Contacts of the helix formed by residues 243 - 255 (chain I) 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 PHE 243 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169I ASN* 5.2 2.7 - - - -
184I VAL* 3.6 29.6 - - + +
188I LEU* 5.7 0.2 - - - +
200I LEU* 3.9 19.2 - - + +
204I SER* 4.2 10.7 + - - -
207I PHE* 3.4 31.7 + - + -
208I LYS 4.5 0.2 - - - -
209I ARG* 3.7 37.0 - - + -
211I PHE* 3.8 21.3 - + - -
242I SER* 1.3 73.4 - - - +
244I GLN* 1.3 63.5 + - - +
246I VAL* 3.1 7.4 + - + +
247I ALA* 3.0 21.7 + - - +
272I TYR* 3.7 5.6 - - - -
401I ADP 3.4 49.8 - + - -
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Residues in contact with GLN 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200I LEU* 4.2 13.7 - - + +
204I SER 4.5 6.9 + - - +
205I GLU* 5.6 5.2 - - - -
242I SER* 3.1 13.1 + - - +
243I PHE* 1.3 79.1 - - - +
245I ALA* 1.3 56.3 + - - +
247I ALA* 3.3 7.8 + - - +
248I ASP* 2.8 66.8 + - - +
259I ILE* 4.2 13.4 - - - +
261I TYR* 3.9 17.2 + - - +
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Residues in contact with ALA 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241I GLU* 4.1 27.6 - - + +
242I SER* 2.9 22.9 + - - +
244I GLN* 1.3 73.6 - - - +
246I VAL* 1.3 66.5 + - - +
248I ASP* 3.2 13.1 + - - +
249I ALA* 3.0 22.7 + - - +
295I VAL* 4.0 7.2 - - + +
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Residues in contact with VAL 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I VAL* 4.9 6.7 - - + -
185I ALA* 4.2 35.2 - - + +
188I LEU* 4.6 6.1 - - + -
211I PHE* 3.7 48.0 - - + -
242I SER 4.2 1.6 - - - +
243I PHE* 3.1 8.4 + - + +
245I ALA* 1.3 77.4 - - - +
247I ALA* 1.3 63.7 + - - +
249I ALA* 3.2 4.3 + - - +
250I THR* 3.0 27.5 + - - +
295I VAL* 3.8 19.0 - - + +
299I VAL* 4.2 9.7 - - + +
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Residues in contact with ALA 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I LEU* 3.8 17.7 - - + +
200I LEU* 4.3 5.8 - - + -
243I PHE 3.0 11.9 + - - +
244I GLN* 3.4 13.2 - - - +
246I VAL* 1.3 77.2 - - - +
248I ASP* 1.3 54.3 + - - +
250I THR* 3.2 1.9 + - - -
251I LEU* 2.8 40.8 + - + +
259I ILE* 3.4 37.0 - - + -
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Residues in contact with ASP 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I GLN* 2.8 52.9 + - - +
245I ALA* 3.3 12.2 - - - +
247I ALA* 1.3 72.9 - - - +
249I ALA* 1.3 62.8 + - - +
251I LEU* 3.9 5.0 - - - +
252I ALA* 3.0 27.0 + - - +
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Residues in contact with ALA 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245I ALA 3.0 9.3 + - - +
246I VAL 3.2 8.0 + - - +
248I ASP* 1.3 79.6 - - - +
250I THR* 1.3 61.3 - - - +
252I ALA* 3.5 6.5 - - - +
253I TYR* 3.2 17.2 + - - +
295I VAL* 4.3 10.1 - - + +
296I ALA* 4.3 16.2 - - + +
299I VAL* 3.7 24.4 - - + +
300I THR* 3.7 16.0 - - + +
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Residues in contact with THR 250 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185I ALA* 4.6 0.9 - - - -
188I LEU* 4.1 21.5 - - + +
189I ASN 4.5 1.3 - - - +
192I LEU* 3.9 21.5 - - + -
246I VAL* 3.0 17.6 + - - +
247I ALA* 3.5 10.1 - - - -
249I ALA* 1.3 73.1 - - - +
251I LEU* 1.3 67.6 + - + +
252I ALA 3.1 0.9 - - - -
253I TYR* 3.1 4.3 + - - +
254I HIS* 3.1 25.3 + - + +
299I VAL* 3.4 17.1 - - - +
303I MET* 3.6 30.1 - - + +
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Residues in contact with LEU 251 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I LEU* 5.5 0.9 - - + -
192I LEU* 3.8 22.4 - - + -
198I PRO* 3.9 18.8 - - + -
247I ALA* 2.8 28.8 + - + +
248I ASP* 4.2 4.5 - - - +
250I THR* 1.3 76.5 - - + +
252I ALA* 1.3 58.0 + - - +
254I HIS* 3.3 2.6 + - - +
255I LYS* 2.8 26.7 + - - -
256I LYS 3.5 18.8 + - - +
257I GLY 3.0 31.0 - - - +
258I GLN* 4.0 8.3 - - - +
259I ILE* 4.4 15.3 - - + +
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Residues in contact with ALA 252 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248I ASP 3.0 19.8 + - - +
249I ALA* 3.5 8.5 - - - +
251I LEU* 1.3 79.0 - - - +
253I TYR* 1.3 61.4 + - - +
255I LYS* 3.2 25.1 - - - +
300I THR* 5.6 3.1 - - + -
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Residues in contact with TYR 253 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249I ALA 3.2 10.2 + - - +
250I THR 3.1 8.7 + - - +
252I ALA* 1.3 81.4 - - - +
254I HIS* 1.3 75.5 + + - +
255I LYS* 3.2 11.8 + - - +
300I THR* 4.3 18.5 - - + +
303I MET* 3.5 40.6 + - + -
304I ALA* 3.4 31.9 + - + +
307I ASN* 4.0 22.3 - - + +
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Residues in contact with HIS 254 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189I ASN* 2.8 32.9 + - - -
192I LEU* 3.8 34.9 - - + +
193I ASN* 3.4 23.7 + - - -
250I THR* 3.1 30.5 + - + +
251I LEU 4.0 3.1 - - - +
253I TYR* 1.3 89.4 - + - +
255I LYS* 1.3 68.5 + - - +
256I LYS* 3.0 28.6 + - + +
303I MET* 3.9 6.5 - - - -
307I ASN* 4.4 7.2 + - - -
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Residues in contact with LYS 255 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251I LEU 2.8 10.1 + - - -
252I ALA* 3.2 24.9 + - - +
253I TYR 3.2 9.5 - - - +
254I HIS* 1.3 80.4 - - - +
256I LYS* 1.3 59.3 + - - +
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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