Contacts of the helix formed by residues 243 - 261 (chain A) in PDB entry 5INQ
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 HIS 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A LYS* 4.4 25.1 - - + +
214A MET* 3.3 23.2 - - + +
238A GLU* 3.8 18.1 - - + +
239A SER 3.2 17.1 + - - +
240A THR* 3.1 27.5 + - + -
241A ARG 3.1 1.0 + - - -
242A GLU* 1.3 86.7 - - + +
244A SER* 1.3 63.6 + - - +
245A ALA* 3.3 3.7 + - - -
246A GLU* 3.4 8.7 + - + +
247A ARG* 3.0 23.8 + - - +
4C A 5.9 5.3 + - + -
5C A 4.9 12.7 + - - -
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Residues in contact with SER 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ARG* 3.1 17.0 + - - -
242A GLU 3.4 2.0 + - - -
243A HIS* 1.3 77.0 - - - +
245A ALA* 1.3 62.4 + - - +
247A ARG* 3.3 13.9 + - - +
248A ILE* 2.9 33.0 + - - +
279A GLU* 2.7 30.9 + - - +
282A LYS* 5.8 1.4 - - - +
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Residues in contact with ALA 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLU 5.3 0.4 + - - -
243A HIS* 3.3 1.4 - - - +
244A SER* 1.3 79.7 - - - +
246A GLU* 1.3 62.8 + - - +
248A ILE* 3.2 9.8 + - - +
249A ARG* 3.0 43.0 + - - +
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Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 4.3 2.9 - - - +
211A ASN* 3.4 23.8 + - - +
212A THR 3.3 13.3 + - - -
238A GLU* 3.8 19.5 - - + +
243A HIS* 3.4 13.6 + - + +
245A ALA* 1.3 74.9 - - - +
247A ARG* 1.3 60.3 + - - +
249A ARG* 2.9 44.6 + - - +
250A GLN* 2.8 66.4 + - - +
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Residues in contact with ARG 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU* 4.0 6.6 - - + +
238A GLU* 2.7 44.9 + - - +
239A SER* 3.8 0.4 - - - +
240A THR 2.8 35.8 + - - +
241A ARG* 3.8 5.5 - - - +
243A HIS 3.0 12.4 + - - +
244A SER* 3.5 12.4 - - - +
246A GLU* 1.3 77.3 - - - +
248A ILE* 1.3 56.5 + - + +
250A GLN* 3.2 8.6 + - - +
251A LEU* 2.9 27.0 + - - +
273A THR 3.2 26.2 - - - +
274A ASN* 3.1 17.7 + - - +
275A LEU* 4.0 12.3 - - + -
276A ARG* 3.6 11.2 - - - +
279A GLU* 2.7 40.4 + - - +
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Residues in contact with ILE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A SER* 2.9 31.9 + - - +
245A ALA* 3.6 10.1 - - - +
247A ARG* 1.3 76.5 - - + +
249A ARG* 1.3 65.9 + - + +
251A LEU* 3.3 8.6 + - + +
252A LYS* 3.1 38.3 + - - +
275A LEU* 5.5 2.0 - - + -
279A GLU* 4.0 27.1 - - + +
282A LYS* 4.1 30.3 - - + +
283A CYS* 4.0 24.0 - - + -
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Residues in contact with ARG 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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211A ASN* 4.5 19.6 + - - +
245A ALA* 3.0 32.8 + - - +
246A GLU* 2.9 51.3 + - - +
248A ILE* 1.3 78.5 - - + +
250A GLN* 1.3 60.9 + - - +
252A LYS* 3.3 16.2 + - + +
253A THR* 3.1 23.7 + - - -
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Residues in contact with GLN 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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209A PHE* 3.3 34.8 - - + -
212A THR* 3.9 5.1 + - - -
216A ARG* 4.4 0.9 - - - +
237A LEU* 3.3 19.0 - - + +
238A GLU* 2.8 51.7 + - - -
246A GLU* 2.8 45.8 + - - +
247A ARG* 3.5 4.0 - - - +
249A ARG* 1.3 74.3 - - - +
251A LEU* 1.3 67.3 + - - +
253A THR* 3.0 10.8 + - - -
254A VAL* 2.9 26.6 + - - +
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Residues in contact with LEU 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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237A LEU* 4.0 17.3 - - + +
247A ARG 2.9 13.7 + - - +
248A ILE* 3.6 10.1 - - - +
250A GLN* 1.3 75.1 - - - +
252A LYS* 1.3 57.0 + - - +
254A VAL* 3.1 8.6 + - + +
255A LEU* 2.8 46.3 + - + +
273A THR* 5.8 0.2 - - + -
275A LEU* 4.0 30.3 - - + -
279A GLU 5.1 0.4 - - - +
280A VAL* 4.4 13.5 - - + -
283A CYS* 3.7 28.0 - - + -
286A LEU* 5.5 1.1 - - + -
329A PHE* 3.9 29.2 - - + -
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Residues in contact with LYS 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 ILE* 3.1 30.4 + - + +
249A ARG* 3.5 16.2 - - + +
250A GLN 3.1 0.4 - - - -
251A LEU* 1.3 75.3 - - - +
253A THR* 1.3 58.3 - - - +
255A LEU* 4.0 6.1 - - + +
256A GLY* 2.9 28.2 + - - -
282A LYS 5.1 3.0 + - - -
283A CYS* 3.5 39.1 - - - +
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Residues in contact with THR 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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207A ILE* 4.0 22.7 - - + -
208A PRO 4.7 2.0 - - - +
209A PHE* 3.8 26.9 - - + -
210A PRO* 6.0 1.9 - - - +
218A LEU* 4.8 2.5 - - + -
249A ARG 3.1 13.5 + - - -
250A GLN* 3.0 11.3 + - - -
252A LYS* 1.3 76.1 - - - +
254A VAL* 1.3 63.8 + - - +
256A GLY* 3.9 1.0 - - - -
257A LYS* 3.0 23.3 + - + +
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A PHE* 4.3 6.7 - - + -
218A LEU* 4.1 24.9 - - + -
233A MET* 3.7 7.1 - - + +
235A SER* 4.8 0.2 - - - -
237A LEU* 4.3 20.6 - - + -
250A GLN 2.9 17.3 + - - +
251A LEU* 3.1 17.9 + - + +
253A THR* 1.3 77.2 - - - +
255A LEU* 1.3 63.8 + - - +
257A LYS* 3.2 5.2 + - - +
258A MET* 3.0 28.3 + - - +
269A PHE* 3.7 37.0 - - + -
329A PHE* 5.0 2.9 - - + -
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Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 2.8 40.6 + - + +
252A LYS* 4.0 5.6 - - - +
254A VAL* 1.3 77.9 - - + +
256A GLY* 1.3 62.5 + - - +
258A MET* 3.4 16.8 + - - +
259A GLN* 3.3 28.0 + - - +
280A VAL* 6.5 0.2 - - + -
283A CYS* 4.7 9.2 - - - -
285A GLY 4.8 5.6 - - - +
286A LEU* 3.9 26.5 - - + -
287A PRO* 3.9 27.3 - - + +
290A VAL* 4.1 18.4 - - + -
329A PHE* 4.4 9.4 - - + -
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Residues in contact with GLY 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 LYS 2.9 16.6 + - - -
253A THR* 3.9 1.8 - - - -
255A LEU* 1.3 78.0 - - - +
257A LYS* 1.3 59.7 + - - +
259A GLN* 3.3 13.5 + - - +
260A GLU* 3.3 31.1 + - - +
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Residues in contact with LYS 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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205A GLU* 2.9 33.9 + - - -
207A ILE* 4.1 17.6 - - + +
218A LEU* 3.8 17.5 - - + -
220A CYS* 4.1 9.6 - - - -
231A CYS* 5.1 9.6 - - - -
233A MET* 3.9 18.7 - - + +
253A THR* 3.0 14.7 + - + +
254A VAL 3.2 8.3 + - - +
256A GLY* 1.3 73.1 - - - +
258A MET* 1.3 64.3 + - - +
260A GLU* 3.1 37.3 + - + +
261A ALA* 3.6 10.9 + - - +
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Residues in contact with MET 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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233A MET* 3.8 18.2 - - + -
254A VAL* 3.0 21.8 + - - +
255A LEU* 3.6 26.0 - - - +
257A LYS* 1.3 75.5 - - - +
259A GLN* 1.3 59.7 + - - +
261A ALA 3.8 2.8 + - - -
267A VAL* 3.9 26.1 - - + +
269A PHE* 4.1 11.4 - - - +
290A VAL* 4.1 14.8 - - + -
329A PHE* 3.6 45.5 - - + +
330A PHE* 3.8 12.8 - - - -
331A ARG* 3.1 36.7 + - + +
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Residues in contact with GLN 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 LEU 3.3 16.4 + - - +
256A GLY* 3.7 12.7 - - - +
257A LYS 3.1 0.6 - - - -
258A MET* 1.3 79.3 - - - +
260A GLU* 1.3 62.5 + - + +
261A ALA 3.7 1.9 - - - +
263A ASP* 5.3 1.2 - - - +
287A PRO* 3.2 33.6 - - - +
289A ASN* 3.7 22.1 + - - +
290A VAL* 4.8 7.0 - - + -
331A ARG* 3.3 15.8 + - - +
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Residues in contact with GLU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A GLY* 3.3 19.2 + - - +
257A LYS* 3.1 33.9 + - + +
259A GLN* 1.3 75.6 - - - +
261A ALA* 1.3 67.9 + - - +
262A PRO* 3.6 2.8 - - - +
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Residues in contact with ALA 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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231A CYS* 4.8 11.2 - - + -
257A LYS* 3.6 10.6 + - - +
258A MET 4.0 2.2 - - - +
259A GLN 3.3 3.3 - - - +
260A GLU* 1.3 81.4 - - - +
262A PRO* 1.3 77.0 - - + +
263A ASP* 3.6 3.6 + - - +
265A THR* 4.7 4.3 - - - -
267A VAL* 3.5 32.8 - - + -
331A ARG* 2.9 18.3 + - - +
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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