Contacts of the helix formed by residues 247 - 267 (chain E) in PDB entry 4P9U
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 247 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239E VAL* 4.9 7.4 - - + +
242E SER* 5.4 5.1 + - - -
244E GLU* 3.4 41.9 + - + +
245E ARG 3.3 0.2 - - - -
246E GLU* 1.3 95.4 - - + +
248E LEU* 1.3 62.6 + - - +
249E PRO* 3.4 0.9 - - - -
250E GLN* 3.2 12.3 + - + +
251E VAL* 3.1 29.9 + - + +
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Residues in contact with LEU 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E PRO* 3.7 24.2 - - + +
113E MET* 4.5 8.3 - - + -
114E ARG* 4.7 6.5 - - + +
117E PHE* 4.0 23.3 - - + -
236E LEU* 3.7 30.3 - - + -
239E VAL* 4.0 18.8 - - + +
245E ARG* 3.3 24.4 + - + +
247E HIS* 1.3 76.7 - - - +
249E PRO* 1.3 67.1 - - + +
250E GLN 3.3 0.2 + - - -
251E VAL* 3.3 6.3 + - + +
252E ILE* 3.0 48.0 + - + +
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Residues in contact with PRO 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E PRO* 4.6 16.1 - - + +
245E ARG 3.5 6.3 - - - +
246E GLU* 3.2 19.1 - - - +
247E HIS 3.5 0.2 - - - -
248E LEU* 1.3 101.5 - - + +
250E GLN* 1.3 57.5 + - + +
252E ILE* 3.3 5.9 + - + +
253E ARG* 2.9 32.7 + - - +
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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
----------------------------------------------------------
246E GLU 5.2 1.1 - - - +
247E HIS* 3.2 15.0 + - + +
248E LEU 3.2 0.2 - - - -
249E PRO* 1.3 79.4 - - + +
251E VAL* 1.3 66.1 + - - +
253E ARG* 3.3 6.2 + - - +
254E GLN* 2.9 58.3 + - - +
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Residues in contact with VAL 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E PHE* 3.6 21.9 - - + -
235E GLN* 3.6 35.6 - - + +
236E LEU* 4.1 12.6 - - + +
239E VAL* 4.3 15.7 - - + -
247E HIS* 3.1 21.3 + - + +
248E LEU* 3.3 8.5 + - - +
250E GLN* 1.3 75.8 - - + +
252E ILE* 1.3 62.5 + - - +
254E GLN* 3.8 10.3 + - - +
255E TYR* 3.0 22.7 + - - +
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Residues in contact with ILE 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E THR* 3.8 29.6 - - + +
109E SER* 3.6 21.1 - - - +
110E PRO* 3.4 33.0 - - + -
113E MET* 3.8 11.7 - - - -
189E PHE* 6.3 0.2 - - + -
232E PHE* 4.0 22.0 - - + -
236E LEU* 4.4 1.6 - - + -
248E LEU* 3.0 38.0 + - + +
249E PRO 3.8 3.8 - - - +
251E VAL* 1.3 77.6 - - - +
253E ARG* 1.3 57.4 + - - +
255E TYR* 3.5 4.6 + - + +
256E GLY* 2.9 22.2 + - - -
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Residues in contact with ARG 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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106E THR* 4.3 17.7 - - + +
249E PRO 2.9 17.8 + - - +
250E GLN* 4.3 6.5 - - - +
252E ILE* 1.3 75.2 - - + +
254E GLN* 1.3 62.0 + - - +
256E GLY* 3.6 1.0 - - - +
257E ILE* 2.9 29.5 + - - +
114F ARG* 5.5 9.1 - - - +
115F TYR* 4.8 12.5 + - - -
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Residues in contact with GLN 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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235E GLN* 5.0 8.1 + - - +
250E GLN* 2.9 57.4 + - - +
251E VAL* 3.8 8.7 - - - +
253E ARG* 1.3 74.8 - - - +
255E TYR* 1.3 65.6 + - - +
257E ILE* 3.2 11.4 - - + +
258E ALA* 2.9 25.8 + - - +
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Residues in contact with TYR 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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105E ARG* 3.7 28.4 + - - -
185E ASP* 4.4 9.1 + - - -
189E PHE* 4.8 3.6 - + - -
219E TYR* 4.3 15.7 + - - -
220E PHE* 4.7 1.0 - - - -
228E LEU* 3.8 22.7 - - + -
229E ALA* 3.9 20.3 - - - +
232E PHE* 3.4 69.5 - + + -
251E VAL 3.0 11.9 + - - +
252E ILE* 3.7 3.6 - - + +
254E GLN* 1.3 75.2 - - - +
256E GLY* 1.3 54.1 + - - +
258E ALA* 4.5 4.9 - - + -
259E SER* 2.6 56.6 + - - -
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Residues in contact with GLY 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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105E ARG* 6.2 0.4 - - - -
106E THR* 4.1 22.4 - - - -
252E ILE 2.9 16.4 + - - -
253E ARG 3.3 3.8 + - - -
254E GLN 3.1 0.4 - - - -
255E TYR* 1.3 80.4 - - - +
257E ILE* 1.3 55.9 + - - +
259E SER* 3.3 6.2 + - - -
260E GLY* 2.9 24.4 + - - -
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Residues in contact with ILE 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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253E ARG 2.9 16.3 + - - +
254E GLN* 3.2 21.3 - - + +
256E GLY* 1.3 73.7 - - - +
258E ALA* 1.3 61.5 + - + +
260E GLY* 3.2 3.0 + - - -
261E HIS* 2.9 56.8 + - + +
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Residues in contact with ALA 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228E LEU* 3.7 22.7 - - + -
254E GLN 2.9 18.4 + - - +
255E TYR* 4.0 4.7 - - + +
257E ILE* 1.3 75.1 - - + +
259E SER* 1.3 66.4 + - - +
260E GLY 3.0 1.1 - - - -
261E HIS* 3.0 20.0 + - - +
262E ILE* 3.0 18.8 + - - +
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Residues in contact with SER 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E LEU* 5.6 2.4 - - - +
105E ARG* 4.7 6.7 + - - -
219E TYR* 3.2 31.6 - - - -
228E LEU* 4.7 1.9 - - - +
255E TYR* 2.6 45.6 + - - -
256E GLY* 3.3 7.3 + - - -
258E ALA* 1.3 77.4 - - - +
260E GLY* 1.3 58.4 + - - +
262E ILE* 3.6 6.6 - - - +
263E TRP* 2.9 29.5 + - - +
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Residues in contact with GLY 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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102E LEU* 5.8 3.8 - - - -
256E GLY 2.9 20.9 + - - -
257E ILE* 3.4 6.1 - - - -
258E ALA 3.0 0.6 - - - -
259E SER* 1.3 78.8 + - - +
261E HIS* 1.3 58.0 + - - +
263E TRP* 3.3 6.9 + - - +
264E ASN* 2.9 36.3 + - - +
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Residues in contact with HIS 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257E ILE* 2.9 43.7 + - + +
258E ALA* 3.0 10.2 + - - +
260E GLY* 1.3 72.0 - - - +
262E ILE* 1.3 66.8 + - + +
264E ASN* 3.1 21.6 + - - +
265E GLN* 3.0 22.3 + - - +
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Residues in contact with ILE 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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219E TYR* 3.5 25.8 - - + +
222E ASN* 4.4 7.6 - - - +
224E GLN* 3.7 17.9 - - + +
225E ALA* 3.7 30.7 - - + +
228E LEU* 3.9 20.9 - - + -
258E ALA 3.0 11.4 + - - +
259E SER* 3.6 7.0 - - - +
261E HIS* 1.3 76.3 - - + +
263E TRP* 1.3 55.7 + - - +
265E GLN* 3.1 13.8 + - - +
266E MET* 2.9 43.0 + - + +
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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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94E ALA 5.3 1.3 - - - -
95E THR* 4.8 3.7 + - - -
98E VAL* 3.6 31.0 - - + +
99E GLU* 3.9 24.3 - - + +
102E LEU* 3.9 26.0 - - + -
215E VAL* 4.7 9.6 - - + -
218E TYR* 3.9 26.0 - + - -
219E TYR* 4.4 21.5 - + + -
259E SER 2.9 18.7 + - - +
260E GLY* 3.6 5.2 - - - +
262E ILE* 1.3 73.8 - - - +
264E ASN* 1.3 69.3 + - - +
266E MET* 4.3 8.1 - - + +
267E LYS* 2.8 53.8 + - + +
270E LEU* 4.0 24.2 - - + -
274E PHE* 4.1 15.7 - + - -
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Residues in contact with ASN 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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99E GLU* 5.2 2.8 - - - +
260E GLY 2.9 24.1 + - - +
261E HIS* 3.1 26.7 + - + +
263E TRP* 1.3 82.4 - - - +
265E GLN* 1.3 60.9 + - - +
267E LYS* 3.5 38.2 + - - +
268E MET* 4.2 11.1 - - - +
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Residues in contact with GLN 265 (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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222E ASN* 3.5 26.5 + - - +
224E GLN* 4.0 16.2 + - - +
261E HIS 3.0 11.5 + - - +
262E ILE* 3.4 14.3 - - - +
263E TRP 3.1 0.2 - - - -
264E ASN* 1.3 78.8 - - - +
266E MET* 1.3 67.4 + - - +
267E LYS 3.2 2.4 + - - -
268E MET* 3.8 16.3 + - - +
269E THR* 4.7 2.9 + - - -
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Residues in contact with MET 266 (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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218E TYR* 2.7 78.4 + - + +
219E TYR* 3.7 23.6 - - - +
221E SER* 4.1 2.2 - - - +
222E ASN* 3.6 38.1 - - + +
262E ILE* 2.9 28.7 + - - +
263E TRP* 3.6 8.3 - - + +
265E GLN* 1.3 80.9 - - - +
267E LYS* 1.3 62.7 + - - +
268E MET 3.3 1.0 + - - -
269E THR* 3.7 10.2 - - - +
270E LEU* 3.9 0.9 - - - +
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Residues in contact with LYS 267 (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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95E THR* 4.0 32.9 - - + +
99E GLU* 4.2 17.6 + - - +
263E TRP* 2.8 32.8 + - + +
264E ASN* 3.5 39.8 + - - +
265E GLN 3.2 0.8 - - - -
266E MET* 1.3 77.3 - - - +
268E MET* 1.3 75.5 + - - +
270E LEU* 3.4 25.9 - - + +
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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
------------------------------------------------------------
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