Contacts of the helix formed by residues 183 - 194 (chain L) in PDB entry 2X86
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 SER 183 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170L VAL 4.2 5.4 - - - -
171L TYR* 3.5 23.9 - - - +
175L GLU* 2.7 35.1 + - - -
181L MET 3.9 1.0 + - - -
182L ALA* 1.3 76.2 - - - +
184L VAL* 1.3 64.5 + - - +
185L ALA* 3.5 9.7 - - - +
186L PHE* 3.0 15.9 + - - +
187L HIS* 3.1 17.8 + - - -
211L PHE* 6.5 0.7 - - - -
401L ADP 5.0 2.5 - - - -
402L BMA 6.1 0.2 - - - -
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Residues in contact with VAL 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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182L ALA 3.7 0.4 + - - -
183L SER* 1.3 70.4 - - - +
185L ALA* 1.3 67.3 + - - +
187L HIS* 3.1 8.9 + - + +
188L LEU* 2.9 44.1 + - + +
199L LYS 4.8 0.7 - - - +
200L LEU* 3.9 22.7 - - + -
211L PHE* 5.6 5.8 - - + -
243L PHE* 3.6 32.3 - - + +
246L VAL* 4.9 8.3 - - + -
401L ADP 3.6 36.7 + - + +
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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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171L TYR* 4.6 11.2 - - + -
183L SER* 3.5 11.0 - - - +
184L VAL* 1.3 78.9 - - - +
186L PHE* 1.3 62.8 + - - +
188L LEU* 3.3 2.9 + - - +
189L ASN* 3.0 23.9 + - - +
246L VAL* 4.2 23.1 - - + +
250L THR* 4.6 2.7 - - - -
299L VAL* 4.7 4.5 - - + -
302L TYR* 4.0 20.0 - - + -
303L MET* 3.6 18.0 - - + +
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Residues in contact with PHE 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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175L GLU* 3.6 8.1 - - + +
176L GLY* 3.5 37.7 - - - -
179L GLY* 5.5 2.2 - - - -
182L ALA* 3.7 20.6 - - + -
183L SER* 3.0 16.4 + - - +
185L ALA* 1.3 79.8 - - - +
187L HIS* 1.3 72.0 + + - +
189L ASN* 3.2 5.7 + - - +
190L THR* 3.1 52.4 + - + +
302L TYR* 3.3 28.9 - - - +
306L LEU* 4.1 21.3 - - + -
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Residues in contact with HIS 187 (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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179L GLY 2.9 26.4 + - - -
180L SER* 3.8 12.0 - - - -
182L ALA* 3.1 23.7 - - - +
183L SER 3.1 12.9 + - - -
184L VAL* 3.1 12.3 + - + +
186L PHE* 1.3 87.3 - + - +
188L LEU* 1.3 58.6 + - + +
190L THR* 3.3 8.6 + - - -
191L GLN* 2.9 47.6 + - - +
199L LYS 6.1 0.4 - - - +
401L ADP 3.2 19.3 + - - -
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Residues in contact with LEU 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 VAL* 2.9 35.5 + - + +
185L ALA 3.7 3.6 - - - +
187L HIS* 1.3 77.1 - - + +
189L ASN* 1.3 64.0 + - - +
191L GLN* 3.4 19.5 + - - +
192L LEU* 3.0 30.8 + - - +
198L PRO* 3.8 14.1 - - + -
199L LYS 3.4 29.2 - - - +
200L LEU* 5.0 2.0 - - + -
243L PHE 5.7 0.2 - - - +
246L VAL* 4.6 2.2 - - + -
247L ALA* 3.8 35.7 - - + +
250L THR* 4.1 19.5 - - + +
251L LEU* 5.5 1.1 - - + -
259L ILE* 4.7 3.8 - - + -
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Residues in contact with ASN 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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185L ALA 3.0 14.0 + - - +
186L PHE 3.6 6.7 - - - +
188L LEU* 1.3 77.9 - - - +
190L THR* 1.3 67.4 + - - +
192L LEU* 3.3 2.6 + - - +
193L ASN* 3.0 43.3 + - - +
250L THR* 4.5 1.7 - - - +
254L HIS* 2.8 35.2 + - - -
303L MET* 3.6 9.8 - - - +
306L LEU* 3.6 39.7 + - + +
307L ASN* 3.4 13.0 + - - -
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Residues in contact with THR 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 PHE* 3.1 48.1 + - + +
187L HIS* 3.4 13.2 + - - -
189L ASN* 1.3 84.6 - - - +
191L GLN* 1.3 67.2 + - - +
193L ASN* 3.4 6.6 + - - +
194L ASN* 3.1 36.3 + - - -
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Residues in contact with GLN 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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187L HIS* 2.9 30.3 + - - +
188L LEU* 3.4 15.5 - - - +
190L THR* 1.3 79.4 + - - +
192L LEU* 1.3 58.5 + - - +
194L ASN* 3.3 6.1 + - - +
196L GLU* 3.0 54.6 + - + +
197L SER 3.9 14.4 - - - +
198L PRO* 3.3 6.3 - - + +
199L LYS* 3.0 49.0 + - + +
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Residues in contact with LEU 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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188L LEU* 3.0 21.1 + - + +
189L ASN 3.7 3.8 - - - +
191L GLN* 1.3 73.8 - - - +
193L ASN* 1.3 62.9 + - - +
194L ASN 3.1 4.9 - - - -
195L GLY 3.2 6.1 + - - -
196L GLU 4.1 5.8 - - - +
198L PRO* 3.8 30.7 - - + -
250L THR* 3.9 8.1 - - + -
251L LEU* 3.8 22.0 - - + -
254L HIS* 3.8 38.6 - - + +
256L LYS* 2.8 44.6 + - - +
257L GLY* 4.1 17.7 - - - -
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Residues in contact with ASN 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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189L ASN* 3.0 40.4 + - - +
190L THR* 3.9 7.2 - - - +
192L LEU* 1.3 75.6 - - - +
194L ASN* 1.3 61.1 + - - +
195L GLY 3.3 1.5 + - - -
254L HIS* 3.4 18.1 + - - -
306L LEU 5.2 1.2 + - - -
307L ASN* 3.4 18.0 + - - +
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Residues in contact with ASN 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 THR* 3.1 26.6 + - - +
191L GLN* 3.6 6.6 - - - +
192L LEU 3.1 1.0 - - - -
193L ASN* 1.3 81.1 - - - +
195L GLY* 1.3 55.4 + - - +
196L GLU* 3.0 32.0 + - - +
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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