Contacts of the helix formed by residues 243 - 258 (chain A) in PDB entry 6Y2G
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 THR 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A LEU* 4.6 3.1 - - - -
241A PRO* 4.4 9.4 - - + +
242A LEU* 1.3 75.5 - - - +
244A GLN* 1.3 65.8 + - - +
245A ASP* 3.2 11.9 + - - +
246A HIS* 3.1 49.4 + - + +
247A VAL* 3.1 17.3 + - - +
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Residues in contact with GLN 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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227A LEU* 4.1 20.0 - - + +
243A THR* 1.3 73.8 - - - +
245A ASP* 1.3 63.8 + - - +
247A VAL* 3.1 24.2 + - - +
248A ASP* 3.0 49.4 + - - +
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Residues in contact with ASP 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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243A THR* 3.1 10.8 + - - +
244A GLN* 1.3 78.6 - - - +
246A HIS* 1.3 66.3 + - + +
248A ASP* 3.1 14.3 + - - +
249A ILE* 3.0 35.5 + - + +
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Residues in contact with HIS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A THR* 6.4 0.4 - - - -
202A VAL* 3.8 34.3 - - + +
240A GLU* 5.8 3.6 - - + -
241A PRO 3.6 16.6 - - - -
242A LEU* 3.4 27.1 - - + +
243A THR* 3.1 36.9 + - + +
245A ASP* 1.3 79.1 - - + +
247A VAL* 1.3 61.3 + - - +
249A ILE* 3.1 15.9 + - + +
250A LEU* 3.1 27.0 + - - +
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Residues in contact with VAL 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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227A LEU* 4.2 14.6 - - + -
242A LEU* 4.2 15.0 - - + -
243A THR 3.1 11.8 + - - +
244A GLN* 3.1 32.4 + - - +
246A HIS* 1.3 74.8 - - - +
248A ASP* 1.3 64.0 + - - +
250A LEU* 3.2 12.6 + - - +
251A GLY* 3.4 8.5 + - - -
261A VAL* 3.9 37.6 - - + +
262A LEU* 5.3 7.0 - - + -
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Residues in contact with ASP 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 GLN* 3.0 42.1 + - - +
245A ASP* 3.1 14.2 + - - +
247A VAL* 1.3 75.8 - - - +
249A ILE* 1.3 58.4 + - + +
251A GLY* 3.1 19.7 + - - -
252A PRO* 4.0 4.2 - - - +
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Residues in contact with ILE 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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202A VAL* 4.7 6.1 - - + -
245A ASP* 3.0 28.3 + - + +
246A HIS* 3.1 17.2 + - + +
248A ASP* 1.3 78.3 - - + +
250A LEU* 1.3 59.0 + - - +
251A GLY 3.2 1.2 + - - -
252A PRO* 3.5 12.2 - - - +
253A LEU* 5.4 1.2 + - - +
293A PRO* 3.7 36.1 - - + +
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Residues in contact with LEU 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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202A VAL* 4.0 26.9 - - + +
205A LEU* 3.8 32.3 - - + -
206A ALA* 4.1 16.8 - - - +
209A TYR* 4.4 10.2 - - + -
242A LEU* 5.0 1.8 - - + -
246A HIS 3.1 15.7 + - - +
247A VAL 3.2 2.4 + - - +
249A ILE* 1.3 76.0 - - - +
251A GLY* 1.3 64.5 + - - +
252A PRO* 3.5 1.1 - - - -
253A LEU* 3.2 16.5 + - + +
254A SER* 3.1 20.3 + - - -
261A VAL* 3.7 31.6 - - + -
293A PRO* 4.0 16.6 - - + -
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Residues in contact with GLY 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 VAL 3.4 6.5 + - - -
248A ASP* 3.1 14.3 + - - -
250A LEU* 1.3 75.6 - - - +
252A PRO* 1.3 65.5 - - - +
254A SER* 3.2 9.6 + - - -
255A ALA* 3.0 21.9 + - - +
261A VAL* 5.0 2.2 - - - -
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Residues in contact with PRO 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 ASP 4.0 5.2 - - - +
249A ILE* 3.5 14.6 - - - +
250A LEU 3.7 0.4 - - - -
251A GLY* 1.3 90.0 - - - +
253A LEU* 1.3 64.1 + - + +
255A ALA* 3.2 8.3 + - + +
256A GLN* 3.1 23.9 + - - +
297A VAL* 5.4 9.6 - - + -
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Residues in contact with LEU 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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206A ALA* 4.1 33.4 - - + +
209A TYR* 3.8 21.4 - - + -
213A ILE* 4.0 19.7 - - + -
249A ILE 5.7 0.9 - - - +
250A LEU* 3.2 19.6 + - + +
252A PRO* 1.3 79.5 - - + +
254A SER* 1.3 61.5 + - - +
256A GLN* 3.6 7.4 + - - +
257A THR* 3.1 29.6 + - - +
293A PRO* 4.3 17.0 - - + +
296A VAL* 3.9 22.9 - - + -
297A VAL* 3.9 22.0 - - + -
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Residues in contact with SER 254 (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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209A TYR* 3.8 11.3 - - - -
250A LEU 3.1 12.6 + - - -
251A GLY* 3.3 11.9 - - - -
253A LEU* 1.3 74.1 - - - +
255A ALA* 1.3 55.7 + - - +
258A GLY* 2.7 35.2 + - - -
259A ILE 2.7 30.8 + - - -
260A ALA* 3.6 8.1 - - - -
261A VAL* 3.9 9.4 + - - +
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Residues in contact with ALA 255 (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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251A GLY 3.0 12.1 + - - +
252A PRO* 3.2 10.5 + - + +
254A SER* 1.3 75.7 + - - +
256A GLN* 1.3 66.0 + - - +
257A THR 3.3 0.5 + - - -
258A GLY* 3.5 7.2 + - - -
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Residues in contact with GLN 256 (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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213A ILE* 3.7 38.2 - - + +
252A PRO 3.1 15.9 + - - +
253A LEU* 3.9 11.3 - - - +
254A SER 3.3 0.2 - - - -
255A ALA* 1.3 78.0 - - - +
257A THR* 1.3 61.9 + - + +
297A VAL* 5.5 3.8 - - - +
301A SER* 3.9 21.6 + - - -
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Residues in contact with THR 257 (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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209A TYR* 3.4 22.5 - - + +
212A VAL* 4.0 26.4 - - + +
213A ILE* 3.6 32.8 - - + -
217A ARG* 5.1 4.7 + - - -
253A LEU 3.1 19.0 + - - +
254A SER 3.5 0.2 + - - -
255A ALA 3.2 0.4 - - - -
256A GLN* 1.3 78.4 - - + +
258A GLY* 1.3 61.9 + - - +
259A ILE* 3.2 19.4 + - - +
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Residues in contact with GLY 258 (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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254A SER 2.7 13.1 + - - -
255A ALA* 3.5 8.0 + - - -
257A THR* 1.3 77.6 - - - +
259A ILE* 1.4 63.1 + - - +
260A ALA 4.0 1.8 + - - -
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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