Contacts of the helix formed by residues 167 - 182 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166F SER* 1.3 72.4 - - - +
168F ASN* 1.3 62.3 + - - +
169F VAL 3.4 2.2 + - - -
170F ARG* 2.8 55.7 + - + +
171F GLY* 3.1 14.9 + - - -
325F ARG* 4.7 14.2 - - + +
326F LEU 3.0 11.8 + - - +
327F GLN* 3.2 19.0 + - - +
328F THR* 2.9 44.7 + - - +
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Residues in contact with ASN 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F ASN 5.0 0.6 + - - -
166F SER* 2.9 31.9 + - - +
167F GLU* 1.3 69.6 - - - +
169F VAL* 1.3 70.2 + - - +
171F GLY 3.5 0.2 + - - -
172F ALA* 3.0 24.8 + - - +
197F MET* 3.8 16.0 - - - +
198F THR* 4.2 9.6 - - - +
201F GLU* 2.7 39.7 + - + +
202F ARG* 2.8 44.5 + - + +
280F PHE* 3.6 11.4 - - - -
325F ARG* 4.4 1.0 - - - +
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Residues in contact with VAL 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F GLU 3.4 0.4 - - - -
168F ASN* 1.3 79.3 - - - +
170F ARG* 1.3 65.8 + - - +
173F ARG* 3.0 23.1 + - + +
201F GLU* 3.5 39.0 - - + +
204F LYS* 4.2 29.6 - - + +
205F GLY* 3.5 21.4 - - - +
208F ALA* 5.6 4.7 - - + -
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Residues in contact with ARG 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F GLU* 2.8 50.5 + - + +
168F ASN 3.3 0.4 - - - -
169F VAL* 1.3 81.6 - - - +
171F GLY* 1.3 63.9 + - - +
173F ARG* 3.6 7.2 + - - +
174F THR* 3.0 33.0 + - - +
327F GLN* 5.9 0.8 - - - +
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Residues in contact with GLY 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F GLU 3.1 13.0 + - - -
168F ASN 4.1 0.7 - - - -
169F VAL 3.3 0.2 - - - -
170F ARG* 1.3 80.9 - - - +
172F ALA* 1.3 57.5 + - - +
174F THR* 3.3 6.4 + - - -
175F ALA* 3.0 29.5 + - - +
280F PHE* 4.1 6.5 - - - -
296F VAL* 4.2 16.4 - - - +
328F THR* 4.1 14.6 + - - -
330F PHE* 5.2 0.3 - - - -
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Residues in contact with ALA 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F ASN 3.0 18.2 + - - +
169F VAL 3.7 2.5 - - - +
171F GLY* 1.3 75.2 - - - +
173F ARG* 1.3 60.3 + - - +
174F THR 3.2 0.3 + - - -
175F ALA* 3.2 4.6 + - - +
176F VAL* 2.8 33.9 + - - +
202F ARG* 3.4 28.3 - - - +
205F GLY* 4.1 4.5 - - - -
250F LEU* 4.0 9.0 - - + -
280F PHE* 3.7 20.7 - - + -
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Residues in contact with ARG 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F VAL* 3.0 17.6 + - + +
170F ARG* 3.8 8.3 - - - +
172F ALA* 1.3 76.8 - - - +
174F THR* 1.3 51.3 + - - +
177F GLU* 2.5 63.8 + - - +
205F GLY* 3.3 19.9 + - - +
208F ALA* 4.2 26.3 - - - +
209F ALA* 3.6 17.1 - - + +
212F ALA* 3.7 23.8 - - - +
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Residues in contact with THR 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F ARG* 3.0 25.6 + - - +
171F GLY* 3.6 7.5 - - - -
172F ALA 3.2 0.4 - - - -
173F ARG* 1.3 73.7 - - - +
175F ALA* 1.3 67.3 + - - +
177F GLU* 3.4 13.3 + - - +
178F TYR* 3.2 20.6 + - - +
330F PHE* 4.0 31.8 - - + -
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Residues in contact with ALA 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171F GLY 3.0 16.9 + - - +
172F ALA 3.8 3.4 - - - +
174F THR* 1.3 78.6 - - - +
176F VAL* 1.3 61.9 + - - +
178F TYR* 3.2 11.8 + - - +
179F LEU* 3.3 16.5 + - - +
250F LEU* 4.4 8.7 - - + -
278F VAL* 3.9 24.7 - - + +
296F VAL* 4.4 9.0 - - + -
330F PHE* 3.6 27.8 - - + -
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Residues in contact with VAL 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F ALA 2.8 19.8 + - - +
175F ALA* 1.3 76.2 - - - +
177F GLU* 1.3 61.9 + - - +
179F LEU* 3.2 7.8 + - + +
180F ILE* 3.1 31.4 + - + +
187F ILE* 4.6 8.5 - - + -
206F PHE* 3.6 36.1 - - + -
209F ALA* 3.6 22.7 - - + -
210F MET* 4.2 10.1 - - - -
250F LEU* 4.0 27.1 - - + -
278F VAL* 5.0 1.6 - - + -
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Residues in contact with GLU 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F ARG* 2.5 63.5 + - - +
174F THR* 3.9 13.6 + - - +
175F ALA 3.3 0.2 - - - -
176F VAL* 1.3 73.3 - - - +
178F TYR* 1.3 60.2 + - - +
180F ILE* 3.6 11.3 - - + +
181F ALA* 2.9 30.5 + - - +
209F ALA* 3.8 16.6 - - + +
212F ALA* 5.2 3.3 - - - +
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Residues in contact with TYR 178 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174F THR 3.2 7.9 + - - +
175F ALA 3.3 8.7 - - - +
176F VAL 3.1 0.6 - - - -
177F GLU* 1.3 79.9 - - - +
179F LEU* 1.3 67.7 + - + +
181F ALA* 3.5 7.0 + - + +
182F ARG* 3.2 60.9 + - + +
278F VAL* 4.2 10.1 - - + -
294F PRO* 3.7 26.8 - - + +
330F PHE* 3.6 31.9 - + + -
332F THR* 3.7 22.3 + - + +
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Residues in contact with LEU 179 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175F ALA 3.3 3.5 + - - +
176F VAL* 3.2 11.7 + - + +
178F TYR* 1.3 81.7 - - + +
180F ILE* 1.3 65.2 + - - +
182F ARG* 3.2 7.7 + - - +
184F HIS* 3.1 49.1 + - + +
187F ILE* 3.9 20.0 - - + -
248F ALA* 3.8 20.4 - - + -
249F LEU 4.0 11.9 - - - +
250F LEU 4.7 0.4 - - - +
276F GLU* 4.3 17.3 - - + +
277F ILE 5.2 0.4 - - - -
278F VAL* 3.4 44.9 - - + +
294F PRO* 6.2 0.2 - - + -
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Residues in contact with ILE 180 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176F VAL* 3.1 17.1 + - + +
177F GLU* 3.6 14.8 - - + +
178F TYR 3.3 0.2 - - - -
179F LEU* 1.3 73.8 - - - +
181F ALA* 1.3 61.9 + - - +
183F GLY* 2.9 21.0 + - - -
184F HIS 3.8 7.9 + - - +
187F ILE* 3.7 16.8 - - + -
209F ALA 3.6 29.6 - - - +
210F MET* 4.1 13.2 - - - -
213F ALA* 3.8 23.8 - - + -
215F LEU* 4.1 12.3 - - + -
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Residues in contact with ALA 181 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177F GLU 2.9 18.3 + - - +
178F TYR* 3.9 7.6 - - + +
179F LEU 3.4 0.4 - - - -
180F ILE* 1.3 77.8 - - - +
182F ARG* 1.3 60.7 + - - +
183F GLY* 3.5 0.6 + - - -
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Residues in contact with ARG 182 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178F TYR* 3.2 55.5 + - + +
179F LEU* 3.2 13.1 + - - +
180F ILE 3.0 1.4 - - - -
181F ALA* 1.3 78.7 - - - +
183F GLY* 1.3 56.9 + - - +
184F HIS* 3.7 8.3 + - + +
276F GLU* 2.7 43.9 + - - -
291F PRO* 4.6 12.7 - - - +
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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