Contacts of the helix formed by residues 247 - 261 (chain A) in PDB entry 5ICN
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 ARG 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A ALA 3.2 12.8 + - - +
244A ALA* 3.7 18.8 - - - +
245A ALA 3.3 2.8 - - - -
246A SER* 1.3 83.3 - - - +
248A ASP* 1.3 67.5 + - - +
249A ILE* 3.3 5.4 - - + -
250A THR* 3.3 13.3 + - - -
251A LEU* 3.5 8.1 + - - +
283A ASP* 2.8 37.9 + - - +
285A MET* 4.1 16.3 - - - +
286A GLU* 5.8 3.6 - - - -
329A MET* 3.5 34.6 + - - +
332A THR* 5.3 4.6 + - - -
330B TYR* 5.7 8.6 + - + -
332B ASP* 3.4 39.9 + - - +
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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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247A ARG* 1.3 74.5 - - - +
249A ILE* 1.3 55.5 + - - +
251A LEU* 2.8 16.7 + - - +
252A PHE* 2.7 48.8 + - + -
40B ASN* 2.8 30.7 + - - +
43B LEU* 4.1 3.5 - - + +
44B ASN* 3.0 29.2 + - - +
331B ASN* 3.9 3.1 - - - +
332B ASP* 2.9 38.1 + - - +
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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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244A ALA 5.5 1.1 - - - +
247A ARG* 4.5 6.1 - - + +
248A ASP* 1.3 78.0 - - - +
250A THR* 1.3 73.0 + - - +
252A PHE* 3.9 8.5 - - - +
253A HIS* 2.9 29.1 + - + +
281A CYS* 4.2 17.7 - - + +
282A ARG 3.9 9.6 - - - +
283A ASP* 3.8 53.2 - - + +
286A GLU* 6.1 0.2 - - - +
325A GLU* 5.5 2.7 - - - +
332B ASP* 4.4 2.4 + - - +
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Residues in contact with THR 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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217A ALA* 3.9 26.6 - - + +
218A ARG* 4.7 2.0 - - + -
221A GLY* 5.3 2.7 - - - -
225A ARG* 4.1 7.5 + - - +
244A ALA 4.1 2.8 + - - -
245A ALA* 3.3 33.3 + - + +
247A ARG 3.3 6.5 + - - -
248A ASP 3.2 0.6 - - - -
249A ILE* 1.3 78.2 - - - +
251A LEU* 1.3 62.1 + - + +
253A HIS* 3.3 8.1 + - + +
254A ALA* 2.9 26.3 + - - +
281A CYS* 3.8 25.2 + - + +
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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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214A LEU* 4.3 30.3 - - + +
217A ALA* 6.1 0.7 - - + -
218A ARG* 3.9 35.7 - - + +
246A SER 4.0 13.0 - - - +
247A ARG 3.7 7.9 - - - +
248A ASP* 2.8 27.6 + - - +
250A THR* 1.3 73.5 - - - +
252A PHE* 1.3 67.2 + - - +
254A ALA* 2.7 18.8 + - + +
255A MET* 2.9 17.4 + - - +
43B LEU* 3.9 15.7 - - + -
44B ASN* 3.9 15.3 - - - +
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Residues in contact with PHE 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* 2.7 33.9 + - + +
249A ILE* 3.9 7.4 - - - +
251A LEU* 1.3 72.7 - - - +
253A HIS* 1.3 61.9 + - - +
255A MET* 3.0 15.6 + - + +
256A ASP* 3.0 23.1 + - - +
39B HIS* 3.2 39.9 - + - -
40B ASN* 3.3 26.7 - - - -
43B LEU* 3.6 34.8 - - + -
48B TYR* 3.5 33.2 - + - -
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Residues in contact with HIS 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 ILE* 2.9 19.2 + - + +
250A THR* 3.5 6.1 - - + +
251A LEU 3.1 0.2 - - - -
252A PHE* 1.3 76.2 - - - +
254A ALA* 1.3 53.5 + - - +
256A ASP* 3.5 11.3 + - + +
257A THR* 2.6 48.6 + - - -
260A LYS* 6.2 1.8 - - - -
272A LEU* 4.8 7.1 - - + +
279A VAL* 4.7 20.0 - - + +
281A CYS* 3.6 30.7 - - - -
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Residues in contact with ALA 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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213A PHE* 3.6 17.3 - - + -
214A LEU* 3.6 19.5 - - + -
217A ALA* 3.5 29.2 - - + -
250A THR 2.9 12.9 + - - +
251A LEU* 2.7 19.2 + - - +
253A HIS* 1.3 70.9 - - - +
255A MET* 1.3 60.8 + - - +
257A THR* 3.6 5.3 + - - -
258A LEU* 3.3 19.8 + - - +
272A LEU* 5.5 1.8 - - - -
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Residues in contact with MET 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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198A VAL 4.3 0.6 - - - +
199A TRP* 3.3 64.0 - - + -
210A ILE* 4.0 12.8 - - + -
214A LEU* 4.0 24.5 - - + -
251A LEU 2.9 15.9 + - - +
252A PHE* 3.6 6.5 - - - +
254A ALA* 1.3 73.9 - - - +
256A ASP* 1.3 65.1 + - - +
258A LEU* 3.7 2.0 - - - +
259A HIS* 3.3 12.1 + - - +
43B LEU* 4.1 20.9 - - + -
48B TYR* 3.7 33.7 - - + +
49B ARG* 4.3 13.0 - - + +
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Residues in contact with ASP 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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198A VAL* 3.3 30.7 - - - +
252A PHE* 3.0 19.4 + - - +
253A HIS* 3.8 13.1 + - + +
255A MET* 1.3 73.6 - - - +
257A THR* 1.3 62.2 + - - +
258A LEU 3.1 1.6 - - - -
259A HIS* 3.1 6.3 + - - +
260A LYS* 2.8 54.8 + - + +
48B TYR* 4.0 4.5 + - - -
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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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213A PHE* 4.5 4.0 - - + -
253A HIS* 2.6 42.3 + - - -
254A ALA* 3.8 8.6 - - - -
255A MET 3.5 0.2 - - - -
256A ASP* 1.3 76.2 - - - +
258A LEU* 1.3 63.7 + - - +
260A LYS* 4.7 4.9 - - - -
261A ASN* 2.7 30.0 + - - +
268A ALA* 3.6 15.8 - - + +
271A ALA* 3.6 31.2 - - + -
272A LEU* 4.3 13.1 - - + +
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Residues in contact with LEU 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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199A TRP* 4.0 26.0 - - + -
205A LEU* 4.0 15.5 - - + -
210A ILE* 4.3 17.0 - - + -
213A PHE* 3.8 28.0 - - + -
214A LEU* 5.3 0.7 - - + -
254A ALA 3.3 12.8 + - - +
255A MET* 3.7 10.8 - - - +
256A ASP 3.1 0.4 - - - -
257A THR* 1.3 79.8 - - - +
259A HIS* 1.3 62.3 + - - +
261A ASN* 3.0 10.9 + - - +
263A TYR* 3.0 31.5 + - + -
265A ILE* 3.9 28.0 - - + -
268A ALA* 4.2 15.7 - - + -
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Residues in contact with HIS 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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197A GLN* 3.3 42.7 + - - +
198A VAL* 3.6 21.5 - - - +
199A TRP* 4.2 4.3 - - - -
200A GLU* 3.7 13.3 + - + -
255A MET 3.3 6.3 + - - +
256A ASP* 3.1 7.2 + - - +
258A LEU* 1.3 77.0 - - - +
260A LYS* 1.3 73.8 + - + +
262A ILE* 3.1 18.9 + - - +
263A TYR* 2.8 42.0 + + - +
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Residues in contact with LYS 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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253A HIS* 6.2 1.6 - - - -
256A ASP* 2.8 40.2 + - + +
257A THR* 4.2 2.2 - - - +
259A HIS* 1.3 82.2 - - + +
261A ASN* 1.3 67.0 + - - +
262A ILE* 3.2 12.7 + - - +
267A LYS* 5.8 0.5 - - - -
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Residues in contact with ASN 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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257A THR* 2.7 26.0 + - - +
258A LEU 3.0 5.4 + - - +
260A LYS* 1.3 82.8 - - - +
262A ILE* 1.3 72.1 + - - +
263A TYR 3.2 2.2 - - - -
264A ASP* 3.2 17.6 + - - +
267A LYS* 3.1 51.4 + - + +
268A ALA* 3.5 20.8 - - + +
271A ALA* 3.9 16.6 - - - +
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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