Contacts of the helix formed by residues 169 - 183 (chain E) in PDB entry 3A13
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 169 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D GLU* 4.5 4.9 - - - -
134D ARG* 3.6 16.0 + - - -
168E TYR* 1.3 75.5 - - - +
170E PRO* 1.3 71.4 - - - +
171E GLU* 3.1 16.1 + - - +
172E GLU* 3.0 37.3 + - - +
173E PHE* 2.9 29.3 + - - +
199E TYR* 3.4 7.6 - - - -
200E ASN* 3.6 3.1 - - - -
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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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134D ARG* 4.4 4.5 - - - +
169E SER* 1.3 88.5 - - - +
171E GLU* 1.3 67.1 + - - +
173E PHE* 3.2 8.1 + - + +
174E GLU* 2.9 24.1 + - - +
199E TYR 3.3 13.7 - - - +
200E ASN* 3.6 25.8 - - - +
201E ARG 4.5 0.2 - - - +
204E GLU* 4.0 24.5 - - + +
205E ARG* 4.1 17.7 - - + +
208E ILE* 3.7 27.5 - - + +
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Residues in contact with GLU 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D ARG* 3.0 29.0 + - - -
357D TYR* 5.5 1.3 - - - -
358D SER* 2.9 39.5 + - - -
169E SER* 3.1 14.0 + - - +
170E PRO* 1.3 81.8 - - - +
172E GLU* 1.3 64.7 + - + +
174E GLU* 3.5 18.8 + - - +
175E LYS* 4.1 4.9 + - - +
204E GLU* 5.1 1.6 - - - +
208E ILE* 4.4 12.3 - - + -
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Residues in contact with GLU 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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130D GLU* 5.7 0.3 - - - +
355D LYS* 5.1 7.6 + - - -
357D TYR* 5.6 4.9 - - - -
167E GLY 4.6 1.6 - - - +
168E TYR* 3.5 16.1 - - + +
169E SER* 3.0 37.8 + - - +
171E GLU* 1.3 77.3 - - + +
173E PHE* 1.3 62.1 + - - +
175E LYS* 3.8 10.4 + - - +
176E LEU* 3.8 10.0 + - - +
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Residues in contact with PHE 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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162E PRO* 3.6 27.1 - - + -
168E TYR* 3.8 27.1 - + + -
169E SER 2.9 17.4 + - - +
170E PRO* 3.4 7.9 - - + +
172E GLU* 1.3 77.0 - - - +
174E GLU* 1.3 67.8 + - - +
175E LYS 3.1 0.3 + - - -
176E LEU* 3.1 10.4 + - + +
177E ALA* 2.8 25.0 + - + +
188E MET* 3.7 34.8 - - + -
189E KCX 5.7 0.7 - - - -
190E ASP* 4.9 3.8 - - - -
205E ARG* 4.6 21.1 - - + -
208E ILE* 5.5 2.2 - - + -
209E MET* 3.4 34.1 - - + -
226E TRP* 4.6 10.5 - - - -
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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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170E PRO 2.9 10.1 + - - +
171E GLU* 3.6 14.4 - - - +
172E GLU 3.4 0.2 - - - -
173E PHE* 1.3 74.6 - - - +
175E LYS* 1.3 59.0 + - + +
177E ALA* 3.3 1.7 + - - -
178E TYR* 2.8 28.6 + - + +
208E ILE* 3.5 35.1 - - + +
211E LYS* 6.1 1.1 - - - +
212E ILE* 2.9 36.1 - - + +
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Residues in contact with LYS 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 GLU 4.1 4.6 + - - +
172E GLU* 3.8 8.4 + - - +
173E PHE 3.2 0.8 - - - -
174E GLU* 1.3 78.1 - - + +
176E LEU* 1.3 62.5 + - - +
178E TYR* 3.4 8.4 + - + +
179E ASP* 2.7 61.9 + - - +
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Residues in contact with LEU 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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162E PRO* 4.1 32.5 - - + -
163E LYS 5.4 3.1 - - - +
172E GLU 3.8 8.9 + - - +
173E PHE* 3.1 13.5 + - + +
175E LYS* 1.3 78.1 - - - +
177E ALA* 1.3 64.2 + - - +
179E ASP* 3.2 6.3 + - + +
180E LEU* 2.9 54.5 + - + +
188E MET* 4.6 1.8 - - + -
395E LEU* 4.3 10.5 - - + -
401E PRO* 4.3 22.2 - - + -
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Residues in contact with ALA 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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173E PHE* 2.8 22.1 + - + +
174E GLU 3.6 4.3 - - - +
176E LEU* 1.3 76.2 - - - +
178E TYR* 1.3 63.8 + - - +
181E LEU* 2.9 31.0 + - + +
188E MET* 3.8 30.3 - - + -
209E MET* 3.8 25.4 - - + -
212E ILE* 4.4 5.2 - - + -
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Residues in contact with TYR 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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174E GLU* 2.8 17.8 + - + +
175E LYS* 3.7 10.1 - - + +
177E ALA* 1.3 76.2 - - - +
179E ASP* 1.3 74.9 + - - +
182E SER* 2.7 50.4 + - - -
212E ILE* 3.9 21.0 - - + +
215E LYS* 3.9 28.0 - - + -
216E VAL* 3.5 22.1 - - + +
219E GLU* 2.7 33.4 + - - -
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Residues in contact with ASP 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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175E LYS* 2.7 54.7 + - - +
176E LEU* 3.8 6.8 - - + +
178E TYR* 1.3 94.5 - - - +
180E LEU* 1.3 63.5 + - + +
182E SER* 4.6 1.1 - - - -
183E ASN* 2.8 33.8 + - - +
401E PRO* 6.2 1.6 - - + -
402E ALA* 4.4 16.5 - - + +
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Residues in contact with LEU 180 (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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160E VAL* 4.1 15.3 - - + -
176E LEU* 2.9 36.0 + - + +
177E ALA 3.9 2.5 - - - +
179E ASP* 1.3 74.2 - - + +
181E LEU* 1.3 66.5 + - - +
183E ASN* 3.0 12.2 + - - -
184E GLY 3.4 1.0 + - - -
185E ALA* 3.3 24.2 + - + +
188E MET* 3.5 37.0 - - + -
394E THR* 3.9 17.0 - - + -
395E LEU* 4.1 4.0 - - + -
401E PRO* 3.6 39.0 - - + +
402E ALA 4.4 0.7 - - - +
405E ALA* 4.1 7.0 - - + +
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Residues in contact with LEU 181 (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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177E ALA 2.9 20.1 + - - +
180E LEU* 1.3 74.6 - - - +
182E SER* 1.3 62.5 + - - +
183E ASN 3.1 1.0 + - - -
184E GLY 3.3 3.5 + - - -
185E ALA* 3.2 22.4 - - + +
186E ASP 3.9 4.3 - - - +
187E TYR* 3.7 33.4 - - - +
188E MET* 4.0 8.1 - - + +
209E MET* 4.2 24.9 - - + -
212E ILE* 4.3 13.5 - - + -
213E ILE* 4.4 5.8 - - + -
216E VAL* 4.0 18.4 - - + -
220E THR* 5.1 0.5 - - - +
224E LYS* 3.0 44.7 + - + -
225E THR 4.7 1.6 - - - +
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Residues in contact with SER 182 (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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178E TYR* 2.7 51.4 + - - -
179E ASP* 3.9 1.3 - - - -
181E LEU* 1.3 77.6 - - - +
183E ASN* 1.3 71.5 + - - +
184E GLY 3.7 0.9 + - - -
216E VAL* 3.6 12.9 - - - +
219E GLU* 4.6 3.0 + - - -
220E THR* 4.2 17.9 - - - +
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Residues in contact with ASN 183 (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 ASP* 2.8 28.0 + - - +
180E LEU 3.0 9.3 + - - +
182E SER* 1.3 89.5 - - - +
184E GLY* 1.3 55.3 + - - +
185E ALA 3.7 0.4 - - - -
402E ALA* 3.6 24.9 - - - +
405E ALA* 3.2 4.1 - - + +
406E ARG* 2.9 67.9 + - - +
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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