Contacts of the helix formed by residues 163 - 179 (chain E) in PDB entry 2ZU6
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 163 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195B GLU* 2.8 31.8 + - - +
164E PHE* 1.3 62.2 + - - +
165E GLU 3.7 1.1 - - - +
166E LYS* 3.7 26.5 - - + +
167E THR* 2.9 31.1 + - - +
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Residues in contact with PHE 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLU* 3.3 18.2 + - - +
163E ALA* 1.3 74.0 - - - +
165E GLU* 1.3 86.1 + - + +
166E LYS 3.0 2.9 - - - -
167E THR* 2.9 21.1 + - - -
168E LEU* 3.0 45.5 + - + +
193E LEU* 5.2 4.3 - - + -
196E MSE 4.4 37.2 - - + -
199E GLY* 3.2 37.2 - - - -
200E VAL* 4.7 2.2 - - + -
203E LEU* 4.5 9.0 - - + -
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Residues in contact with GLU 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLU* 5.0 5.6 + - - +
138D THR* 5.5 11.6 + - - +
163E ALA* 4.7 0.4 - - - +
164E PHE* 1.3 94.9 - - + +
166E LYS* 1.3 60.1 + - + +
167E THR 3.4 0.2 - - - -
169E THR* 2.6 39.9 + - - +
203E LEU* 4.2 21.7 - - + +
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Residues in contact with LYS 166 (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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163E ALA* 3.8 26.2 - - + +
164E PHE 3.0 1.2 - - - -
165E GLU* 1.3 82.5 - - + +
167E THR* 1.3 57.9 + - - +
169E THR* 5.0 0.2 - - - -
170E PRO* 3.2 23.5 - - - +
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Residues in contact with THR 167 (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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163E ALA* 2.9 17.6 + - - +
164E PHE* 2.9 5.7 + - - -
166E LYS* 1.3 78.1 - - - +
168E LEU* 1.3 63.6 + - + +
170E PRO* 3.2 17.0 - - - +
171E ILE* 3.9 14.7 + - + +
187E MSE 6.2 0.7 - - + -
191E LEU* 3.6 36.1 - - + -
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Residues in contact with LEU 168 (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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164E PHE* 3.0 42.4 + - + +
167E THR* 1.3 81.3 - - + +
169E THR* 1.3 65.4 + - - +
171E ILE* 3.2 11.8 + - + +
172E ILE* 3.0 30.0 + - + +
188E LEU* 3.6 23.6 - - + -
191E LEU* 4.1 22.0 - - + -
193E LEU* 4.8 7.2 - - + -
200E VAL* 3.3 32.3 - - + -
203E LEU* 3.7 19.7 - - + -
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Residues in contact with THR 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E GLU* 2.6 25.8 + - - +
166E LYS* 5.0 0.2 - - - -
167E THR 3.3 0.2 - - - -
168E LEU* 1.3 77.2 - - - +
170E PRO* 1.3 64.8 - - + +
172E ILE* 3.0 5.1 + - - +
173E GLN* 2.9 55.6 + - + +
203E LEU* 3.6 23.8 - - - +
207E LEU* 4.2 15.3 - - + +
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Residues in contact with PRO 170 (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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282D ARG* 4.3 25.6 - - - +
331D LEU* 5.7 1.8 - - + -
166E LYS* 3.2 25.1 - - - +
167E THR* 3.2 10.1 - - - +
169E THR* 1.3 92.9 - - + +
171E ILE* 1.3 65.3 + - - +
173E GLN* 4.1 12.5 - - + +
174E GLU* 2.9 32.0 + - + +
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Residues in contact with ILE 171 (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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282D ARG* 5.6 7.0 - - - +
167E THR* 4.0 15.3 - - + +
168E LEU* 3.2 16.5 + - + +
169E THR 3.2 0.2 - - - -
170E PRO* 1.3 80.1 - - - +
172E ILE* 1.3 66.6 + - + +
174E GLU* 3.5 4.9 - - - +
175E TYR* 3.0 26.2 + - - +
178E HIS* 4.9 1.2 + - - -
184E VAL* 4.3 27.5 - - + +
187E MSE 3.6 55.2 - - + -
188E LEU* 4.2 18.4 - - + -
191E LEU* 4.6 11.0 - - + -
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Residues in contact with ILE 172 (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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168E LEU* 3.0 16.6 + - + +
169E THR 3.0 8.1 + - - +
171E ILE* 1.3 85.3 - - + +
173E GLN* 1.3 61.3 + - - +
175E TYR* 3.3 14.3 - - + +
176E PHE* 3.0 45.7 + - + -
184E VAL* 5.6 2.5 - - + -
200E VAL* 4.4 18.2 - - + +
203E LEU* 4.5 10.1 - - + -
204E ALA* 3.6 38.1 - - + +
207E LEU* 3.8 15.0 - - + -
222E LEU* 4.8 10.8 - - + -
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Residues in contact with GLN 173 (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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111D GLU* 3.9 23.0 + - - +
331D LEU* 3.9 29.3 - - + +
169E THR* 2.9 36.4 + - + +
170E PRO* 4.1 8.4 - - - +
172E ILE* 1.3 72.3 - - - +
174E GLU* 1.3 60.1 + - - +
176E PHE* 2.7 38.5 + - + +
177E GLU* 3.1 9.7 + - - +
207E LEU* 4.3 16.2 - - + +
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Residues in contact with GLU 174 (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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280D ASN 4.8 0.7 - - - +
282D ARG* 2.6 41.9 + - - +
329D THR* 2.9 27.4 + - - +
330D ASP* 5.8 0.2 - - - +
331D LEU* 3.7 22.4 + - + +
332D LEU* 2.8 23.7 - - - +
170E PRO* 2.9 28.1 + - + +
171E ILE* 3.5 4.5 - - - +
173E GLN* 1.3 74.4 - - - +
175E TYR* 1.3 63.7 + - - +
177E GLU* 3.0 8.5 + - - +
178E HIS* 2.8 39.6 + - + +
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Residues in contact with TYR 175 (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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171E ILE 3.0 14.1 + - - +
172E ILE* 3.3 14.6 - - + +
174E GLU* 1.3 75.5 - - - +
176E PHE* 1.3 72.3 + + - +
178E HIS* 3.4 11.1 + - + -
179E GLY* 2.7 53.7 + - - -
180E ASP 3.6 11.7 - - - -
181E THR* 3.8 18.9 - - - +
184E VAL* 3.7 25.8 - - + -
218E MSE 2.6 52.5 + - + +
219E THR* 4.9 0.2 - - - -
221E LYS* 4.4 4.0 - - - +
222E LEU* 3.7 32.1 + - + +
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Residues in contact with PHE 176 (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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352D ASN* 5.6 2.9 + - - -
172E ILE* 3.0 36.4 + - + -
173E GLN* 2.7 29.5 + - + +
175E TYR* 1.3 85.6 - + - +
177E GLU* 1.3 64.1 + - - +
204E ALA 4.5 1.8 - - - -
207E LEU* 4.0 18.2 - - + -
208E ALA* 4.3 9.4 - - + -
215E HIS* 3.3 55.7 + + + +
218E MSE 3.3 38.6 - - + +
219E THR* 3.3 19.7 - - - -
222E LEU* 6.3 0.4 - - + -
321E GLN* 5.0 0.2 - - - +
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Residues in contact with GLU 177 (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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330D ASP* 4.3 22.9 - - + +
331D LEU* 3.8 33.6 - - + +
334D ARG* 4.0 12.7 + - - -
351D THR* 3.9 2.1 + - - -
352D ASN* 4.2 11.1 + - - +
355D ASN* 3.2 26.9 + - - +
173E GLN 3.1 7.3 + - - +
174E GLU* 3.0 9.1 + - - +
176E PHE* 1.3 85.4 - - - +
178E HIS* 1.3 65.7 + - + +
179E GLY 3.4 0.3 + - - -
215E HIS* 5.2 7.1 - - - -
321E GLN* 3.4 16.6 - - - +
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Residues in contact with HIS 178 (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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280D ASN* 3.0 46.1 - - + +
281D THR* 3.9 11.9 - - + +
330D ASP* 5.9 1.8 - - - +
351D THR* 2.9 28.1 + - - +
171E ILE 4.9 1.0 + - - -
174E GLU* 2.8 37.8 + - + +
175E TYR* 3.4 25.6 + - + +
177E GLU* 1.3 74.0 - - + +
179E GLY* 1.3 58.0 + - - +
180E ASP* 3.0 51.0 + - + +
183E GLU* 3.7 19.3 + - + +
184E VAL* 4.8 1.7 - - + +
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Residues in contact with GLY 179 (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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351D THR* 4.3 4.3 - - - -
175E TYR* 2.7 43.5 + - - -
177E GLU 3.3 3.7 - - - -
178E HIS* 1.3 72.5 + - - +
180E ASP* 1.3 54.7 + - - +
181E THR* 3.5 7.6 + - - +
218E MSE 5.0 6.5 - - - -
321E GLN* 4.4 10.3 - - - -
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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