Contacts of the helix formed by residues 240 - 251 (chain I) in PDB entry 1YC0
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 GLN 240 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238I GLN* 4.2 15.9 - - + +
239I HIS* 1.3 79.8 - - + +
241I HIS* 1.3 57.4 + - - +
242I GLN 3.0 2.5 - - - -
243I MET* 2.7 31.0 + - + +
244I HIS* 3.0 35.5 + - + +
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Residues in contact with HIS 241 (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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238I GLN 3.4 25.3 - - - +
239I HIS 3.6 0.4 - - - -
240I GLN* 1.3 77.3 - - - +
242I GLN* 1.3 57.5 + - - +
244I HIS* 3.9 14.1 + - + +
245I GLN* 2.9 72.6 + - + +
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Residues in contact with GLN 242 (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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238I GLN 4.1 9.5 + - - +
239I HIS* 3.9 9.3 + - - +
240I GLN 3.0 0.8 - - - -
241I HIS* 1.3 81.2 + - - +
243I MET* 1.3 81.7 + - + +
245I GLN* 3.9 7.6 - - + +
246I THR* 2.9 30.8 + - - +
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Residues in contact with MET 243 (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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239I HIS 3.8 15.0 - - - +
240I GLN* 2.7 17.8 + - + +
242I GLN* 1.3 107.5 - - + +
244I HIS* 1.3 63.1 + - + +
245I GLN 3.2 0.2 - - - -
246I THR* 3.2 12.0 + - - +
247I GLU* 2.9 40.0 + - - +
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Residues in contact with HIS 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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240I GLN* 3.0 40.1 + - + +
241I HIS* 3.9 13.4 - - + +
243I MET* 1.3 80.8 - - + +
245I GLN* 1.3 58.2 + - + +
247I GLU* 3.4 19.9 + - - +
248I ASP* 2.9 40.9 + - - +
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Residues in contact with GLN 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 HIS* 2.9 56.2 + - + +
242I GLN* 3.9 8.7 - - + +
244I HIS* 1.3 74.5 - - + +
246I THR* 1.3 59.4 + - - +
248I ASP* 3.4 5.0 + - - -
249I TYR* 2.9 60.3 + - + +
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Residues in contact with THR 246 (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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242I GLN* 2.9 22.2 + - - +
243I MET* 3.2 18.2 + - - +
245I GLN* 1.3 77.3 - - - +
247I GLU* 1.3 58.2 + - + +
249I TYR* 4.9 0.7 - - - -
250I CYS* 2.8 45.3 + - + +
251I LEU* 3.5 7.9 + - + +
303I VAL* 3.7 24.0 - - + +
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Residues in contact with GLU 247 (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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243I MET* 2.9 25.0 + - - +
244I HIS* 3.6 23.9 - - - +
246I THR* 1.3 76.5 - - - +
248I ASP* 1.3 60.7 + - - +
251I LEU* 3.0 46.5 + - + +
252I ALA* 3.0 13.6 + - - +
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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
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244I HIS* 2.9 24.6 + - - +
245I GLN* 3.9 5.2 + - - +
247I GLU* 1.3 79.9 - - - +
249I TYR* 1.3 69.2 + - + +
252I ALA* 3.5 18.1 - - - +
286I ASN* 5.2 0.2 - - - +
287I LYS* 3.4 18.6 + - + +
288I ASN 3.4 16.8 + - - -
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Residues in contact with TYR 249 (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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245I GLN* 2.9 54.0 + - + +
246I THR* 4.9 0.7 - - - -
248I ASP* 1.3 83.1 - - + +
250I CYS* 1.3 66.2 + - - +
287I LYS* 3.5 58.8 - - + +
288I ASN* 3.3 21.0 - - - +
290I TYR* 2.7 36.9 + + - +
299I ALA* 5.6 3.1 - - + -
300I CYS* 3.7 0.2 - - - -
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Residues in contact with CYS 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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246I THR* 2.8 26.1 + - + +
249I TYR* 1.3 88.1 - - - +
251I LEU* 1.3 61.3 + - + +
268I TYR* 3.1 28.2 - - + +
270I PRO* 3.9 3.5 - - - +
288I ASN* 3.4 13.6 + - - +
299I ALA* 3.9 7.6 - - - -
300I CYS* 2.0 55.0 - - + -
303I VAL* 4.3 11.9 - - - +
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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
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246I THR* 3.5 7.4 + - + +
247I GLU* 3.0 37.3 + - + +
250I CYS* 1.3 79.8 - - + +
252I ALA* 1.3 68.2 + - - +
253I SER* 3.5 2.6 + - - -
270I PRO* 3.7 37.0 - - + +
303I VAL* 3.7 24.2 - - + -
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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