Contacts of the helix formed by residues 178 - 194 (chain L) in PDB entry 2B4X
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 ASN 178 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174L ASP* 2.7 42.4 + - + +
177L GLU* 1.3 82.5 - - - +
179L ALA* 1.3 64.8 + - - +
180L GLU 2.9 4.9 + - - +
181L GLN* 3.0 27.7 + - + +
182L SER* 3.0 20.7 + - - +
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Residues in contact with ALA 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174L ASP 3.4 3.2 + - - -
175L PHE* 3.8 10.2 + - - +
177L GLU 3.6 3.8 + - - -
178L ASN* 1.3 74.2 - - - +
180L GLU* 1.3 57.5 + - - +
182L SER* 3.1 21.5 - - - -
183L ARG* 3.2 9.2 + - - +
207L ILE* 3.0 34.6 - - - +
208L ASN* 3.6 23.8 - - - -
209L GLU 4.2 0.9 - - - +
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Residues in contact with GLU 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178L ASN* 2.9 2.0 + - - -
179L ALA* 1.3 75.5 - - - +
181L GLN* 1.3 63.6 + - - +
182L SER 2.8 5.6 + - - -
183L ARG* 3.2 17.8 + - - +
184L ALA* 3.3 18.7 + - - +
204L SER* 3.7 19.2 + - - -
205L GLU* 4.7 5.9 + - - -
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Residues in contact with GLN 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173L LEU* 6.0 0.2 - - - -
178L ASN* 3.0 29.2 + - + +
180L GLU* 1.3 79.6 - - - +
182L SER* 1.3 56.4 + - - +
184L ALA* 3.8 7.2 - - + +
185L ALA* 2.9 27.6 + - + +
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Residues in contact with SER 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173L LEU* 3.6 17.0 - - - +
174L ASP 3.4 14.0 + - - -
175L PHE* 3.5 29.9 - - - -
178L ASN* 3.0 13.5 + - - +
179L ALA 3.1 11.7 - - - -
180L GLU 2.8 1.0 - - - -
181L GLN* 1.3 77.1 - - - +
183L ARG* 1.3 54.2 + - - -
185L ALA* 2.8 9.7 + - - +
186L ILE* 2.7 40.0 + - - +
207L ILE* 4.7 0.2 - - - -
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Residues in contact with ARG 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179L ALA 3.2 8.5 + - - +
180L GLU* 3.2 16.3 + - - +
182L SER* 1.3 75.2 - - - +
184L ALA* 1.3 58.2 + - - +
186L ILE* 2.7 25.4 + - - +
187L ASN* 2.7 29.8 + - - +
202L ILE* 4.7 5.4 - - + -
203L PRO 4.3 12.6 - - - +
204L SER* 5.7 1.6 - - - -
205L GLU 6.0 2.0 - - - +
207L ILE* 4.2 23.0 - - + +
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Residues in contact with ALA 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180L GLU* 3.3 20.4 + - - +
181L GLN* 3.9 8.3 - - + +
183L ARG* 1.3 79.1 - - - +
185L ALA* 1.3 62.6 + - - +
187L ASN* 4.2 6.5 - - - +
188L LYS* 2.8 38.1 + - + +
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Residues in contact with ALA 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147L PHE* 5.0 2.7 - - - -
171L GLN* 5.5 2.5 - - - +
173L LEU* 3.9 23.3 - - + -
181L GLN* 2.9 20.6 + - + +
182L SER* 2.8 18.5 + - - +
184L ALA* 1.3 79.4 - - - +
186L ILE* 1.3 60.2 + - - +
188L LYS* 3.7 4.3 + - - +
189L TRP* 3.6 13.5 + - - +
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Residues in contact with ILE 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147L PHE* 3.6 50.7 - - + -
173L LEU* 3.8 7.2 - - + -
175L PHE* 4.3 3.6 - - + -
182L SER 2.7 18.7 + - - +
183L ARG 2.7 6.2 + - - +
185L ALA* 1.3 67.2 - - - +
187L ASN* 1.3 66.7 + - - +
188L LYS 3.1 1.6 - - - -
189L TRP* 2.9 19.1 + - - +
190L VAL* 3.5 8.6 + - + +
201L VAL* 6.2 0.4 - - + -
202L ILE* 3.8 18.6 - - + -
207L ILE* 3.7 30.1 - - + -
214L VAL* 3.9 19.7 - - + -
216L VAL* 4.0 14.1 - - + -
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Residues in contact with ASN 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183L ARG* 2.7 30.8 + - - +
184L ALA* 4.2 3.2 - - - +
186L ILE* 1.3 71.7 - - - +
188L LYS* 1.3 66.8 + - + +
190L VAL* 3.4 6.1 + - - +
191L SER* 3.0 24.2 + - - -
198L ILE 4.3 2.6 - - - +
199L THR* 4.6 3.9 - - - -
200L ASP* 4.0 18.1 - - - +
201L VAL* 3.4 10.0 + - - +
202L ILE* 2.6 56.2 + - - +
203L PRO 4.0 4.6 + - - -
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Residues in contact with LYS 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184L ALA* 2.8 34.3 + - + +
185L ALA 3.9 3.8 - - - +
186L ILE 3.0 0.8 + - - -
187L ASN* 1.3 81.9 - - + +
189L TRP* 1.3 59.6 + - - +
190L VAL 3.0 2.2 - - - -
191L SER* 2.8 12.4 + - - -
192L ASN* 2.8 31.3 + - - +
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Residues in contact with TRP 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143L ALA* 3.5 35.9 - - + -
144L ASN 3.5 9.2 - - - -
145L ARG* 3.5 60.9 - - + +
147L PHE* 4.2 19.3 - + + -
171L GLN* 5.4 1.6 - - - -
185L ALA 3.6 7.7 + - - +
186L ILE 2.9 10.9 + - - +
188L LYS* 1.3 77.8 - - - +
190L VAL* 1.3 66.6 + - + +
192L ASN* 3.5 9.7 + - + +
193L LYS* 3.1 50.5 + - + +
216L VAL* 4.1 17.5 - - + -
218L THR* 4.1 7.9 - - + -
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Residues in contact with VAL 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186L ILE* 4.0 11.7 - - + +
187L ASN 3.4 2.2 + - - +
188L LYS 3.0 0.4 - - - -
189L TRP* 1.3 76.6 - - + +
191L SER* 1.3 57.5 - - - +
192L ASN 2.9 4.3 - - - -
193L LYS 2.9 1.5 + - - +
194L THR* 2.7 46.5 + - + +
198L ILE* 3.8 7.6 - - + -
201L VAL* 3.4 28.3 - - + -
216L VAL* 3.8 20.4 - - + -
218L THR* 3.5 16.8 - - + -
385L SER* 3.2 35.7 - - - +
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Residues in contact with SER 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NAG 4.6 2.1 - - - +
187L ASN 3.0 14.8 + - - -
188L LYS* 2.8 21.5 + - - -
190L VAL* 1.3 77.7 - - - +
192L ASN* 1.3 55.1 + - - +
194L THR* 3.9 0.7 - - - -
195L GLU* 4.2 0.2 - - - -
196L GLY* 2.7 34.4 + - - -
198L ILE 3.1 15.9 + - - -
199L THR* 2.9 29.3 - - - +
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Residues in contact with ASN 192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B NAG 1.5 74.9 + - - +
188L LYS 2.8 12.8 + - - +
189L TRP* 3.7 10.7 - - + +
190L VAL 2.9 0.2 - - - -
191L SER* 1.3 77.5 - - - +
193L LYS* 1.3 75.3 + - - +
194L THR 3.2 5.5 + - - -
195L GLU* 3.8 10.4 + - - +
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Residues in contact with LYS 193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141L VAL* 4.9 8.1 - - + +
143L ALA* 3.6 25.4 - - + +
189L TRP* 3.1 41.1 + - + +
190L VAL* 2.9 6.1 + - - +
192L ASN* 1.3 88.7 - - - +
194L THR* 1.3 62.1 + - - +
195L GLU* 3.8 4.8 - - - +
218L THR* 3.8 20.3 + - + +
219L ILE 5.5 0.3 - - - -
220L TYR* 4.1 13.2 - - - +
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Residues in contact with THR 194 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L VAL* 2.7 36.1 + - + +
191L SER* 3.9 0.9 - - - -
193L LYS* 1.3 86.7 - - - +
195L GLU* 1.3 57.4 + - - +
196L GLY 3.1 0.7 - - - -
197L ARG* 2.6 37.4 + - - +
198L ILE* 3.0 37.7 + - + -
218L THR* 4.0 14.4 - - - -
219L ILE 4.5 4.5 - - - +
220L TYR* 3.9 9.6 - - - -
383L ALA* 4.1 9.4 - - + -
384L ALA 4.4 5.2 - - - +
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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