Contacts of the helix formed by residues 241 - 261 (chain A) in PDB entry 2RCY
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 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A LEU 3.3 1.5 + - - -
238A GLU* 3.2 12.1 + - - +
239A LYS 3.3 0.7 + - - -
240A ASN* 1.3 78.2 - - - +
242A PHE* 1.3 57.4 + - - +
243A LYS* 3.3 2.7 - - - +
244A TYR* 3.4 15.2 + - - +
245A THR* 2.8 33.4 + - - -
238B GLU 3.5 21.3 + - - -
239B LYS 3.7 7.9 + - - -
241B SER* 2.8 23.4 + - - +
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Residues in contact with PHE 242 (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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176A PHE* 3.8 12.6 - + - -
237A LEU* 2.8 51.0 + - + +
238A GLU* 5.0 0.2 - - - +
240A ASN 3.3 1.2 + - - -
241A SER* 1.3 72.5 - - - +
243A LYS* 1.3 62.6 + - - +
245A THR* 3.3 6.1 + - - -
246A VAL* 3.1 33.1 + - + +
172E TYR 4.1 4.0 - - - -
175E LEU* 3.8 25.1 - - + -
176E PHE* 3.6 50.9 - + + -
179E SER* 4.4 1.6 - - - -
242E PHE* 3.4 28.3 - + - -
245E THR* 3.9 15.7 - - + -
246E VAL* 3.7 15.0 - - + -
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Residues in contact with LYS 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLU* 5.6 5.3 - - - +
241A SER* 3.3 0.4 - - - -
242A PHE* 1.3 80.7 - - - +
244A TYR* 1.3 56.5 + - - +
246A VAL* 3.3 4.2 + - - +
247A MSE 3.0 41.0 + - - +
220B LYS* 3.9 17.8 - - - +
238B GLU* 3.4 38.8 + - + +
178C GLU* 5.7 0.2 + - - -
175E LEU* 4.5 12.7 - - + +
178E GLU* 2.7 37.4 + - - +
179E SER* 3.3 26.2 - - - +
182E ASP* 2.9 29.4 + - - -
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Residues in contact with TYR 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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241A SER* 3.4 15.0 + - - +
243A LYS* 1.3 78.3 - - - +
245A THR* 1.3 59.2 + - - +
247A MSE 4.3 5.2 - - - -
248A ASN* 2.7 56.0 + - + +
235B TYR* 3.4 43.3 + + - -
238B GLU* 3.5 28.7 + - + +
239B LYS* 3.5 55.7 - - + +
240E ASN* 4.2 23.3 + - - -
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Residues in contact with THR 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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240A ASN 3.9 4.7 + - - -
241A SER* 2.8 26.1 + - - -
242A PHE* 3.5 9.0 - - - -
243A LYS 3.3 0.2 - - - -
244A TYR* 1.3 79.0 - - - +
246A VAL* 1.3 61.2 + - - +
248A ASN* 3.9 1.6 - - - +
249A ALA* 3.1 22.7 + - - +
236E SER* 4.7 0.9 + - - +
237E LEU* 3.8 9.8 - - + +
240E ASN* 3.4 43.9 + - + +
242E PHE* 3.8 36.1 - - + -
245E THR* 5.0 1.2 + - - -
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Residues in contact with VAL 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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172A TYR* 6.0 1.8 - - + -
242A PHE* 3.1 20.0 + - + +
243A LYS 3.7 6.1 - - - +
245A THR* 1.3 73.1 - - - +
247A MSE 1.3 64.3 + - - +
249A ALA* 3.2 4.2 + - - +
250A VAL* 3.1 23.9 + - + +
176E PHE* 3.9 19.3 - - + -
179E SER* 3.8 18.2 - - - -
180E LEU* 3.8 37.7 - - + +
237E LEU* 4.5 7.0 - - + -
242E PHE* 3.8 27.4 - - + -
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Residues in contact with MSE 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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243A LYS* 3.0 35.2 + - + +
244A TYR* 3.8 3.1 - - - +
246A VAL* 1.3 75.5 - - - +
248A ASN* 1.3 57.4 + - - +
250A VAL* 3.5 2.8 + - - +
251A GLU* 3.0 30.0 + - - +
231B ALA 5.1 1.6 - - - +
235B TYR* 3.6 38.9 - - + +
238B GLU* 4.7 12.3 - - - -
179E SER 3.4 20.6 - - - +
182E ASP* 3.5 40.6 - - + +
183E ALA* 3.8 14.8 - - + +
186E LYS* 3.9 15.5 - - + -
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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 TYR* 2.7 43.2 + - + +
245A THR 3.9 3.6 - - - +
247A MSE 1.3 70.1 - - - +
249A ALA* 1.3 59.2 + - - +
251A GLU* 3.8 2.8 - - - +
252A ALA* 2.9 31.7 + - - +
235B TYR* 2.8 28.0 + - - +
236E SER* 3.0 17.7 + - - +
239E LYS* 5.6 3.5 - - - +
240E ASN* 3.3 15.3 + - - +
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Residues in contact with ALA 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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172A TYR* 4.5 8.3 - - + -
245A THR 3.1 19.0 + - - +
246A VAL* 3.2 5.4 + - - +
248A ASN* 1.3 73.7 - - - +
250A VAL* 1.3 64.6 + - + +
252A ALA* 3.5 1.2 + - - +
253A ALA* 3.1 22.9 + - - +
233E GLY* 3.5 27.7 - - - +
236E SER* 3.3 13.4 + - - +
237E LEU* 3.6 20.4 - - + -
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Residues in contact with VAL 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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161A ILE* 3.6 27.8 - - + -
164A ALA* 3.3 12.0 - - + +
165A ILE* 3.8 15.7 - - + -
172A TYR* 4.1 20.0 - - + -
246A VAL* 3.1 14.9 + - + +
247A MSE 3.8 1.1 - - - +
249A ALA* 1.3 75.1 - - + +
251A GLU* 1.3 58.1 + - - +
253A ALA 3.3 1.9 + - - -
254A CYS* 2.9 24.3 + - - +
180E LEU* 3.8 27.1 - - + -
183E ALA* 3.7 25.6 - - + +
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Residues in contact with GLU 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 MSE 3.0 17.4 + - - +
248A ASN* 4.0 7.4 - - - +
250A VAL* 1.3 73.3 - - - +
252A ALA* 1.3 60.2 + - - +
254A CYS* 3.2 8.0 + - + +
255A GLU* 2.9 45.6 + - + +
235B TYR* 4.2 16.9 + - - +
186E LYS* 2.7 42.9 + - - +
187E ASN* 3.5 28.5 + - - +
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Residues in contact with ALA 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* 2.9 22.9 + - - +
249A ALA 3.7 4.7 - - - +
251A GLU* 1.3 74.9 - - - +
253A ALA* 1.3 62.0 + - - +
255A GLU* 3.5 12.3 + - - +
256A LYS 3.2 16.5 + - - -
232E VAL* 3.4 26.1 - - + +
236E SER* 4.1 16.8 - - - +
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Residues in contact with ALA 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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164A ALA* 3.8 8.5 - - + -
168A CYS* 4.4 1.1 - - - -
172A TYR* 3.6 22.9 - - - +
249A ALA 3.1 9.0 + - - +
250A VAL 3.4 8.7 - - - +
252A ALA* 1.3 74.5 - - - +
254A CYS* 1.3 58.6 + - - +
256A LYS* 3.2 2.9 + - - +
257A SER* 3.0 23.9 + - - -
229E ILE* 3.1 42.6 - - + +
232E VAL* 4.3 2.2 - - - +
233E GLY* 4.3 3.6 - - - +
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Residues in contact with CYS 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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160A ASP* 3.9 15.0 - - - +
161A ILE* 3.7 35.9 - - + -
164A ALA* 3.8 6.7 - - + +
250A VAL 2.9 14.5 + - - +
251A GLU* 3.2 14.1 + - + +
253A ALA* 1.3 77.9 - - - +
255A GLU* 1.3 60.6 + - - +
257A SER* 3.5 3.8 + - - -
258A LYS* 3.2 37.5 + - - +
187E ASN* 4.3 16.4 - - - -
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Residues in contact with GLU 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 GLU* 2.9 40.0 + - + +
252A ALA* 3.7 9.6 - - - +
253A ALA 3.3 0.2 - - - -
254A CYS* 1.3 74.1 - - + +
256A LYS* 1.3 56.2 + - - +
258A LYS* 3.3 8.8 + - + +
259A ALA* 2.8 34.9 + - - +
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Residues in contact with LYS 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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252A ALA 3.2 11.2 + - - +
253A ALA* 3.2 10.6 + - - +
255A GLU* 1.3 77.8 - - - +
257A SER* 1.3 63.0 + - - +
259A ALA* 4.2 8.7 - - + +
260A MSE 3.1 50.9 + - + +
186D LYS 5.8 0.8 + - - -
227E GLY* 3.8 24.0 + - - -
228E GLY 3.9 6.3 - - - -
229E ILE* 3.8 16.6 - - - -
232E VAL* 3.7 31.4 - - + +
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Residues in contact with SER 257 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A GLY* 3.3 22.5 + - - -
111A TRP* 5.0 1.4 - - - -
160A ASP* 2.7 43.5 + - - +
163A THR* 4.4 5.6 + - - -
253A ALA 3.0 13.0 + - - -
254A CYS 3.6 8.7 - - - -
256A LYS* 1.3 76.9 - - - +
258A LYS* 1.3 56.0 + - - +
261A GLY* 3.1 20.1 + - - -
229E ILE* 3.8 24.4 - - - +
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Residues in contact with LYS 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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157A LYS 4.7 9.6 + - - -
160A ASP* 3.4 35.4 - - - +
161A ILE 5.7 0.2 - - - +
254A CYS* 3.2 27.4 + - - +
255A GLU* 3.7 8.1 - - + +
257A SER* 1.3 74.5 - - - +
259A ALA* 1.3 64.9 + - - +
261A GLY* 3.1 11.2 + - - +
262A SER* 3.2 18.2 + - - -
187E ASN* 5.3 8.5 + - - +
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Residues in contact with ALA 259 (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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255A GLU 2.8 17.5 + - - +
256A LYS* 3.4 15.5 + - + +
258A LYS* 1.3 77.0 - - - +
260A MSE 1.3 61.2 + - + +
262A SER* 3.3 22.8 + - - +
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Residues in contact with MSE 260 (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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68A PRO* 3.7 35.7 - - + -
69A ASP 5.8 0.2 - - - +
92A GLY 3.9 6.7 - - - +
93A GLY* 4.1 10.4 - - - +
94A LEU* 4.4 9.5 - - + +
98A LYS* 2.9 22.2 + - - -
256A LYS* 3.1 41.7 + - + +
257A SER 4.0 4.0 - - - +
259A ALA* 1.3 76.4 - - + +
261A GLY* 1.3 56.0 + - - +
262A SER* 3.2 2.3 - - - +
227E GLY 4.0 16.2 - - - +
228E GLY* 4.6 5.4 - - - -
229E ILE* 3.7 26.7 - - + -
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Residues in contact with GLY 261 (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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93A GLY 3.3 19.1 - - - -
95A ASN* 3.2 25.1 + - - +
98A LYS* 3.9 8.4 + - - +
160A ASP* 5.7 0.7 - - - -
257A SER 3.1 11.6 + - - -
258A LYS* 3.1 10.8 + - - -
260A MSE 1.3 77.9 - - - +
262A SER* 1.3 57.2 - - - +
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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