Contacts of the helix formed by residues 183 - 194 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170E VAL 4.1 5.8 - - - -
171E TYR* 3.5 24.2 - - - +
175E GLU* 2.7 35.9 + - - -
181E MET 3.9 0.4 + - - -
182E ALA* 1.3 76.4 - - - +
184E VAL* 1.3 63.8 + - - +
185E ALA* 3.5 9.8 - - - +
186E PHE* 3.0 15.6 + - - +
187E HIS* 3.1 18.7 + - - -
211E PHE* 6.5 0.7 - - - -
401E ADP 5.4 1.1 - - - -
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Residues in contact with VAL 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E ALA 3.7 0.2 + - - -
183E SER* 1.3 69.9 - - - +
185E ALA* 1.3 67.0 + - - +
187E HIS* 3.1 9.7 + - + +
188E LEU* 2.9 41.7 + - + +
199E LYS 4.8 0.9 - - - +
200E LEU* 3.8 26.0 - - + -
211E PHE* 5.6 4.8 - - + -
243E PHE* 3.6 33.9 - - + -
246E VAL* 4.9 8.3 - - + -
401E ADP 3.7 34.5 - - + +
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Residues in contact with ALA 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E TYR* 4.6 10.8 - - + -
183E SER* 3.5 10.7 - - - +
184E VAL* 1.3 79.5 - - - +
186E PHE* 1.3 63.5 + - - +
188E LEU* 3.3 2.7 + - - +
189E ASN* 3.0 23.9 + - - +
246E VAL* 4.2 22.5 - - + +
250E THR* 4.6 2.5 - - - -
299E VAL* 4.7 5.2 - - + -
302E TYR* 4.0 19.3 - - + -
303E MET* 3.6 18.1 - - + +
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Residues in contact with PHE 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E GLU* 3.6 7.0 - - + +
176E GLY* 3.5 39.7 - - - -
179E GLY* 5.6 2.2 - - - -
182E ALA* 3.8 20.0 - - + -
183E SER* 3.0 15.7 + - - +
185E ALA* 1.3 79.9 - - - +
187E HIS* 1.3 71.4 + + - +
189E ASN* 3.2 6.1 + - - +
190E THR* 3.0 55.0 + - + +
302E TYR* 3.3 29.0 - - - +
306E LEU* 4.1 20.9 - - + -
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Residues in contact with HIS 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179E GLY 2.9 27.5 + - - -
180E SER* 3.8 12.6 - - - -
182E ALA* 3.1 23.0 - - - +
183E SER 3.1 12.1 + - - -
184E VAL* 3.1 12.7 + - + +
186E PHE* 1.3 89.1 - + - +
188E LEU* 1.3 59.0 + - + +
190E THR* 3.3 9.4 + - - -
191E GLN* 2.9 47.6 + - - +
199E LYS 6.1 0.4 - - - +
401E ADP 3.1 20.2 + - - -
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Residues in contact with LEU 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E VAL* 2.9 36.4 + - + +
185E ALA 3.7 3.4 - - - +
187E HIS* 1.3 77.1 - - + +
189E ASN* 1.3 64.2 + - - +
191E GLN* 3.4 16.6 + - - +
192E LEU* 3.0 31.1 + - + +
198E PRO* 3.8 14.4 - - + -
199E LYS 3.4 32.8 - - - +
200E LEU* 5.0 1.3 - - + -
246E VAL* 4.6 2.5 - - + -
247E ALA* 3.8 35.7 - - + +
250E THR* 4.1 19.1 - - + +
251E LEU* 5.5 0.9 - - + -
259E ILE* 4.7 4.0 - - + -
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Residues in contact with ASN 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E ALA 3.0 14.0 + - - +
186E PHE 3.2 7.6 + - - +
188E LEU* 1.3 77.4 - - - +
190E THR* 1.3 67.1 + - - +
192E LEU* 3.3 2.3 + - - +
193E ASN* 3.0 43.0 + - - +
250E THR* 4.5 1.3 - - - +
254E HIS* 2.8 35.3 + - - -
303E MET* 3.6 10.2 - - - +
306E LEU* 3.5 40.3 + - + +
307E ASN* 3.4 13.0 + - - -
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Residues in contact with THR 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E PHE* 3.0 47.6 + - + +
187E HIS* 3.4 13.0 + - - -
189E ASN* 1.3 84.7 - - - +
191E GLN* 1.3 68.4 + - - +
193E ASN* 3.4 6.3 + - - +
194E ASN* 3.1 36.7 + - - -
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Residues in contact with GLN 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E HIS* 2.9 30.1 + - - +
188E LEU* 3.5 15.3 - - - +
190E THR* 1.3 78.8 + - - +
192E LEU* 1.3 58.3 + - - +
194E ASN* 3.3 5.5 + - - +
196E GLU* 2.9 55.2 + - - +
197E SER 3.9 14.8 - - - +
198E PRO* 3.3 7.5 - - + +
199E LYS* 3.0 49.2 + - + +
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Residues in contact with LEU 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E LEU 3.0 22.0 + - - +
189E ASN 3.7 2.9 - - - +
191E GLN* 1.3 74.4 - - - +
193E ASN* 1.3 62.5 + - - +
194E ASN 3.1 4.7 - - - -
195E GLY* 3.2 6.4 + - - -
196E GLU 4.2 5.4 - - - +
198E PRO* 3.9 31.0 - - + -
250E THR* 3.9 8.3 - - + +
251E LEU* 3.8 22.0 - - + -
254E HIS* 3.8 38.4 - - + +
256E LYS* 2.8 44.0 + - - +
257E GLY* 4.1 18.2 - - - -
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Residues in contact with ASN 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E ASN* 3.0 40.2 + - - +
190E THR* 3.9 6.8 - - - +
192E LEU* 1.3 75.7 - - - +
194E ASN* 1.3 60.6 + - - +
195E GLY 3.3 1.9 + - - -
254E HIS* 3.4 18.1 + - - -
256E LYS* 5.2 0.4 - - - +
306E LEU 5.1 1.6 + - - -
307E ASN* 3.4 18.2 + - - +
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Residues in contact with ASN 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E THR* 3.1 27.7 + - - +
191E GLN* 3.6 6.8 - - - +
192E LEU 3.1 1.2 - - - -
193E ASN* 1.3 81.9 - - - +
195E GLY* 1.3 55.1 + - - +
196E GLU* 3.0 32.3 + - - +
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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