Contacts of the helix formed by residues 241 - 261 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237E LEU 3.2 4.5 + - - -
238E GLU* 3.3 8.7 + - - +
239E LYS 3.2 8.7 + - - -
240E ASN* 1.3 78.4 - - - +
242E PHE* 1.3 56.3 + - - +
243E LYS 3.3 3.3 + - - +
244E TYR* 3.4 23.0 + - - +
245E THR* 2.7 35.1 + - - -
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Residues in contact with PHE 242 (chain E).
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* 4.1 5.4 - - + -
175A LEU* 3.7 24.9 - - + -
176A PHE* 3.6 50.0 - + + -
242A PHE* 3.4 29.8 - + - -
245A THR* 3.8 16.4 - - + -
246A VAL* 3.8 14.6 - - + -
176E PHE* 3.9 11.0 - + - -
237E LEU* 2.9 50.5 + - + +
238E GLU* 5.1 0.2 - - - +
240E ASN 3.4 1.4 - - - -
241E SER* 1.3 72.0 - - - +
243E LYS* 1.3 63.3 + - - +
245E THR* 3.4 5.7 + - - -
246E VAL* 3.1 29.3 + - + +
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Residues in contact with LYS 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A LEU* 4.7 12.8 - - + +
178A GLU* 2.8 41.0 + - - +
179A SER* 3.3 24.3 + - - +
182A ASP* 2.6 32.4 + - - -
238E GLU* 5.5 10.0 - - - +
241E SER 3.3 0.8 - - - -
242E PHE* 1.3 78.1 - - - +
244E TYR* 1.3 59.3 + - - +
246E VAL* 3.4 3.8 + - - +
247E MSE 3.0 46.6 + - - +
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Residues in contact with TYR 244 (chain E).
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* 4.2 20.6 - - - -
241E SER* 3.4 24.6 + - - +
243E LYS* 1.3 76.1 - - - +
245E THR* 1.3 60.0 + - - +
247E MSE 4.4 9.2 - - + -
248E ASN* 2.7 71.0 + - + +
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Residues in contact with THR 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A SER* 4.7 0.3 + - - -
237A LEU* 3.8 20.6 - - + -
240A ASN* 3.6 46.4 + - + +
242A PHE* 3.9 21.8 - - + -
245A THR* 5.0 1.3 + - - -
240E ASN 3.9 4.3 + - - -
241E SER* 2.7 25.1 + - - -
242E PHE* 3.4 9.5 - - - -
243E LYS 3.3 0.2 - - - -
244E TYR* 1.3 78.8 - - - +
246E VAL* 1.3 61.7 + - - +
248E ASN* 3.9 1.6 - - - +
249E ALA* 3.1 24.3 + - - +
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Residues in contact with VAL 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PHE* 4.0 18.4 - - + +
179A SER* 3.8 18.6 - - - -
180A LEU* 3.8 35.0 - - + +
237A LEU* 4.4 6.7 - - + -
242A PHE* 3.7 27.8 - - + -
172E TYR* 6.1 1.8 - - + -
242E PHE* 3.1 21.2 + - + +
243E LYS 3.8 7.0 - - - +
245E THR* 1.3 75.4 - - - +
247E MSE 1.3 62.5 + - - +
249E ALA* 3.3 3.9 + - - +
250E VAL* 3.2 24.3 + - + +
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Residues in contact with MSE 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A SER 3.3 21.3 - - - +
182A ASP* 3.7 39.0 - - + +
183A ALA* 3.9 16.7 - - + +
186A LYS* 4.2 21.1 - - + -
187A ASN* 5.6 0.2 - - - +
243E LYS* 3.0 40.6 + - - +
244E TYR* 3.8 9.6 - - + +
246E VAL* 1.3 75.7 - - - +
248E ASN* 1.3 57.3 + - - +
250E VAL* 3.6 2.4 + - - +
251E GLU* 3.1 31.6 + - - +
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Residues in contact with ASN 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A SER* 3.0 17.0 + - - -
239A LYS* 5.7 3.5 - - - +
240A ASN* 3.3 15.1 + - - +
244E TYR* 2.7 55.1 + - + +
245E THR 3.9 3.8 - - - +
247E MSE 1.3 71.7 - - - +
249E ALA* 1.3 60.2 + - - +
251E GLU* 3.9 7.8 - - - +
252E ALA* 3.0 30.2 + - - +
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Residues in contact with ALA 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A GLY* 3.4 31.7 - - - +
236A SER* 3.4 14.3 + - - +
237A LEU* 3.6 20.4 - - + -
172E TYR* 3.6 9.8 + - + -
245E THR 3.1 17.6 + - - +
246E VAL 3.6 5.8 - - - +
247E MSE 3.3 0.2 - - - -
248E ASN* 1.3 75.5 - - - +
250E VAL* 1.3 63.8 + - + +
252E ALA* 3.5 0.7 + - - +
253E ALA 3.2 16.6 + - - -
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Residues in contact with VAL 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 3.9 26.5 - - + -
183A ALA* 3.8 22.7 - - + -
187A ASN* 5.4 0.2 - - - +
161E ILE* 3.6 27.8 - - + -
164E ALA* 3.3 12.8 - - + +
165E ILE* 3.7 17.9 - - + -
172E TYR* 4.0 20.2 - - + -
246E VAL 3.2 15.3 + - - +
247E MSE 3.6 0.6 + - - +
249E ALA* 1.3 75.6 - - - +
251E GLU* 1.3 58.5 + - - +
253E ALA 3.3 1.4 + - - -
254E CYS* 2.8 25.1 + - - +
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Residues in contact with GLU 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ALA* 5.5 0.5 - - - +
186A LYS* 2.9 39.5 + - - +
187A ASN* 3.3 29.6 + - - +
247E MSE 3.1 20.0 + - - +
248E ASN* 3.9 10.8 - - - +
250E VAL* 1.3 73.7 - - - +
252E ALA* 1.3 60.5 + - - +
254E CYS* 3.7 7.0 - - + +
255E GLU* 2.9 37.5 + - + +
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Residues in contact with ALA 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A VAL* 3.3 26.9 - - + +
236A SER* 4.0 17.5 - - - +
248E ASN* 3.0 20.3 + - - +
249E ALA 3.7 5.2 - - - +
251E GLU* 1.3 74.8 - - - +
253E ALA* 1.3 57.8 + - - +
255E GLU* 3.4 11.0 + - - +
256E LYS 3.0 22.0 + - - -
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Residues in contact with ALA 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ILE* 3.1 40.4 - - + +
232A VAL* 4.2 0.4 - - - +
233A GLY* 4.1 4.5 - - - +
164E ALA* 3.9 8.3 - - + -
168E CYS* 4.2 2.5 - - - -
172E TYR* 3.3 26.2 - - - +
249E ALA 3.2 4.6 + - - +
250E VAL 3.5 6.7 - - - +
252E ALA* 1.3 78.1 - - - +
254E CYS* 1.3 59.4 + - - +
256E LYS* 3.3 2.8 + - - -
257E SER* 2.9 24.6 + - - -
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Residues in contact with CYS 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ASN* 4.6 12.1 - - - -
160E ASP* 3.7 19.5 - - - +
161E ILE* 3.6 38.4 - - + -
164E ALA* 3.6 6.0 - - + +
250E VAL 2.8 17.8 + - - +
251E GLU* 3.7 9.6 - - + +
253E ALA* 1.3 75.4 - - - +
255E GLU* 1.3 62.1 + - - +
257E SER* 3.4 2.9 + - - -
258E LYS* 3.1 40.0 + - - +
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Residues in contact with GLU 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E GLU* 2.9 24.7 + - + +
252E ALA* 3.5 10.4 - - - +
253E ALA 3.2 0.2 - - - -
254E CYS* 1.3 77.2 - - - +
256E LYS* 1.3 56.1 + - - +
258E LYS* 3.3 8.8 + - - +
259E ALA* 3.0 28.6 + - + +
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Residues in contact with LYS 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLY 4.0 11.3 + - - -
228A GLY 3.9 17.9 - - - +
229A ILE* 4.0 8.7 - - - -
232A VAL* 3.6 31.8 - - + +
186C LYS 5.9 0.4 + - - -
252E ALA 3.0 16.6 + - - +
253E ALA* 3.3 5.6 + - - +
255E GLU* 1.3 73.8 - - - +
257E SER* 1.3 65.2 + - - +
259E ALA* 3.3 10.1 + - + +
260E MSE 3.1 53.0 + - + +
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Residues in contact with SER 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ILE* 3.7 28.8 - - - +
93E GLY* 3.4 17.8 + - - +
111E TRP* 5.1 1.0 - - - -
160E ASP* 2.7 43.9 + - - +
163E THR* 4.4 5.5 + - - -
253E ALA 2.9 13.2 + - - -
254E CYS 3.5 9.2 - - - -
256E LYS* 1.3 78.1 - - - +
258E LYS* 1.3 59.8 + - - +
260E MSE 4.9 0.2 - - - -
261E GLY* 3.2 15.6 + - - -
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Residues in contact with LYS 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ASN* 5.3 10.7 + - - +
157E LYS 4.7 9.5 + - - -
160E ASP* 3.4 35.2 - - - +
161E ILE* 6.5 0.4 - - - -
254E CYS* 3.1 30.9 + - - +
255E GLU* 3.8 7.2 - - - +
256E LYS 3.3 0.2 - - - -
257E SER* 1.3 74.2 - - - +
259E ALA* 1.3 61.9 + - - +
260E MSE 3.4 0.2 - - - -
261E GLY* 3.4 2.7 + - - +
262E SER* 2.9 28.2 + - - -
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Residues in contact with ALA 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E GLU 3.0 18.0 + - - +
256E LYS* 3.3 15.7 + - + +
258E LYS* 1.3 78.0 - - - +
260E MSE 1.3 61.7 + - + +
262E SER* 3.4 22.8 + - - +
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Residues in contact with MSE 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLY 4.0 16.2 - - - +
228A GLY* 4.6 4.7 - - - -
229A ILE* 3.8 25.4 - - + -
68E PRO* 3.7 36.6 - - + -
92E GLY 3.8 6.7 - - - +
93E GLY* 4.1 8.5 - - - -
94E LEU* 4.3 16.0 - - + +
98E LYS* 5.8 0.3 - - - +
256E LYS* 3.1 43.4 + - + +
257E SER 4.1 3.6 - - - +
259E ALA* 1.3 76.6 - - + +
261E GLY* 1.3 59.0 + - - +
262E SER* 3.2 6.9 + - - +
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Residues in contact with GLY 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E GLY 3.2 22.2 + - - -
94E LEU* 5.0 1.1 - - - -
95E ASN* 3.0 26.2 + - - +
98E LYS* 4.8 7.1 - - - +
257E SER 3.2 13.0 + - - -
258E LYS* 3.4 6.0 + - - -
259E ALA 3.2 0.4 - - - -
260E MSE 1.3 75.9 - - - +
262E SER* 1.3 60.5 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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