Contacts of the helix formed by residues 256 - 273 (chain B) in PDB entry 5EGO
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 256 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B SER* 4.1 1.1 - - - -
254B SER 4.4 0.2 + - - -
255B LEU* 1.3 75.2 - - - +
257B GLU* 1.3 64.9 + - - +
258B ARG* 4.0 9.3 - - - +
259B GLN* 2.9 51.1 + - - +
260B ILE* 3.3 11.8 + - - +
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Residues in contact with GLU 257 (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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246B ARG* 3.3 33.5 - - + +
247B ARG* 2.7 57.9 + - - +
250B SER* 3.7 14.5 + - - -
255B LEU 3.6 2.2 + - - -
256B SER* 1.3 72.4 - - - +
258B ARG* 1.3 60.1 + - - +
260B ILE* 2.9 26.2 - - - +
261B THR* 3.0 14.2 + - - -
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Residues in contact with ARG 258 (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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256B SER* 3.1 9.3 + - - +
257B GLU* 1.3 79.4 - - - +
259B GLN* 1.3 66.4 + - + +
261B THR* 3.1 13.4 + - - +
262B ILE* 2.9 56.6 + - + +
33D 5CM 3.6 38.7 + - - +
34D G 4.9 13.5 + - - -
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Residues in contact with GLN 259 (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 LYS* 5.2 5.3 - - - +
221B ILE* 5.5 3.6 - - - +
223B TYR* 3.5 19.8 + - + +
254B SER 5.1 0.3 - - - +
255B LEU* 3.4 26.0 - - + +
256B SER* 2.9 42.1 + - - +
258B ARG* 1.3 81.6 - - + +
260B ILE* 1.3 58.6 + - + +
262B ILE* 3.6 7.1 + - - +
263B TRP* 2.9 25.6 + - - +
32D A 3.0 34.1 + - - +
33D 5CM 5.8 3.1 - - - +
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Residues in contact with ILE 260 (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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223B TYR* 6.4 0.2 - - + -
231B LEU* 4.4 8.7 - - + -
241B ILE* 5.2 4.9 - - + +
246B ARG* 2.8 55.0 - - + +
249B ILE* 3.8 28.7 - - + -
250B SER* 4.4 1.8 - - - +
253B THR* 4.6 0.2 - - - +
255B LEU* 4.1 25.6 - - + +
256B SER 3.8 7.6 - - - +
257B GLU* 2.9 27.8 - - - +
259B GLN* 1.3 76.4 - - - +
261B THR* 1.3 64.9 + - - +
262B ILE 3.2 1.3 - - - -
263B TRP* 3.9 5.8 - - - -
264B PHE* 3.0 35.6 + - + -
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Residues in contact with THR 261 (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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241B ILE* 5.2 5.8 - - + -
246B ARG* 2.8 39.8 + - - +
257B GLU 3.0 10.5 + - - -
258B ARG* 3.4 15.8 - - - +
260B ILE* 1.3 79.0 - - - +
262B ILE* 1.3 57.8 + - + +
264B PHE* 3.5 4.9 + - - +
265B GLN* 3.1 37.6 + - - +
1E C 4.4 7.0 - - - +
2E C 3.3 23.0 + - - +
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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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258B ARG* 2.9 65.7 + - + +
259B GLN* 3.9 6.3 - - - +
261B THR* 1.3 75.9 - - + +
263B TRP* 1.3 59.9 + - - +
265B GLN* 3.2 15.9 + - - +
266B ASN* 2.8 51.7 + - - +
31D T 5.4 3.8 - - + -
32D A 3.7 20.0 - - + -
33D 5CM 3.4 32.3 - - + +
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Residues in contact with TRP 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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223B TYR* 3.9 26.7 - + + -
228B LEU* 3.9 14.1 - - + +
231B LEU* 3.5 45.3 - - + +
232B GLU* 3.9 21.1 - - - -
235B TYR* 4.1 11.2 - - + -
259B GLN 2.9 18.9 + - - +
260B ILE* 3.7 8.7 - - - +
261B THR 3.4 0.2 - - - -
262B ILE* 1.3 77.5 - - - +
264B PHE* 1.3 79.2 + + - +
266B ASN* 3.2 8.4 + - + +
267B ARG* 2.7 70.6 + - + -
31D T 4.0 13.6 + - - -
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Residues in contact with PHE 264 (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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231B LEU* 4.4 13.9 - - + -
234B GLU* 3.8 25.4 - - + -
235B TYR* 3.7 35.8 - + + -
238B ASN 3.8 10.1 - - - -
239B LYS 3.5 19.5 - - - -
241B ILE* 4.0 35.9 - - + -
249B ILE* 5.5 4.9 - - + -
260B ILE* 3.0 33.1 + - + +
261B THR* 3.8 4.9 - - - +
263B TRP* 1.3 92.0 - + - +
265B GLN* 1.3 67.6 + - - +
267B ARG* 3.6 2.1 - - - +
268B ARG* 3.0 39.8 + - - +
2E C 6.1 0.4 - - - +
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Residues in contact with GLN 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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261B THR* 3.1 29.0 + - - +
262B ILE* 3.4 23.9 - - - +
264B PHE* 1.3 78.8 - - - +
266B ASN* 1.3 64.8 + - - +
268B ARG* 3.6 16.5 + - - +
269B VAL* 3.3 23.7 + - - +
33D 5CM 4.7 6.2 + - - +
34D G 4.9 1.6 - - - +
1E C 3.9 1.8 + - - -
2E C 2.8 44.4 + - - +
3E T 3.3 36.5 + - + +
4E 5CM 4.8 5.7 + - - +
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Residues in contact with ASN 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* 2.8 39.2 + - - +
263B TRP* 3.7 7.5 + - + +
265B GLN* 1.3 78.6 - - - +
267B ARG* 1.3 64.9 + - - +
269B VAL* 3.3 15.7 - - + +
270B LYS* 3.2 20.3 + - - +
31D T 3.8 26.6 - - + +
32D A 3.1 36.0 + - - +
33D 5CM 4.7 5.7 + - - -
4E 5CM 5.2 2.8 + - - -
5E G 4.7 2.4 + - - -
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Residues in contact with ARG 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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232B GLU* 1.8 43.1 + - - +
235B TYR* 3.2 48.6 - - + -
263B TRP* 2.7 52.0 + - + +
264B PHE 3.2 5.1 + - - +
266B ASN* 1.3 72.2 - - - +
268B ARG* 1.3 64.2 + - - +
270B LYS* 3.2 33.9 + - - +
271B GLU* 3.1 32.9 + - - +
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Residues in contact with ARG 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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235B TYR* 3.4 22.0 - - + +
239B LYS* 2.8 33.7 + - + +
240B PHE* 3.3 42.7 - - - +
241B ILE 4.9 0.2 - - - +
264B PHE* 3.0 30.2 + - - +
265B GLN* 3.7 21.2 - - - +
267B ARG* 1.3 72.5 - - - +
269B VAL* 1.3 63.9 + - - +
271B GLU* 3.3 2.4 + - - +
272B LYS* 2.9 25.9 + - - +
2E C 3.5 27.5 + - - -
3E T 2.8 32.7 + - - +
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Residues in contact with VAL 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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265B GLN 3.3 15.1 + - - +
266B ASN* 3.3 18.8 - - - +
267B ARG 3.2 0.6 - - - -
268B ARG* 1.3 79.8 - - - +
270B LYS* 1.3 63.0 + - - +
272B LYS* 3.3 8.9 + - - +
273B LYS* 3.3 42.2 + - - +
3E T 5.8 1.6 - - + +
4E 5CM 3.4 32.3 - - + +
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Residues in contact with LYS 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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232B GLU* 5.5 2.8 + - - -
266B ASN 3.2 8.1 + - - +
267B ARG* 3.2 35.8 + - - +
269B VAL* 1.3 82.5 - - + +
271B GLU* 1.3 63.6 + - - +
273B LYS* 3.1 25.4 + - + +
274B VAL* 3.2 13.3 + - + +
29D T 4.5 2.9 + - - -
30D T 2.9 40.7 + - - +
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Residues in contact with GLU 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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235B TYR* 3.0 35.4 + - + +
239B LYS* 2.6 34.2 + - - +
267B ARG* 3.1 20.2 + - - +
268B ARG 3.3 4.5 + - - +
270B LYS* 1.3 78.4 - - - +
272B LYS* 1.3 59.4 + - - +
274B VAL* 3.0 36.3 + - + +
275B LEU* 3.5 6.1 + - - +
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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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268B ARG 2.9 16.4 + - - +
269B VAL* 3.6 8.3 - - - +
270B LYS 3.2 0.4 - - - -
271B GLU* 1.3 77.8 - - - +
273B LYS* 1.3 58.5 + - - +
274B VAL 3.4 0.7 - - - -
275B LEU* 3.3 36.6 - - + +
4E 5CM 3.0 38.6 + - - +
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Residues in contact with LYS 273 (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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269B VAL* 3.3 31.1 + - - +
270B LYS* 3.1 21.1 + - + +
271B GLU 3.1 0.6 - - - -
272B LYS* 1.3 76.5 - - - +
274B VAL* 1.3 58.0 + - - +
275B LEU 3.2 9.2 - - - +
276B ALA* 4.2 10.7 - - - +
29D T 5.8 4.5 - - - +
30D T 5.4 10.1 - - - +
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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