + -
206E VAL* 2.9 22.6 + - + +
207E GLU 3.7 4.5 - - - +
209E LEU* 1.3 78.1 - - + +
211E ALA* 1.3 57.2 + - - +
213E ARG* 3.4 1.5 + - - -
214E ASN* 3.0 8.8 + - - -
215E ILE* 2.8 69.5 + - + +
217E TRP* 3.9 12.6 - + + -
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Residues in contact with ALA 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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200A GLY* 3.6 37.1 + - - +
201A ALA* 4.3 2.9 - - - +
367A ARG* 5.9 0.7 + - - -
370A VAL* 4.4 2.8 - - - +
207E GLU 2.9 18.1 + - - +
208E ASP* 3.6 9.4 - - - +
209E LEU 3.2 0.2 - - - -
210E PHE* 1.3 74.5 - - - +
212E GLU* 1.3 64.1 + - - +
213E ARG 3.3 0.7 + - - -
214E ASN* 3.3 11.8 + - - +
217E TRP* 5.7 1.7 - - - +
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Residues in contact with GLU 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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200A GLY* 4.2 8.7 - - - -
201A ALA* 4.9 7.0 - - + +
369A ARG* 5.2 2.8 - - - -
370A VAL* 3.4 31.5 + - + +
372A THR* 5.5 4.5 + - - +
208E ASP* 2.8 35.8 + - + +
209E LEU* 3.3 14.0 + - - +
211E ALA* 1.3 72.9 - - - +
213E ARG* 1.3 77.7 + - - +
214E ASN* 3.4 0.6 + - - +
374E MET* 5.6 2.8 - - - +
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Residues in contact with ARG 213 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ARG 4.9 0.8 - - - +
165E LEU* 3.6 27.6 + - - +
168E HIS* 3.3 41.5 + - + +
172E LYS* 5.7 1.8 - - - +
177E ARG* 3.1 18.9 + - - -
209E LEU* 3.1 46.0 + - - +
210E PHE 4.3 1.6 - - - +
212E GLU* 1.3 95.3 + - - +
214E ASN* 1.3 67.8 + - - +
215E ILE* 3.3 8.5 + - + +
351E PHE* 5.0 4.4 - - - +
354E ASP* 3.5 30.9 + - - -
374E MET* 5.1 2.8 - - - +
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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