Contacts of the helix formed by residues 257 - 272 (chain B) in PDB entry 4BEJ
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 257 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B ARG* 4.9 0.7 - - - +
255B LYS* 3.1 28.6 + - - +
256B LYS* 1.3 75.9 - - - +
258B VAL* 1.3 65.7 + - - +
259B THR* 4.1 9.0 - - - -
260B ASP* 2.9 39.3 + - - +
261B SER* 3.0 20.4 + - - -
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Residues in contact with VAL 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU* 3.7 21.1 - - + +
44B SER* 3.9 13.2 - - - +
47B GLY* 3.5 36.8 + - - +
48B ARG* 4.2 15.7 - - - -
49B ASP* 4.2 2.5 - - + +
247B ARG* 3.9 29.8 - - + +
256B LYS 3.5 1.2 + - - -
257B SER* 1.3 71.8 - - - +
259B THR* 1.3 57.0 + - - +
261B SER* 3.2 8.3 + - - -
262B ILE* 2.9 37.6 + - + +
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Residues in contact with THR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLY* 4.0 12.0 + - - -
257B SER* 3.1 7.5 - - - -
258B VAL* 1.3 80.2 - - - +
260B ASP* 1.3 67.7 + - - +
262B ILE* 3.1 28.8 - - + +
263B ARG* 3.4 10.6 + - - +
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Residues in contact with ASP 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LYS* 4.8 6.7 - - + +
257B SER* 2.9 27.4 + - - +
259B THR* 1.3 84.3 - - - +
261B SER* 1.3 57.7 + - - +
263B ARG* 3.2 31.6 + - - +
264B ASP* 2.8 37.5 + - - +
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Residues in contact with SER 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B VAL 4.6 1.8 + - - +
246B ASN* 4.0 6.4 - - - -
247B ARG* 3.6 30.1 + - - +
251B ASP* 4.7 0.2 + - - -
256B LYS* 4.0 20.3 - - - +
257B SER 3.0 13.2 + - - -
258B VAL* 3.2 13.0 + - - -
260B ASP* 1.3 77.8 - - - +
262B ILE* 1.3 59.2 + - - +
264B ASP* 3.2 9.6 + - - +
265B GLU* 2.9 27.4 + - - +
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B SER* 3.2 31.0 - - - +
47B GLY* 5.8 3.8 - - - -
245B VAL 5.7 0.2 - - - -
258B VAL* 2.9 25.4 + - + +
259B THR* 3.1 31.2 - - + +
261B SER* 1.3 74.9 - - - +
263B ARG* 1.3 63.8 + - - +
265B GLU* 3.4 17.2 + - - +
266B TYR* 3.3 19.6 + - - +
282B THR* 4.3 13.9 - - + +
283B LYS 6.1 0.2 - - - +
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Residues in contact with ARG 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B THR 3.6 9.4 - - - +
260B ASP* 3.2 37.6 + - - +
262B ILE* 1.3 80.3 - - + +
264B ASP* 1.3 88.3 + - - +
266B TYR* 3.3 16.2 + - - +
267B ALA* 3.5 12.1 + - - +
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Residues in contact with ASP 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B LYS* 2.6 37.1 + - - -
260B ASP* 2.8 19.8 + - - +
261B SER* 3.3 11.2 - - - +
263B ARG* 1.3 101.6 + - - +
265B GLU* 1.3 59.4 + - - +
267B ALA* 3.5 8.3 + - - +
268B PHE* 3.2 21.3 + - - +
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Residues in contact with GLU 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B VAL* 3.5 11.4 - - - +
245B VAL* 2.7 58.3 + - + +
261B SER 2.9 13.9 + - - +
262B ILE* 3.4 14.8 - - - +
264B ASP* 1.3 75.6 - - - +
266B TYR* 1.3 66.2 + - - +
268B PHE* 3.3 5.7 + - - +
269B LEU* 3.2 25.2 + - + +
281B GLY* 3.7 10.0 - - - -
282B THR* 2.7 43.2 + - - -
283B LYS* 5.9 0.3 - - - +
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Residues in contact with TYR 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B ILE 3.3 9.7 + - - +
263B ARG* 3.3 10.0 + - - +
265B GLU* 1.3 81.0 - - - +
267B ALA* 1.3 66.4 + - + +
269B LEU* 3.3 9.8 + - + +
270B GLN* 3.1 65.6 + - + +
277B ALA* 5.4 10.8 - - + -
283B LYS* 3.7 33.0 - - + -
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Residues in contact with ALA 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B ARG 3.5 8.3 + - - +
264B ASP* 3.6 11.9 - - - +
265B GLU 3.3 0.2 - - - -
266B TYR* 1.3 84.3 - - - +
268B PHE* 1.3 61.9 + - - +
270B GLN* 3.3 7.7 + - - +
271B LYS* 3.3 41.4 + - - +
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Residues in contact with PHE 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B LEU* 4.4 4.5 - - + -
218B ASP* 3.4 44.0 - - + -
245B VAL* 4.5 12.6 - - + -
264B ASP 3.2 10.9 + - - +
265B GLU* 3.5 11.9 - - - +
266B TYR 3.2 0.2 - - - -
267B ALA* 1.3 79.2 - - - +
269B LEU* 1.3 71.9 + - + +
271B LYS* 3.3 5.3 + - - +
272B LYS* 3.0 52.4 + - + +
273B TYR* 3.8 31.0 - + - -
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B LEU* 4.1 22.2 - - + -
243B GLY 4.9 0.9 - - - +
245B VAL* 5.5 0.9 - - + -
265B GLU* 3.2 21.4 + - + +
266B TYR* 3.8 7.6 - - + +
267B ALA 3.3 0.2 - - - -
268B PHE* 1.3 94.2 - - + +
270B GLN* 1.3 61.7 + - - +
272B LYS 2.6 17.0 - - - +
273B TYR* 2.9 33.0 - - + +
274B PRO* 3.5 1.0 - - - +
276B LEU* 6.1 0.7 - - + -
277B ALA* 4.0 19.5 - - + +
280B ASN* 3.7 18.8 - - + +
281B GLY* 3.6 34.1 - - - +
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Residues in contact with GLN 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B TYR* 3.1 62.5 + - + +
267B ALA* 3.6 10.1 - - - +
268B PHE 3.3 0.4 - - - -
269B LEU* 1.3 78.3 - - - +
271B LYS* 1.3 59.6 + - + +
274B PRO* 3.4 22.6 - - - +
277B ALA* 4.5 11.5 - - + +
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Residues in contact with LYS 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B ALA* 3.3 27.3 + - - +
268B PHE* 3.3 4.3 + - - +
269B LEU 3.2 0.2 - - - -
270B GLN* 1.3 79.9 - - + +
272B LYS* 1.3 64.8 + - + +
274B PRO* 3.3 19.6 - - - +
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Residues in contact with LYS 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B ASP 4.3 15.0 + - - -
220B MET 4.6 6.3 + - - -
268B PHE* 3.0 38.8 + - + +
269B LEU* 2.6 24.6 - - - +
271B LYS* 1.3 79.0 - - + +
273B TYR* 1.3 102.2 + - + +
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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