Contacts of the helix formed by residues 251 - 267 (chain A) in PDB entry 5E2Q
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 TYR 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ALA* 4.2 13.5 - - + -
50A LEU* 3.6 34.3 - - + -
51A GLN* 3.3 23.4 + - + +
197A ASN 5.8 0.9 - - - -
199A ARG* 3.2 38.6 + - - +
217A ALA* 3.8 16.2 - - + -
249A GLY 3.6 1.0 + - - -
250A ASP* 1.3 101.5 + - - +
252A ALA* 1.3 58.1 + - - +
253A PRO* 3.5 4.0 - - - -
254A ILE* 3.1 17.8 + - + -
255A LEU* 2.9 32.0 + - + +
314A PHE* 3.8 28.0 - + - -
718A LEU* 4.2 19.4 - - + +
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Residues in contact with ALA 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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218A SER 3.4 12.1 - - - +
219A VAL* 3.4 28.9 - - - +
249A GLY* 3.2 18.5 + - - +
250A ASP 3.0 1.6 - - - -
251A TYR* 1.3 76.1 - - - +
253A PRO* 1.4 73.2 - - + +
255A LEU* 3.4 2.2 + - - +
256A GLN* 3.0 23.4 + - - +
718A LEU* 4.8 0.6 - - - +
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Residues in contact with PRO 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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251A TYR 3.6 1.8 - - - -
252A ALA* 1.4 93.6 - - + +
254A ILE* 1.3 60.5 + - - +
256A GLN* 3.2 20.2 - - + +
257A LYS* 3.3 14.6 + - - +
714A ILE* 3.7 35.9 - - + +
717A GLN* 4.4 12.3 - - - +
718A LEU* 4.0 16.6 - - + -
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Residues in contact with ILE 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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43A TYR* 3.3 29.2 - - + +
44A GLY* 4.0 9.4 - - - -
46A LEU* 4.5 5.6 - - + -
47A ALA* 4.3 18.4 - - + +
50A LEU* 4.0 9.4 - - + -
251A TYR* 3.1 10.9 + - + +
253A PRO* 1.3 73.2 - - - +
255A LEU* 1.3 63.5 + - + +
256A GLN 3.1 1.6 - - - -
257A LYS* 3.0 24.5 + - - +
258A VAL* 3.1 10.7 + - - +
711A LEU* 5.9 4.9 - - + -
714A ILE* 3.9 18.4 - - + -
715A LEU* 3.7 30.3 - - + -
718A LEU* 3.8 17.5 - - + -
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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
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44A GLY* 5.5 0.7 - - - -
217A ALA* 3.8 15.0 - - + +
218A SER* 3.6 22.4 - - - +
219A VAL* 3.6 15.9 - - + +
250A ASP 3.6 20.9 - - - +
251A TYR* 2.9 20.3 + - + +
252A ALA 4.0 1.3 - - - +
254A ILE* 1.3 76.4 - - + +
256A GLN* 1.3 60.4 + - - +
258A VAL* 3.1 13.8 + - + +
259A VAL* 3.0 32.7 + - - +
285A PHE* 3.8 23.3 - - + +
314A PHE* 4.8 4.0 - - + -
328A PHE* 3.9 30.3 - - + -
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Residues in contact with GLN 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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219A VAL* 3.5 26.5 - - + +
252A ALA 3.0 14.1 + - - +
253A PRO* 3.2 17.5 - - + +
255A LEU* 1.3 76.9 - - - +
257A LYS* 1.3 62.6 + - + +
259A VAL* 3.2 20.1 - - - +
260A GLU* 3.1 34.8 + - - +
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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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43A TYR* 3.3 41.3 - - + +
253A PRO 3.5 13.2 - - - +
254A ILE* 3.0 10.8 + - - +
256A GLN* 1.3 77.6 - - + +
258A VAL* 1.3 62.3 + - - +
260A GLU* 3.5 26.0 + - - +
261A GLN* 3.4 15.6 + - - +
707A ASP* 2.4 36.0 + - - +
710A GLU* 3.2 38.4 + - - -
711A LEU* 4.4 14.6 - - + -
714A ILE* 4.6 6.3 - - + -
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Residues in contact with VAL 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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40A ALA* 3.6 25.1 - - + +
43A TYR* 3.9 1.8 - - + -
44A GLY* 3.5 35.7 - - - +
254A ILE 3.1 15.4 + - - +
255A LEU* 3.1 19.7 + - + +
257A LYS* 1.3 74.9 - - - +
259A VAL* 1.3 60.7 + - - +
261A GLN 3.2 2.6 + - - -
262A LEU* 2.9 45.1 + - + +
285A PHE* 4.1 13.2 - - + -
312A ILE* 4.2 8.3 - - + -
328A PHE* 4.6 2.5 - - + -
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Residues in contact with VAL 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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219A VAL* 4.3 7.4 - - + -
255A LEU 3.0 17.6 + - - +
256A GLN* 3.2 32.5 - - - +
258A VAL* 1.3 72.2 - - - +
260A GLU* 1.3 61.4 + - - +
262A LEU* 3.8 8.5 - - - +
263A GLU* 3.0 32.7 + - - +
282A ILE* 4.0 23.7 - - + +
285A PHE* 3.8 26.0 - - + -
286A THR* 3.8 20.2 - - - +
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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
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43A TYR* 5.6 0.5 - - - -
256A GLN* 3.1 43.5 + - - +
257A LYS* 3.5 30.0 + - - +
258A VAL 3.1 0.4 - - - -
259A VAL* 1.3 78.9 - - - +
261A GLN* 1.3 68.6 + - - +
263A GLU* 3.8 7.3 - - - +
264A LYS* 3.2 38.0 + - - +
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Residues in contact with GLN 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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36A HIS* 3.0 50.8 + - - +
39A ARG* 3.5 47.2 - - + +
40A ALA* 3.7 11.4 - - + +
43A TYR* 3.6 18.1 - - + -
257A LYS 3.5 11.7 - - - +
258A VAL 3.2 2.9 + - - +
260A GLU* 1.3 83.6 + - - +
262A LEU* 1.3 62.2 + - - +
264A LYS* 3.5 20.7 + - - +
265A ALA* 3.0 28.9 + - - +
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Residues in contact with LEU 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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37A LEU* 3.7 26.5 - - + -
40A ALA* 3.9 13.0 - - + -
258A VAL* 2.9 24.6 + - + +
259A VAL* 3.9 3.4 - - - +
261A GLN* 1.3 77.8 - - - +
263A GLU* 1.3 57.8 + - - +
265A ALA* 3.3 5.9 + - - +
266A LYS* 3.0 26.5 + - - +
278A LEU* 3.8 20.4 - - + +
281A TYR* 4.2 12.8 - - + -
282A ILE* 3.9 20.9 - - + -
285A PHE* 3.7 37.2 - - + -
312A ILE* 4.6 12.8 - - + -
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Residues in contact with GLU 263 (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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259A VAL* 3.0 21.2 + - - +
260A GLU* 3.8 7.2 - - - +
261A GLN 3.3 0.2 - - - -
262A LEU* 1.3 78.3 - - - +
264A LYS* 1.3 61.2 + - + +
266A LYS* 3.3 35.9 + - - +
267A ALA* 3.7 6.2 + - - +
282A ILE* 3.8 15.0 - - + +
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Residues in contact with LYS 264 (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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36A HIS* 3.8 35.6 - - + +
39A ARG* 5.5 2.8 - - - +
260A GLU* 3.2 24.2 + - - +
261A GLN* 3.8 19.0 - - - +
263A GLU* 1.3 74.1 - - + +
265A ALA* 1.3 64.3 + - - +
267A ALA* 3.3 11.7 + - - +
268A TYR* 3.2 22.7 - - + -
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Residues in contact with ALA 265 (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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33A TYR* 3.4 24.5 - - + +
36A HIS* 3.7 17.4 - - + +
37A LEU* 3.9 30.7 - - + -
261A GLN 3.0 17.9 + - - +
262A LEU 3.6 5.4 - - - +
264A LYS* 1.3 74.7 - - - +
266A LYS* 1.3 60.0 + - - +
268A TYR* 3.0 20.7 + - - -
269A ALA 3.4 0.9 + - - -
278A LEU* 4.2 3.8 - - + -
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Residues in contact with LYS 266 (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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262A LEU 3.0 12.4 + - - +
263A GLU* 3.3 30.6 + - - +
264A LYS 3.2 0.6 - - - -
265A ALA* 1.3 78.0 - - - +
267A ALA* 1.3 55.8 + - - +
268A TYR 3.1 4.5 + - - -
269A ALA* 3.4 16.0 + - - +
275A GLY* 3.6 32.0 - - - +
278A LEU* 3.8 13.4 - - + +
279A ALA* 4.2 21.7 - - + +
282A ILE* 3.8 18.7 - - + +
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Residues in contact with ALA 267 (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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263A GLU 3.7 4.5 + - - +
264A LYS* 3.3 14.5 + - - +
265A ALA 3.1 1.0 - - - -
266A LYS* 1.3 77.8 - - - +
268A TYR* 1.3 73.1 + - + +
269A ALA 3.6 0.9 - - - -
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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