Contacts of the helix formed by residues 253 - 271 (chain B) in PDB entry 1R4N
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 ASP 253 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B ASP* 2.8 33.6 + - + +
252B ASP* 1.3 73.1 - - - +
254B PRO* 1.3 60.1 - - - +
255B GLU* 3.1 28.0 + - - +
256B HIS* 2.6 52.7 + - + +
257B ILE* 3.3 4.8 + - - +
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Residues in contact with PRO 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLN* 5.8 5.6 - - - +
252B ASP 2.9 18.7 - - - +
253B ASP* 1.3 78.4 - - - +
255B GLU* 1.3 58.7 + - + +
256B HIS 2.8 1.2 + - - -
257B ILE* 2.8 6.5 + - + +
258B GLN* 2.6 37.0 + - - +
278B TYR* 3.8 17.1 + - - +
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Residues in contact with GLU 255 (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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243B PHE* 3.4 33.0 - - + -
253B ASP* 3.0 13.3 + - - +
254B PRO* 1.3 80.2 - - + +
256B HIS* 1.3 56.8 + - - +
258B GLN* 3.7 9.2 - - - +
259B TRP* 3.1 20.3 + - - +
14F GLU* 4.6 5.4 - - + +
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Residues in contact with HIS 256 (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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237B TRP* 3.4 19.4 - + - -
243B PHE* 3.2 41.0 - + - +
247B VAL* 5.0 5.5 - - + +
248B PRO 3.5 10.3 - - - -
249B LEU* 3.8 10.1 - - + -
250B ASP* 2.8 50.9 + - + +
253B ASP* 2.6 34.3 + - + +
255B GLU* 1.3 69.6 - - - +
257B ILE* 1.3 60.3 - - + +
259B TRP* 3.1 5.0 + - - +
260B ILE* 2.8 33.8 + - - +
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Residues in contact with ILE 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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251B GLY* 2.9 32.8 - - - +
252B ASP 4.7 5.2 - - - +
253B ASP 4.2 7.0 - - - +
254B PRO* 2.8 10.0 + - + +
256B HIS* 1.3 70.1 - - + +
258B GLN* 1.3 55.9 + - - +
260B ILE* 3.0 8.9 + - + -
261B PHE* 2.5 38.3 + - - +
278B TYR* 3.3 28.9 - - + +
281B THR* 4.0 17.3 - - + +
282B GLN* 3.6 43.3 - - + +
285B VAL* 5.1 9.4 - - + -
286B LYS* 4.3 4.0 - - + -
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Residues in contact with GLN 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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254B PRO* 2.6 20.8 + - + +
255B GLU* 3.7 11.0 - - - +
257B ILE* 1.3 73.3 - - - +
259B TRP* 1.3 57.9 + - - +
261B PHE* 3.4 22.9 - - - +
262B GLN* 2.9 41.6 + - - +
278B TYR* 3.8 20.4 - - + +
81E ILE* 5.6 5.9 - - - +
13F TRP* 6.4 0.2 - - - -
14F GLU* 3.9 20.7 - - + +
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Residues in contact with TRP 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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232B VAL* 4.0 21.1 - - + -
236B GLN* 3.8 26.7 - - + -
237B TRP* 3.5 26.2 - + + -
240B GLU* 4.3 14.8 + - + -
242B PRO* 3.3 39.0 - - + +
243B PHE* 4.3 9.6 - + + -
255B GLU 3.1 15.2 + - - +
256B HIS 3.3 7.0 - - - +
257B ILE 3.1 0.4 - - - -
258B GLN* 1.3 74.9 - - - +
260B ILE* 1.3 70.8 + - + +
262B GLN* 2.9 6.2 + - + +
263B LYS* 2.7 66.2 + - + +
14F GLU* 3.1 39.2 - - - +
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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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229B ILE* 4.2 4.3 - - + +
232B VAL* 3.5 27.6 - - + +
233B ARG* 4.7 3.6 - - + +
237B TRP* 4.4 0.7 - - + -
249B LEU* 3.4 45.1 - - + -
256B HIS 2.8 20.4 + - - +
257B ILE* 3.5 7.9 - - + +
259B TRP* 1.3 87.7 - - + +
261B PHE* 1.3 51.7 + - - +
264B SER* 2.7 47.1 + - - +
281B THR* 3.6 17.5 - - + -
285B VAL* 3.8 23.1 - - + -
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Residues in contact with PHE 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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257B ILE 2.5 20.7 + - - +
258B GLN* 3.4 25.6 - - - +
260B ILE* 1.3 73.1 - - - +
262B GLN* 1.3 55.2 + - - +
264B SER* 3.0 4.2 + - - -
265B LEU* 2.7 61.6 + - + +
276B VAL* 3.7 21.3 - - + -
277B THR* 3.5 5.6 - - - -
278B TYR* 3.2 46.0 - + + -
281B THR* 3.1 31.6 - - + +
81E ILE* 4.6 11.4 - - + -
82E GLY* 4.9 10.1 - - - -
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Residues in contact with GLN 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 GLN* 2.9 26.7 + - - +
259B TRP* 2.9 12.3 + - + +
261B PHE* 1.3 79.6 - - - +
263B LYS* 1.3 61.2 + - + +
265B LEU* 3.2 10.2 - - - +
266B GLU* 3.0 42.1 + - - +
66E SER* 2.5 22.0 + - - +
67E GLY* 2.3 44.3 + - - +
68E GLU 3.7 1.2 - - - +
81E ILE* 4.7 6.8 - - - +
13F TRP* 5.4 0.2 - - - -
14F GLU* 3.4 25.7 - - + +
15F GLY* 4.6 4.5 - - - -
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Residues in contact with LYS 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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232B VAL* 3.3 22.5 - - + +
236B GLN* 3.0 33.0 + - - +
240B GLU* 5.1 8.3 + - - -
259B TRP* 2.7 55.8 + - + +
262B GLN* 1.3 72.3 - - - +
264B SER* 1.3 61.4 + - - +
265B LEU 3.1 1.3 - - - -
266B GLU* 3.3 32.0 + - - +
267B ARG* 2.9 23.2 + - - +
68E GLU* 5.3 0.2 + - - -
446E SER* 5.7 1.6 + - - -
14F GLU* 5.5 1.8 - - - -
15F GLY* 6.3 1.3 - - - -
18F ASN* 4.1 18.8 - - - +
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Residues in contact with SER 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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228B CYS* 3.8 3.9 - - - +
229B ILE* 3.0 47.6 - - - +
232B VAL* 3.3 14.4 - - - +
260B ILE* 2.7 30.6 + - - +
261B PHE* 3.6 4.5 - - - -
263B LYS* 1.3 73.2 - - - +
265B LEU* 1.3 57.9 + - - +
267B ARG* 3.7 3.6 - - - +
268B ALA* 2.9 31.2 + - - +
276B VAL* 4.1 8.5 - - - +
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Residues in contact with LEU 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 PHE* 2.7 48.1 + - + +
262B GLN* 3.2 16.8 - - - +
264B SER* 1.3 80.0 - - - +
266B GLU* 1.3 61.1 + - + +
268B ALA* 3.7 4.3 - - + +
269B SER* 3.3 20.3 + - - -
276B VAL* 4.3 9.6 - - + +
64E GLN* 3.7 45.3 - - + +
65E VAL 3.5 20.6 - - - +
66E SER* 4.1 11.8 - - - -
81E ILE* 4.7 2.5 - - + -
82E GLY* 4.9 3.1 - - - +
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Residues in contact with GLU 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 GLN* 3.0 28.7 + - - +
263B LYS* 3.6 37.3 + - - +
264B SER 3.3 0.2 - - - -
265B LEU* 1.3 75.8 - - - +
267B ARG* 1.3 64.4 + - - +
269B SER* 3.1 10.1 + - - -
270B GLN* 3.0 28.1 + - - +
66E SER* 3.9 18.5 + - - +
68E GLU* 3.3 36.1 - - - +
445E VAL* 5.6 6.2 - - - +
15F GLY* 5.5 1.6 - - - -
18F ASN* 5.0 1.2 + - - -
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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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218B ILE 3.0 21.0 + - - -
219B ALA* 3.6 19.6 + - - +
222B PRO* 3.8 16.3 - - - +
227B HIS 3.9 7.1 + - - -
228B CYS* 3.9 15.1 - - + +
231B TYR* 2.9 59.8 - - + +
232B VAL* 4.5 4.0 - - + -
236B GLN* 5.3 2.0 - - - +
263B LYS 2.9 17.4 + - - +
264B SER* 3.7 6.1 - - - +
266B GLU* 1.3 74.4 - - - +
268B ALA* 1.3 68.4 + - - +
270B GLN* 2.9 40.5 + - - +
271B TYR* 3.3 25.0 + - + -
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Residues in contact with ALA 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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228B CYS* 3.4 16.3 - - - -
264B SER 2.9 18.8 + - - +
265B LEU* 3.7 7.2 - - + +
267B ARG* 1.3 77.7 - - - +
269B SER* 1.3 52.7 + - - +
271B TYR 3.3 0.9 + - - -
272B ASN 2.6 30.5 + - - -
273B ILE* 2.8 33.0 + - - +
276B VAL* 3.6 19.7 - - + -
64E GLN* 5.7 1.6 - - - +
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Residues in contact with SER 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 LEU* 3.3 11.6 + - - -
266B GLU* 3.1 13.6 + - - -
267B ARG 3.1 0.8 - - - -
268B ALA* 1.3 77.9 - - - +
270B GLN* 1.3 67.8 + - - +
272B ASN* 2.9 16.6 + - - +
63E ASN* 2.7 33.5 + - - +
64E GLN 5.9 2.5 - - - -
85E ARG* 5.2 4.0 + - - -
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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 GLU* 3.0 16.0 + - - +
267B ARG* 2.9 30.6 + - - +
269B SER* 1.3 77.8 - - - +
271B TYR* 1.3 75.7 + - + +
272B ASN* 3.3 4.0 + - - +
436E HIS* 5.5 7.9 + - - +
440E GLY 3.0 27.3 - - - +
441E ARG* 3.8 16.5 - - - +
442E TYR* 6.4 2.5 - - + -
445E VAL* 5.8 7.2 - - - +
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Residues in contact with TYR 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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336A SER* 2.9 31.5 + - - +
337A GLY* 5.9 0.3 - - - -
340A ILE* 3.2 14.9 - - - +
219B ALA 4.0 13.7 + - - -
220B SER 3.9 10.7 + - - -
222B PRO* 3.4 28.7 - - + -
267B ARG* 3.3 33.8 + - + +
268B ALA 3.4 1.8 - - - +
270B GLN* 1.3 95.1 + - + +
272B ASN* 1.3 78.6 + - - +
273B ILE* 3.3 15.6 + - + +
439E GLN 5.1 1.2 + - - -
440E GLY* 4.1 20.6 + - - -
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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