Contacts of the helix formed by residues 167 - 182 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D SER* 1.3 70.4 - - - +
168D ASN* 1.3 56.1 + - - +
169D VAL 3.5 2.0 - - - -
170D ARG* 2.9 53.2 + - + +
171D GLY* 3.0 22.2 + - - -
325D ARG* 4.7 14.7 - - + +
326D LEU 3.1 14.2 + - - +
327D GLN* 3.4 15.9 + - - +
328D THR* 2.8 48.0 + - - +
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Residues in contact with ASN 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ASN 4.9 0.4 + - - -
166D SER* 3.0 27.2 + - - +
167D GLU* 1.3 70.0 - - - +
169D VAL* 1.3 67.3 + - - +
172D ALA* 3.0 27.4 + - - +
197D MET* 3.7 16.4 - - - +
198D THR* 4.1 11.1 - - - +
201D GLU* 2.9 36.6 + - + +
202D ARG* 2.7 45.1 + - + +
280D PHE* 3.5 10.2 - - - -
325D ARG* 4.4 1.0 - - - +
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Residues in contact with VAL 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D GLU 3.5 0.2 - - - -
168D ASN* 1.3 78.0 - - - +
170D ARG* 1.3 64.5 + - - +
172D ALA 3.2 0.2 + - - -
173D ARG* 3.0 26.4 + - + +
201D GLU* 3.5 39.2 + - + +
204D LYS* 4.2 29.4 - - + +
205D GLY* 3.6 20.9 - - - +
208D ALA* 5.5 4.0 - - + -
325D ARG* 6.1 0.4 - - - +
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Residues in contact with ARG 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D GLU* 2.9 47.1 + - + +
168D ASN 3.4 0.6 - - - -
169D VAL* 1.3 79.6 - - - +
171D GLY* 1.3 64.5 + - - +
173D ARG* 3.4 6.8 + - - +
174D THR* 3.0 34.2 + - - +
327D GLN* 6.0 0.6 - - - +
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Residues in contact with GLY 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D GLU 3.0 14.1 + - - -
168D ASN 4.0 0.4 - - - -
170D ARG* 1.3 78.3 - - - +
172D ALA* 1.3 62.1 + - - +
174D THR* 3.2 6.8 + - - -
175D ALA* 3.0 22.5 + - - +
280D PHE* 4.2 4.3 - - - -
296D VAL* 4.1 16.7 - - - +
328D THR* 3.8 19.6 + - - -
330D PHE* 5.4 0.2 - - - -
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Residues in contact with ALA 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ASN 3.0 19.0 + - - +
169D VAL 3.7 2.2 - - - +
171D GLY* 1.3 74.9 - - - +
173D ARG* 1.3 57.3 + - - +
175D ALA* 3.3 5.3 + - - +
176D VAL* 2.9 34.4 + - - +
202D ARG* 3.3 28.5 - - - +
205D GLY* 4.2 5.8 - - - -
206D PHE 4.2 0.2 - - - +
250D LEU* 4.0 8.7 - - + -
280D PHE* 3.6 22.6 - - + -
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Residues in contact with ARG 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D VAL* 3.0 19.2 + - + +
170D ARG* 3.7 7.6 - - + +
172D ALA* 1.3 74.9 - - - +
174D THR* 1.3 52.6 + - - +
176D VAL 3.3 0.3 + - - -
177D GLU* 2.7 60.1 + - - +
205D GLY* 3.4 23.6 + - - +
208D ALA* 4.3 24.8 + - - +
209D ALA* 3.7 12.9 - - + +
212D ALA* 3.8 23.8 - - - +
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Residues in contact with THR 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D ARG* 3.0 19.8 + - - +
171D GLY* 3.2 11.4 + - - -
173D ARG* 1.3 77.0 - - - +
175D ALA* 1.3 62.6 + - - +
177D GLU* 3.4 13.3 + - - +
178D TYR* 3.1 21.8 + - - +
330D PHE* 3.8 35.0 - - + -
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Residues in contact with ALA 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D GLY 3.0 12.0 + - - +
172D ALA 3.6 7.2 - - - +
174D THR* 1.3 76.0 - - - +
176D VAL* 1.3 63.3 + - - +
178D TYR* 3.4 5.4 - - - +
179D LEU* 3.3 22.7 + - - +
250D LEU* 4.1 9.6 - - + -
278D VAL* 3.7 25.9 - - + +
296D VAL* 4.4 10.3 - - + -
330D PHE* 3.6 26.0 - - + -
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Residues in contact with VAL 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D ALA 2.9 20.5 + - - +
175D ALA* 1.3 74.5 - - - +
177D GLU* 1.3 65.6 + - - +
179D LEU* 3.1 11.5 + - + +
180D ILE* 3.0 31.6 + - + +
187D ILE* 4.6 7.9 - - + -
206D PHE* 3.7 38.8 - - + -
209D ALA* 3.5 22.9 - - + -
210D MET* 4.2 9.6 - - - -
250D LEU* 4.0 22.2 - - + -
278D VAL* 5.1 1.1 - - + -
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Residues in contact with GLU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D ARG* 2.7 56.6 + - - +
174D THR* 3.4 14.5 + - - +
176D VAL* 1.3 77.3 - - - +
178D TYR* 1.3 57.4 + - - +
180D ILE* 3.2 12.1 + - + +
181D ALA* 2.8 31.3 + - - +
209D ALA* 3.9 16.2 - - + +
212D ALA* 5.3 3.3 - - - +
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Residues in contact with TYR 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D THR 3.1 8.3 + - - +
175D ALA 3.4 8.5 - - - +
176D VAL 3.2 0.2 - - - -
177D GLU* 1.3 75.9 - - - +
179D LEU* 1.3 67.5 + - + +
181D ALA* 3.4 9.6 + - + +
182D ARG* 3.3 59.2 + - + +
278D VAL* 4.2 10.1 - - + -
294D PRO* 3.7 27.4 - - + +
330D PHE* 3.6 32.5 - + + -
332D THR* 3.8 23.7 + - + -
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Residues in contact with LEU 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ALA 3.3 3.5 + - - +
176D VAL* 3.1 12.8 + - + +
178D TYR* 1.3 82.1 - - + +
180D ILE* 1.3 64.6 + - - +
182D ARG* 3.1 10.1 + - - -
183D GLY 3.3 0.3 + - - -
184D HIS* 3.2 35.7 + - + +
187D ILE* 3.9 22.2 - - + -
248D ALA* 3.8 29.6 - - + -
249D LEU 4.1 8.5 - - - +
250D LEU 4.8 0.4 - - - +
276D GLU* 4.1 20.6 - - + +
277D ILE 4.9 0.2 - - - +
278D VAL* 3.5 44.9 - - + -
294D PRO* 6.1 0.4 - - + -
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Residues in contact with ILE 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D VAL* 3.0 30.8 + - + +
177D GLU* 3.2 13.4 + - + +
179D LEU* 1.3 75.9 - - - +
181D ALA* 1.3 61.4 + - - +
183D GLY* 2.8 22.3 + - - -
184D HIS 3.9 8.1 - - - +
187D ILE* 3.6 16.6 - - + -
209D ALA 3.7 23.3 - - - +
210D MET* 4.1 9.6 - - - -
213D ALA* 4.0 22.7 - - + -
215D LEU* 4.0 14.4 - - + -
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Residues in contact with ALA 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D GLU 2.8 15.8 + - - +
178D TYR* 3.7 10.1 - - + +
179D LEU 3.2 0.2 - - - -
180D ILE* 1.3 79.5 - - - +
182D ARG* 1.3 58.4 + - - +
183D GLY* 3.1 1.0 + - - -
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Residues in contact with ARG 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178D TYR* 3.3 51.0 + - + +
179D LEU* 3.1 12.5 + - - +
180D ILE 3.1 1.0 - - - -
181D ALA* 1.3 75.3 - - - +
183D GLY* 1.3 59.1 + - - +
184D HIS* 3.7 7.9 - - + +
276D GLU* 2.7 43.1 + - - -
291D PRO* 4.6 13.2 - - - +
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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