Contacts of the helix formed by residues 247 - 264 (chain E) in PDB entry 3IKM
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 THR 247 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E PRO* 2.9 5.0 + - - +
245E PRO 3.7 1.3 - - - -
246E ARG* 1.3 91.9 + - - +
248E SER* 1.3 71.4 + - - +
250E GLN* 2.8 51.6 - - + +
251E TRP* 2.6 58.8 + - + +
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Residues in contact with SER 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E THR* 3.2 27.1 - - - +
244E PRO 2.4 39.3 + - - -
245E PRO* 3.5 13.0 + - - -
247E THR* 1.3 62.1 - - - +
249E ASN* 1.3 63.1 + - - +
250E GLN 2.8 3.6 - - - +
251E TRP* 2.4 31.7 + - - +
252E LEU* 3.0 7.3 + - - -
305E ASN* 4.1 6.1 + - - -
334E CYS* 3.3 20.4 - - - -
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Residues in contact with ASN 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248E SER* 1.3 82.7 + - - +
250E GLN* 1.3 62.5 + - - +
252E LEU* 2.7 32.3 + - - +
253E ASP* 2.9 19.4 - - - +
285E LYS* 2.7 45.6 - - - +
305E ASN* 4.1 10.2 - - - +
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Residues in contact with GLN 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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245E PRO 5.7 0.2 - - - +
246E ARG 5.6 0.2 - - - +
247E THR* 2.8 51.8 - - + +
248E SER 2.7 0.6 + - - -
249E ASN* 1.3 81.5 - - - +
251E TRP* 1.3 91.5 + - - -
253E ASP* 3.5 18.0 + - - +
254E PHE 4.2 1.7 + - - -
257E ARG* 4.3 11.4 + - - -
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Residues in contact with TRP 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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205E PRO* 5.3 9.1 - - + +
241E TRP* 5.8 3.4 - - + +
243E THR* 3.5 20.6 - - + +
244E PRO* 5.4 1.3 - - + +
247E THR* 2.6 48.2 + - + -
248E SER 2.4 22.7 + - - +
250E GLN* 1.3 85.3 - - - +
252E LEU* 1.3 62.3 + - - -
253E ASP 3.0 3.5 + - - -
254E PHE* 3.2 31.2 + + + +
255E TRP* 3.0 32.8 + - + +
257E ARG* 5.2 2.7 - - - -
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Residues in contact with LEU 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E THR* 5.8 0.6 - - - +
248E SER 3.0 4.6 + - - +
249E ASN* 2.7 36.5 + - - +
251E TRP* 1.3 75.9 - - - +
253E ASP* 1.3 64.6 + - - +
255E TRP* 3.6 9.8 - - + +
256E LEU* 3.2 23.5 + - + +
285E LYS* 4.9 5.2 - - - -
287E ASN* 4.4 20.0 - - - +
303E LEU* 4.8 14.3 - - + +
304E TRP 3.9 20.2 - - - +
305E ASN* 3.8 24.5 - - + +
336E LEU* 4.5 17.9 - - + -
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Residues in contact with ASP 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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249E ASN* 2.9 31.0 - - - +
250E GLN* 3.5 10.6 - - - +
251E TRP 3.0 0.6 - - - -
252E LEU* 1.3 79.9 - - - +
254E PHE* 1.3 52.1 - - - +
255E TRP 3.1 1.3 - - - -
256E LEU* 2.7 19.5 + - + +
257E ARG* 2.2 42.9 + - - +
285E LYS* 5.9 1.2 - - - -
287E ASN* 5.9 0.5 + - - -
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Residues in contact with PHE 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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539D PHE* 6.5 0.9 - + - -
122E ARG* 4.2 26.2 - - - -
251E TRP* 3.2 30.2 + + + +
253E ASP* 1.3 72.7 - - - +
255E TRP* 1.3 71.0 + + - +
256E LEU 2.8 1.6 - - - -
257E ARG* 2.9 44.9 - - + +
258E HIS* 2.2 82.3 + + + +
261E GLN* 4.0 7.2 - - - -
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Residues in contact with TRP 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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117E SER 5.4 0.2 - - - -
118E VAL* 3.7 30.1 - - + -
122E ARG* 4.7 14.4 - - + -
239E LEU* 4.0 18.5 - - + +
241E TRP* 3.2 65.0 - + - +
251E TRP* 3.0 22.8 + - + +
252E LEU* 3.6 9.0 - - + +
254E PHE* 1.3 85.3 - + - +
256E LEU* 1.3 50.8 + - - +
258E HIS* 4.2 26.7 - + + -
259E ARG* 2.6 45.1 + - - +
303E LEU* 4.3 7.5 - - + +
336E LEU* 3.7 25.6 - - + -
338E VAL* 5.8 1.1 - - + -
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Residues in contact with LEU 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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252E LEU* 3.2 14.5 + - + +
253E ASP* 2.7 24.1 + - - +
255E TRP* 1.3 78.7 - - - +
257E ARG* 1.3 53.4 + - - +
259E ARG* 3.0 5.0 - - + +
260E LEU* 2.6 46.5 + - + +
275E SER* 4.7 22.9 - - - +
287E ASN* 4.5 24.5 - - + +
289E LEU* 5.2 12.3 - - + -
303E LEU* 4.0 21.3 - - + -
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Residues in contact with ARG 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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250E GLN* 4.3 16.6 + - - -
251E TRP* 5.1 4.0 - - - -
253E ASP* 2.2 28.0 + - - +
254E PHE* 2.9 53.7 - - + +
256E LEU* 1.3 66.9 - - - +
258E HIS* 1.3 67.3 + - - +
260E LEU* 3.3 6.5 + - - +
261E GLN* 2.9 42.2 + - + +
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Residues in contact with HIS 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E SER* 3.1 47.1 + - - -
118E VAL* 5.7 0.2 - - + -
121E PHE* 4.8 5.9 - - - -
122E ARG* 4.0 15.0 + - - -
254E PHE* 2.2 62.6 + + + +
255E TRP* 4.2 20.4 - + + +
257E ARG* 1.3 70.3 - - - +
259E ARG* 1.3 67.4 + - - +
261E GLN* 3.0 35.0 + - + +
262E TRP* 3.1 8.3 + - + +
265E LYS* 4.8 4.8 + - - -
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Residues in contact with ARG 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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114E TRP* 2.5 34.2 - - - +
239E LEU* 6.2 0.4 - - - -
255E TRP* 2.6 30.7 + - - +
256E LEU* 3.0 11.9 - - + +
258E HIS* 1.3 78.8 + - - +
260E LEU* 1.3 55.8 - - - +
262E TRP* 2.6 49.8 + - - +
263E TRP* 2.6 45.4 + - + +
289E LEU* 5.6 5.6 - - + -
301E GLU* 2.5 44.7 + - - +
303E LEU* 4.1 16.8 - - + -
338E VAL* 3.8 8.6 - - - +
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Residues in contact with LEU 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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256E LEU* 2.6 26.0 + - + +
257E ARG* 3.7 6.1 - - - +
259E ARG* 1.3 72.9 - - - +
261E GLN* 1.3 62.5 + - + +
262E TRP 3.2 0.7 + - - -
263E TRP* 3.8 3.0 + - - -
264E ARG* 3.0 71.2 + - + +
273E PHE* 4.8 1.3 - - + -
274E SER* 4.7 21.8 - - - +
275E SER* 5.3 7.2 - - - +
289E LEU* 4.9 13.7 - - + -
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Residues in contact with GLN 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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539D PHE* 4.2 25.9 - - - -
254E PHE* 4.0 9.9 - - - -
257E ARG* 2.9 34.3 + - + +
258E HIS* 3.0 32.9 + - + +
259E ARG 2.8 1.0 + - - -
260E LEU* 1.3 77.8 - - + +
262E TRP* 1.3 53.9 + - - -
264E ARG* 4.1 1.7 - - - +
265E LYS* 2.9 33.4 + - - +
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Residues in contact with TRP 262 (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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110E LEU* 4.0 20.0 - - + -
113E GLU* 3.6 18.2 + - + +
114E TRP* 3.4 50.9 - + + -
117E SER* 3.9 15.2 - - - +
258E HIS* 3.1 10.1 + - + +
259E ARG* 2.6 30.3 + - - +
261E GLN* 1.3 66.8 - - - +
263E TRP* 1.3 112.0 + + - +
265E LYS* 2.5 54.6 - - + +
266E PHE* 3.0 39.0 - + - -
342E LEU* 5.5 1.6 - - + -
349E TYR* 5.1 1.1 - - - -
378E LEU* 6.0 0.2 - - + -
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Residues in contact with TRP 263 (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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110E LEU* 5.9 3.6 - - + -
114E TRP* 4.3 4.0 - + - -
259E ARG* 2.6 63.4 + - + +
260E LEU* 4.5 2.2 - - - +
262E TRP* 1.3 91.8 - + - +
264E ARG* 1.3 63.1 + - + +
265E LYS 2.4 16.4 + - - -
266E PHE* 2.7 13.9 + - - -
273E PHE* 4.8 15.7 - + + -
289E LEU* 6.3 2.0 - - + -
300E ILE* 3.2 40.8 - - + -
301E GLU* 3.3 14.2 + - - -
340E GLY* 4.9 2.9 - - - -
341E ASP 4.2 18.4 - - - -
342E LEU* 5.2 8.3 - - + -
345E GLY* 4.5 13.9 - - - -
349E TYR* 2.7 39.6 + + - +
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Residues in contact with ARG 264 (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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260E LEU* 3.0 52.5 - - + +
261E GLN* 4.1 2.2 - - - +
263E TRP* 1.3 79.6 - - + +
265E LYS* 1.3 56.2 + - - +
266E PHE 3.0 7.4 + - - -
267E ALA 3.6 6.2 + - - +
270E PRO* 2.6 47.5 + - + +
271E SER* 3.6 9.1 + - - +
273E PHE* 2.5 66.5 + - + +
274E SER* 5.3 0.8 - - - +
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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
------------------------------------------------------------
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