Contacts of the helix formed by residues 246 - 262 (chain A) in PDB entry 2IKS
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 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A ARG* 5.0 2.5 - - - +
220A TYR* 3.6 25.9 - - - +
244A THR* 3.3 2.7 + - - -
245A THR* 1.3 81.8 + - - +
247A PHE* 1.3 65.0 + - - +
248A ALA* 3.3 16.6 + - - +
249A LEU* 3.2 26.5 + - - +
250A LEU 3.2 8.7 + - - -
272A THR* 3.6 5.6 + - - -
273A PHE* 3.6 11.2 - - - -
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Residues in contact with PHE 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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246A SER* 1.3 75.0 - - - +
248A ALA* 1.3 56.3 + - - +
250A LEU* 3.1 15.0 + - + +
251A GLN* 2.8 60.7 + - + +
254A MSE 4.5 10.5 - - + -
272A THR* 3.8 18.2 - - + -
273A PHE 3.1 12.3 + - - +
274A GLY* 4.2 17.5 - - - -
275A ASP 4.2 4.9 - - - +
276A ASN* 4.0 28.7 - - + -
279A LEU* 3.7 33.4 - - + -
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Residues in contact with ALA 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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220A TYR 3.9 15.7 - - - +
221A GLU* 4.2 0.9 - - - -
222A ARG* 3.3 30.9 - - + +
246A SER* 3.2 10.6 + - - +
247A PHE* 1.3 79.0 - - - +
249A LEU* 1.3 60.0 + - - +
251A GLN* 3.3 17.4 + - - +
252A GLY 3.2 17.2 + - - -
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Residues in contact with LEU 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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185A LEU* 3.6 20.4 - - + +
186A GLY 3.6 22.0 - - - +
187A ALA* 4.4 0.2 - - + -
217A ALA* 4.2 11.0 - - + -
219A SER 3.8 22.2 - - - +
220A TYR* 4.0 12.3 - - + -
221A GLU 3.9 9.4 - - - +
225A ALA* 3.6 23.6 - - + +
244A THR* 4.3 7.0 - - - -
245A THR* 3.5 24.0 - - - +
246A SER* 3.2 19.3 + - - +
248A ALA* 1.3 72.5 - - - +
250A LEU* 1.3 66.3 + - - +
252A GLY 3.2 2.4 + - - -
253A VAL* 3.2 24.6 + - - +
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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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242A LEU* 3.8 20.6 - - + -
244A THR* 3.4 20.3 - - - +
246A SER 3.2 2.6 + - - -
247A PHE* 3.1 25.7 + - + +
249A LEU* 1.3 78.5 - - - +
251A GLN* 1.3 63.1 + - - +
253A VAL* 3.1 3.4 + - + +
254A MSE 2.9 51.0 + - + +
270A ILE* 3.6 30.3 - - + -
272A THR* 3.8 30.1 - - + +
279A LEU* 4.7 6.7 - - + -
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Residues in contact with GLN 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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222A ARG* 3.5 31.1 + - + +
247A PHE* 2.8 47.5 + - + +
248A ALA* 3.5 23.1 - - - +
249A LEU 3.3 0.2 - - - -
250A LEU* 1.3 72.5 - - - +
252A GLY* 1.3 56.7 + - - +
254A MSE 3.3 15.2 + - + +
255A ASP* 2.8 34.1 + - - +
277B GLU* 3.4 23.4 + - - +
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Residues in contact with GLY 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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222A ARG* 3.3 28.9 - - - +
225A ALA* 4.2 0.2 - - - -
226A ALA* 3.5 15.2 - - - +
248A ALA 3.2 9.1 + - - -
249A LEU 3.2 3.5 + - - -
250A LEU 3.2 0.4 - - - -
251A GLN* 1.3 78.5 - - - +
253A VAL* 1.3 61.8 + - - +
255A ASP* 3.4 4.7 + - - +
256A VAL* 3.1 27.2 + - - +
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Residues in contact with VAL 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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185A LEU* 3.4 33.0 - - + -
225A ALA* 5.2 0.4 - - + -
229A PHE* 3.7 45.1 - - + -
238A MSE 6.0 0.2 - - - -
239A PRO* 6.2 0.2 - - + -
242A LEU* 3.8 32.8 - - + -
244A THR* 4.6 0.7 - - + -
249A LEU 3.2 6.3 + - - +
250A LEU* 3.1 9.1 + - + +
252A GLY* 1.3 75.0 - - - +
254A MSE 1.3 61.2 + - + +
256A VAL* 3.2 4.2 + - - +
257A THR* 2.9 36.9 + - - +
268A LEU* 6.4 1.3 - - + -
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Residues in contact with MSE 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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247A PHE* 4.5 9.9 - - + -
250A LEU* 2.9 52.4 + - + +
251A GLN* 3.8 25.1 - - + +
253A VAL* 1.3 79.1 - - + +
255A ASP* 1.3 56.2 + - - +
257A THR* 3.8 5.6 - - - -
258A LEU* 2.9 39.2 + - - +
264A LEU* 4.3 14.6 - - + -
270A ILE* 4.8 4.0 - - + -
279A LEU* 4.7 4.5 - - + -
282A LEU* 4.4 15.9 - - - -
281B PHE* 3.7 39.9 - - + -
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Residues in contact with ASP 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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222A ARG* 2.8 48.0 + - - +
223A GLU* 5.4 3.3 - - - +
226A ALA* 4.8 3.8 - - + +
251A GLN 2.8 17.6 + - - +
252A GLY* 3.4 9.9 - - - +
254A MSE 1.3 77.6 - - - +
256A VAL* 1.3 57.7 + - - +
258A LEU* 4.0 6.7 - - - +
259A ARG* 3.0 44.7 + - - +
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Residues in contact with VAL 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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226A ALA* 3.3 35.2 - - + +
229A PHE* 3.8 20.6 - - + -
230A GLU* 4.1 20.9 - - + -
233A LEU* 3.9 18.8 - - + -
252A GLY 3.1 14.3 + - - +
253A VAL 3.2 6.5 + - - +
255A ASP* 1.3 73.8 - - - +
257A THR* 1.3 61.6 + - - +
259A ARG* 3.2 18.6 + - - +
260A ARG* 2.8 35.0 + - + +
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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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229A PHE* 3.7 14.2 - - - -
238A MSE 3.9 27.6 - - + -
253A VAL* 2.9 22.9 + - - +
254A MSE 3.8 3.1 - - - -
256A VAL* 1.3 74.7 - - - +
258A LEU* 1.3 58.2 + - - +
260A ARG* 3.9 1.3 - - - +
261A ASP* 2.9 33.0 + - - +
263A LYS 3.6 17.8 - - - +
264A LEU* 3.9 21.8 - - + +
265A PRO* 3.9 15.0 - - + -
268A LEU* 5.7 1.8 - - + +
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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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254A MSE 2.9 21.6 + - - +
255A ASP* 4.0 6.3 - - - +
257A THR* 1.3 76.4 - - - +
259A ARG* 1.3 57.9 + - - +
262A GLY* 2.8 31.6 + - - +
263A LYS* 3.5 34.8 - - - +
264A LEU* 4.0 4.7 - - + +
280B ASP* 4.2 25.6 - - + +
281B PHE* 3.7 52.0 - - + -
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Residues in contact with ARG 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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223A GLU* 5.3 6.3 + - - -
226A ALA* 4.3 11.9 - - - +
230A GLU* 3.2 33.5 + - - -
255A ASP* 3.0 21.3 + - - +
256A VAL* 3.6 31.8 - - - +
258A LEU* 1.3 77.4 - - - +
260A ARG* 1.3 61.8 + - - +
262A GLY 4.7 0.5 + - - -
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Residues in contact with ARG 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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230A GLU* 6.3 1.1 - - - -
233A LEU* 3.7 43.3 + - - +
236A HIS 5.5 0.8 + - - -
237A PRO* 6.0 0.6 - - - +
238A MSE 2.7 45.7 - - - +
256A VAL* 2.8 24.4 + - + +
257A THR 3.9 2.0 - - - +
259A ARG* 1.3 75.7 - - - +
261A ASP* 1.3 81.4 + - - +
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Residues in contact with ASP 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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238A MSE 3.3 25.0 - - - +
257A THR* 2.9 15.2 + - - +
260A ARG* 1.3 99.1 + - - +
262A GLY* 1.3 63.5 + - - +
263A LYS* 3.4 27.9 + - + +
265A PRO* 5.1 5.4 - - - +
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Residues in contact with GLY 262 (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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258A LEU* 2.8 31.1 + - - +
259A ARG 4.6 0.6 + - - -
260A ARG 3.9 0.2 - - - -
261A ASP* 1.3 72.2 - - - +
263A LYS* 1.3 63.3 + - - +
280B ASP 5.4 1.6 - - - +
283B GLN* 3.1 19.1 + - - +
330B VAL* 6.0 0.7 - - - +
333B ARG* 6.3 2.9 - - - -
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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