Contacts of the helix formed by residues 167 - 182 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B SER* 1.3 70.5 - - - +
168B ASN* 1.3 62.6 + - - +
169B VAL 3.5 2.2 - - - -
170B ARG* 2.6 56.8 + - + +
171B GLY* 3.2 13.2 + - - -
325B ARG* 4.6 13.0 - - + +
326B LEU 3.1 12.8 + - - +
327B GLN* 3.4 14.9 + - - +
328B THR* 2.9 49.6 + - - +
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Residues in contact with ASN 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ASN 4.9 0.4 + - - -
166B SER* 3.0 29.1 + - - +
167B GLU* 1.3 69.6 - - - +
169B VAL* 1.3 66.6 + - - +
171B GLY 3.3 0.5 + - - -
172B ALA* 3.0 27.5 + - - +
197B MET* 3.8 15.0 - - - +
198B THR* 4.3 7.9 - - - +
201B GLU* 2.9 38.6 + - + +
202B ARG* 2.9 43.3 + - + +
280B PHE* 3.6 11.1 - - - -
325B ARG* 3.7 3.2 - - - +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU 3.5 0.4 - - - -
168B ASN* 1.3 74.0 - - - +
170B ARG* 1.3 63.3 + - - +
173B ARG* 3.0 24.6 + - + +
201B GLU* 3.5 40.6 - - + +
204B LYS* 4.1 29.4 - - + +
205B GLY* 3.4 21.9 - - - -
208B ALA* 5.6 4.5 - - + -
325B ARG* 6.0 0.4 - - - +
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Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 2.6 52.3 + - + +
168B ASN 3.3 0.4 - - - -
169B VAL* 1.3 79.9 - - - +
171B GLY* 1.3 64.9 + - - +
173B ARG* 3.8 7.9 - - - +
174B THR* 3.0 34.5 + - - +
327B GLN* 5.6 2.0 - - - +
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Residues in contact with GLY 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B GLU 3.2 10.7 + - - -
168B ASN 3.9 1.8 - - - -
169B VAL 3.3 0.4 - - - -
170B ARG* 1.3 79.5 - - - +
172B ALA* 1.3 56.6 + - - +
174B THR* 3.3 6.7 + - - -
175B ALA* 3.0 27.5 + - - +
280B PHE* 4.1 6.1 - - - -
296B VAL* 4.2 13.8 - - - +
328B THR* 3.8 20.3 + - - -
330B PHE* 5.3 1.1 - - - +
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ASN 3.0 17.8 + - - +
169B VAL 3.9 2.7 - - - +
171B GLY* 1.3 73.4 - - - +
173B ARG* 1.3 65.3 + - - +
175B ALA* 3.0 5.1 + - - +
176B VAL* 3.0 30.0 + - - +
202B ARG* 3.2 32.8 - - - +
205B GLY* 4.1 3.1 - - - -
206B PHE 4.2 0.2 - - - +
250B LEU* 3.9 14.4 - - + -
280B PHE* 3.7 13.7 - - + -
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Residues in contact with ARG 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B VAL* 3.0 21.5 + - + +
170B ARG* 3.8 8.1 - - - +
172B ALA* 1.3 75.7 - - - +
174B THR* 1.3 52.7 + - - +
177B GLU* 2.5 59.8 + - - +
205B GLY* 3.4 18.7 + - - +
208B ALA* 4.4 21.4 + - - +
209B ALA* 3.7 20.0 - - + +
212B ALA* 3.7 24.5 - - - +
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Residues in contact with THR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ARG* 3.0 25.2 + - - +
171B GLY* 3.6 6.9 - - - -
172B ALA 3.2 0.2 - - - -
173B ARG* 1.3 74.2 - - - +
175B ALA* 1.3 66.2 + - - +
177B GLU* 3.6 13.5 + - - +
178B TYR* 3.2 20.1 + - - +
330B PHE* 3.9 32.5 - - + -
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B GLY 3.0 14.7 + - - +
172B ALA 3.0 5.2 + - - +
174B THR* 1.3 77.9 - - - +
176B VAL* 1.3 63.2 + - - +
178B TYR* 3.2 16.8 - - - +
179B LEU* 3.3 5.0 + - - +
250B LEU* 4.3 9.9 - - + -
278B VAL* 3.6 33.9 - - + +
296B VAL* 4.4 9.0 - - + -
330B PHE* 3.7 25.4 - - + -
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ALA 3.0 18.5 + - - +
175B ALA* 1.3 74.9 - - - +
177B GLU* 1.3 65.1 + - - +
178B TYR 3.1 1.1 - - - -
179B LEU* 3.1 10.7 + - + +
180B ILE* 2.9 31.0 + - + +
187B ILE* 4.5 8.7 - - + -
206B PHE* 3.7 35.0 - - + -
209B ALA* 3.5 23.1 - - + -
210B MET* 4.1 16.4 - - - -
250B LEU* 4.1 21.8 - - + -
278B VAL* 5.1 0.4 - - + -
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Residues in contact with GLU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B ARG* 2.5 58.4 + - - +
174B THR* 3.9 13.7 + - - +
175B ALA 3.4 0.2 - - - -
176B VAL* 1.3 75.6 - - - +
178B TYR* 1.3 52.7 + - - +
180B ILE* 3.1 12.4 + - + +
181B ALA* 2.7 36.4 + - - +
209B ALA* 3.9 13.7 - - + +
212B ALA* 5.3 3.3 - - - +
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Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B THR 3.2 5.9 + - - +
175B ALA 3.2 9.4 - - - +
176B VAL 3.1 0.8 - - - -
177B GLU* 1.3 78.0 - - - +
179B LEU* 1.3 69.2 + - + +
181B ALA* 3.4 8.0 + - + +
182B ARG* 3.2 63.2 + - + +
278B VAL* 4.2 10.8 - - + -
294B PRO* 3.6 26.7 - - + +
330B PHE* 3.6 33.9 - + + -
332B THR* 3.8 22.7 + - + -
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ALA 3.3 2.6 + - - +
176B VAL* 3.1 13.2 + - + +
178B TYR* 1.3 84.9 - - + +
180B ILE* 1.3 63.0 + - - +
182B ARG* 3.2 7.8 + - - +
184B HIS* 3.2 45.9 + - + +
187B ILE* 3.9 18.4 - - + -
248B ALA* 3.8 18.2 - - + -
249B LEU 3.8 17.7 - - - +
250B LEU 4.7 0.2 - - - +
276B GLU* 4.2 20.0 - - + +
277B ILE 5.0 0.4 - - - +
278B VAL* 3.6 42.4 - - + -
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Residues in contact with ILE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B VAL* 2.9 31.5 + - + +
177B GLU* 3.5 13.7 - - + +
179B LEU* 1.3 72.1 - - - +
181B ALA* 1.3 62.2 + - - +
183B GLY* 2.9 21.3 + - - -
184B HIS 3.8 8.0 + - - +
187B ILE* 3.7 15.5 - - + -
209B ALA 3.9 22.7 - - - +
210B MET* 4.1 9.2 - - - -
213B ALA* 4.0 24.0 - - + -
215B LEU* 4.0 14.1 - - + -
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Residues in contact with ALA 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B GLU 2.7 20.7 + - - +
178B TYR* 3.7 9.0 - - + +
180B ILE* 1.3 74.4 - - - +
182B ARG* 1.3 61.6 + - - +
183B GLY 3.2 0.7 + - - -
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Residues in contact with ARG 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B TYR* 3.2 56.6 + - + +
179B LEU* 3.5 12.8 - - - +
180B ILE 3.1 1.4 - - - -
181B ALA* 1.3 77.5 - - - +
183B GLY* 1.3 58.9 + - - +
184B HIS* 4.1 7.7 + - + -
276B GLU* 2.6 42.9 + - - -
291B PRO* 4.7 13.0 - - - +
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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