Contacts of the helix formed by residues 167 - 182 (chain E) in PDB entry 3EGC
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 GLU 167 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166E SER* 1.3 68.7 - - - +
168E ASN* 1.3 62.6 + - - +
169E VAL 3.5 1.8 - - - -
170E ARG* 2.4 58.1 + - + -
171E GLY* 3.2 14.0 + - - -
325E ARG* 4.7 13.6 - - + +
326E LEU 3.0 12.5 + - - +
327E GLN* 3.5 19.0 + - - +
328E THR* 3.1 44.4 + - - +
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Residues in contact with ASN 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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153E ASN 5.1 0.6 + - - -
166E SER* 3.1 29.4 + - - +
167E GLU* 1.3 70.1 - - - +
169E VAL* 1.3 72.3 + - - +
171E GLY 3.4 0.2 + - - -
172E ALA* 3.0 24.1 + - - +
197E MET* 3.8 13.7 - - - +
198E THR* 4.4 8.3 - - - +
201E GLU* 2.6 40.0 + - + +
202E ARG* 3.0 43.9 + - + -
280E PHE* 3.7 10.0 - - - -
325E ARG* 3.8 2.4 - - - +
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Residues in contact with VAL 169 (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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167E GLU 3.5 0.4 - - - -
168E ASN* 1.3 81.6 - - - +
170E ARG* 1.3 63.5 + - - +
172E ALA 3.1 0.2 + - - -
173E ARG* 3.0 22.5 + - + +
201E GLU* 3.6 36.5 + - + +
204E LYS* 4.2 29.2 - - + +
205E GLY* 3.6 24.4 - - - +
208E ALA* 5.6 3.8 - - + -
325E ARG* 6.0 0.4 - - - +
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Residues in contact with ARG 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E GLU* 2.4 55.0 + - + +
168E ASN 3.4 0.6 - - - -
169E VAL* 1.3 78.9 - - - +
171E GLY* 1.3 60.6 + - - +
173E ARG* 3.6 8.0 + - - +
174E THR* 2.9 32.8 + - - +
327E GLN* 5.5 2.2 - - - +
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Residues in contact with GLY 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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167E GLU* 3.2 12.2 + - - -
168E ASN 3.9 0.7 - - - -
169E VAL 3.2 0.2 + - - -
170E ARG* 1.3 77.4 - - - +
172E ALA* 1.3 56.9 + - - +
174E THR* 3.1 8.1 + - - -
175E ALA* 2.9 27.5 + - - +
280E PHE* 4.2 4.5 - - - -
296E VAL* 4.3 16.1 - - - +
328E THR* 3.9 18.6 + - - -
330E PHE* 5.3 0.5 - - - -
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Residues in contact with ALA 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 ASN 3.0 17.5 + - - +
169E VAL 3.6 2.7 - - - +
171E GLY* 1.3 77.5 - - - +
173E ARG* 1.3 59.0 + - - +
175E ALA* 4.0 4.5 - - - +
176E VAL* 3.1 30.3 + - - +
202E ARG* 3.2 29.2 - - - +
205E GLY* 4.2 4.0 - - - -
206E PHE 4.2 0.2 - - - +
250E LEU* 4.0 9.2 - - + -
280E PHE* 3.7 21.5 - - + -
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Residues in contact with ARG 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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169E VAL* 3.0 17.5 + - - +
170E ARG* 3.9 9.2 - - - +
172E ALA* 1.3 73.6 - - - +
174E THR* 1.3 61.7 + - - +
177E GLU* 2.6 57.2 + - - +
205E GLY* 3.5 22.3 + - - +
208E ALA* 4.2 28.4 + - - +
209E ALA* 3.9 12.5 - - + +
212E ALA* 3.8 23.0 - - - +
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Residues in contact with THR 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 ARG* 2.9 20.7 + - - +
171E GLY* 3.1 12.1 + - - -
173E ARG* 1.3 79.8 - - - +
175E ALA* 1.3 61.9 + - - +
177E GLU* 3.4 11.9 + - - +
178E TYR* 3.1 22.0 + - - +
330E PHE* 3.8 34.1 - - + -
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Residues in contact with ALA 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 GLY 2.9 15.2 + - - +
172E ALA 4.1 3.4 - - - +
173E ARG 3.3 0.2 - - - -
174E THR* 1.3 76.5 - - - +
176E VAL* 1.3 62.4 + - - +
178E TYR* 3.3 16.1 - - - +
179E LEU* 3.3 5.9 + - - +
250E LEU* 4.2 9.6 - - + -
278E VAL* 3.8 31.9 - - + +
279E SER 5.6 0.2 - - - +
296E VAL* 4.4 9.9 - - + -
330E PHE* 3.6 27.3 - - + -
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Residues in contact with VAL 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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172E ALA 3.1 18.4 + - - +
175E ALA* 1.3 74.6 - - - +
177E GLU* 1.3 60.7 - - - +
179E LEU* 3.1 9.3 + - + +
180E ILE* 2.9 37.1 + - + +
187E ILE* 4.7 8.5 - - + -
206E PHE* 3.7 29.6 - - + -
209E ALA* 3.5 24.5 - - + -
210E MET* 4.2 14.6 - - - -
250E LEU* 4.0 24.2 - - + -
278E VAL* 5.0 1.1 - - + -
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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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173E ARG* 2.6 61.1 + - - +
174E THR* 3.8 11.7 + - - +
176E VAL* 1.3 74.6 - - - +
178E TYR* 1.3 54.2 + - - +
180E ILE* 3.1 12.0 + - + +
181E ALA* 2.7 36.6 + - - +
209E ALA* 3.9 14.8 - - + +
212E ALA* 5.4 2.6 - - - +
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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 THR 3.1 12.9 + - - +
175E ALA 3.3 9.4 - - - +
176E VAL 3.2 0.2 - - - -
177E GLU* 1.3 77.9 - - - +
179E LEU* 1.3 67.4 + - + +
181E ALA* 3.4 7.7 + - + +
182E ARG* 3.2 61.0 + - + +
278E VAL* 4.2 10.1 - - + -
294E PRO* 3.7 27.9 - - + +
330E PHE* 3.7 27.8 - + + -
332E THR* 3.7 23.6 + - + +
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Residues in contact with LEU 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 ALA 3.3 2.4 + - - +
176E VAL* 3.1 11.9 + - + +
178E TYR* 1.3 83.6 - - + +
180E ILE* 1.3 64.8 + - - +
182E ARG* 3.3 5.8 + - - -
184E HIS* 3.1 41.6 + - + +
187E ILE* 4.1 20.9 - - + -
248E ALA* 3.7 28.5 - - + -
249E LEU 3.9 9.2 - - - +
250E LEU 4.7 0.4 - - - +
276E GLU* 4.2 20.4 - - + +
278E VAL* 3.4 44.9 - - + -
294E PRO* 6.2 0.2 - - + -
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Residues in contact with ILE 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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176E VAL* 2.9 36.8 + - + +
177E GLU* 3.1 12.3 + - + +
179E LEU* 1.3 73.8 - - - +
181E ALA* 1.3 57.7 + - - +
182E ARG 3.0 1.8 - - - -
183E GLY* 2.7 25.8 + - - -
184E HIS 3.8 6.5 + - - +
187E ILE* 3.7 15.5 - - + -
209E ALA 4.2 17.7 - - - +
210E MET* 3.9 11.7 - - - -
213E ALA* 4.1 23.1 - - + -
215E LEU* 3.8 15.9 - - + -
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Residues in contact with ALA 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 GLU 2.7 20.6 + - - +
178E TYR* 3.8 8.3 - - + +
179E LEU 3.4 0.2 - - - -
180E ILE* 1.3 73.7 - - - +
182E ARG* 1.3 59.8 + - + +
183E GLY 3.2 0.9 + - - -
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Residues in contact with ARG 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* 3.2 56.0 + - + +
179E LEU* 3.6 12.3 - - - +
180E ILE 3.0 1.4 - - - -
181E ALA* 1.3 76.5 - - - +
183E GLY* 1.3 59.8 + - - +
184E HIS* 3.6 8.7 + - + -
276E GLU* 2.7 43.1 + - - -
291E PRO* 4.7 12.2 - - - +
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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