Contacts of the helix formed by residues 243 - 253 (chain A) in PDB entry 2W3C
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 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A GLY* 3.7 12.7 + - - -
201A GLN* 2.7 43.3 + - - +
202A LYS* 3.8 10.1 - - - +
239A LEU 3.5 12.3 + - - +
240A LEU 3.3 13.0 + - - +
241A LYS 3.2 2.6 - - - +
242A ASN* 1.3 78.0 + - - +
244A ASN* 1.3 57.8 + - - +
245A SER* 3.6 9.9 + - - -
246A ASN* 3.1 29.1 + - - +
247A GLN* 3.1 27.1 + - - +
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Residues in contact with ASN 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ASN* 5.2 3.2 + - - -
243A ASN* 1.3 73.0 + - - +
245A SER* 1.3 66.7 + - - +
246A ASN 3.2 0.4 - - - -
247A GLN* 3.3 13.8 + - - +
248A ASN* 2.9 26.0 + - - +
295A ASN* 4.3 10.7 - - - +
296A PRO* 3.7 35.2 - - + +
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Residues in contact with SER 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LYS* 3.4 36.6 - - - +
206A PHE* 5.6 4.9 - - - -
243A ASN 3.4 0.2 - - - -
244A ASN* 1.3 78.4 - - - +
246A ASN* 1.3 59.1 + - - +
248A ASN* 3.5 6.6 + - - +
249A PHE* 3.0 26.2 + - - +
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Residues in contact with ASN 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLN 3.3 28.7 + - - -
202A LYS* 3.6 20.9 - - - +
205A ALA* 3.7 20.0 - - - +
206A PHE* 5.0 4.0 - - - -
210A PHE* 3.7 7.8 - - + -
239A LEU* 2.9 35.4 + - - +
240A LEU* 3.5 4.8 - - - +
243A ASN* 3.1 17.1 + - - +
245A SER* 1.3 77.0 + - - +
247A GLN* 1.3 58.1 + - - +
248A ASN 3.3 0.2 - - - -
249A PHE* 3.8 6.5 - - - +
250A PHE* 3.0 28.6 + - - +
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Residues in contact with GLN 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A LEU* 2.8 35.3 + - + +
242A ASN* 4.4 4.2 - - - +
243A ASN 3.1 21.9 + - - +
244A ASN* 3.6 14.8 + - - +
246A ASN* 1.3 72.6 - - - +
248A ASN* 1.3 65.3 + - - +
250A PHE* 3.4 2.9 + - - +
251A LYS* 3.1 23.7 + - - +
289A VAL* 3.5 22.7 + - + +
290A LEU* 3.8 25.4 - - + +
295A ASN* 3.0 34.5 + - - -
299A ALA* 5.3 6.9 - - + +
303A CYS* 5.0 4.1 - - - -
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Residues in contact with ASN 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ASN 2.9 18.1 + - - +
245A SER* 3.6 6.1 - - - +
247A GLN* 1.3 77.4 - - - +
249A PHE* 1.3 52.5 + - - +
251A LYS* 3.3 18.8 + - - +
252A GLU* 2.8 60.1 + - - +
299A ALA* 6.2 4.3 - - + +
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Residues in contact with PHE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ALA* 3.3 35.2 - - + -
206A PHE* 4.7 20.2 - + + -
210A PHE* 3.6 28.5 - + + -
245A SER 3.0 17.7 + - - +
246A ASN* 3.8 9.0 - - - +
248A ASN* 1.3 76.7 + - - +
250A PHE* 1.3 55.9 - - - +
252A GLU* 3.8 6.9 - - + -
253A GLY* 2.9 26.5 + - - -
255A TYR* 4.2 14.7 - + - -
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Residues in contact with PHE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PHE* 3.8 34.8 - + + -
214A LEU* 4.4 13.0 - - + -
236A LEU* 4.9 6.1 - - + -
240A LEU* 3.9 20.4 - - + -
246A ASN 3.0 18.3 + - - +
247A GLN* 3.5 5.2 - - - +
248A ASN 3.2 0.2 - - - -
249A PHE* 1.3 74.6 - - - +
251A LYS* 1.3 67.6 + - - +
253A GLY 3.5 0.3 + - - -
255A TYR* 3.2 60.7 + + + -
256A ILE* 3.5 22.7 - - + -
259A MET* 4.0 19.5 - - + -
262A TRP* 5.7 0.4 - + - -
290A LEU* 3.6 33.0 - - + -
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Residues in contact with LYS 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLN 3.1 13.0 + - - +
248A ASN* 3.6 19.9 - - - +
250A PHE* 1.3 75.0 - - + +
252A GLU* 1.3 79.3 + - - +
254A SER* 2.8 28.4 + - - -
256A ILE* 3.8 31.0 - - + +
299A ALA* 5.4 0.9 - - - +
302A SER* 3.2 41.6 + - - +
303A CYS* 4.1 13.7 - - - +
306A ALA* 4.8 4.9 - - + -
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Residues in contact with GLU 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ASN* 2.8 36.5 + - - +
249A PHE* 3.8 9.4 - - + +
251A LYS* 1.3 101.0 + - - +
253A GLY* 1.3 59.8 + - - +
254A SER* 3.5 4.3 + - - -
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Residues in contact with GLY 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A PHE* 2.9 18.8 + - - -
251A LYS 3.0 1.0 + - - -
252A GLU* 1.3 74.5 - - - +
254A SER* 1.3 70.5 + - - +
255A TYR* 3.3 28.2 + - - -
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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