Contacts of the helix formed by residues 239 - 260 (chain B) in PDB entry 1M1B
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 ASN 239 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B GLU* 3.3 11.4 - - - -
48B LEU* 4.5 19.0 - - + +
49B SER* 3.9 11.0 - - - +
124B LEU* 4.4 12.1 - - - +
217B THR* 3.7 25.5 + - - +
237B TRP 3.7 0.2 - - - -
238B ALA* 1.3 82.2 - - - +
240B HIS* 1.3 67.5 + - - +
242B LEU* 3.4 5.9 + - + +
243B ARG* 2.6 71.2 + - + +
997B SPV 4.8 3.8 + - - +
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Residues in contact with HIS 240 (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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24B MET* 4.1 11.0 - - + +
25B GLU* 3.4 1.0 + - - -
217B THR* 4.9 14.9 - - + +
220B TYR* 6.3 1.0 - - - +
237B TRP* 3.9 27.1 - + + +
238B ALA 3.9 10.3 - - - -
239B ASN* 1.3 92.5 + - - +
241B ASN* 1.3 58.2 + - - +
243B ARG* 3.4 30.4 + - - +
244B ALA* 2.7 35.0 + - - +
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Residues in contact with ASN 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B MET* 3.4 27.4 - - - +
25B GLU* 2.8 35.0 + - - +
26B ALA* 5.0 0.4 - - - +
27B HIS* 4.0 8.2 - - + -
31B SER* 5.1 8.8 + - - -
34B ILE* 5.8 6.2 - - - +
35B VAL* 3.7 10.9 - - - +
240B HIS* 1.3 77.0 - - - +
242B LEU* 1.3 57.5 + - - +
244B ALA* 3.7 6.6 - - - +
245B SER* 2.8 29.3 + - - -
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Residues in contact with LEU 242 (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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25B GLU* 3.1 6.2 + - - +
27B HIS* 3.6 26.2 - - + +
48B LEU* 4.8 6.7 - - + +
49B SER* 3.3 49.8 - - - +
52B ALA* 3.7 25.1 - - + -
53B GLN* 4.2 6.5 - - + +
239B ASN* 3.6 11.4 - - + +
240B HIS 3.2 0.2 - - - -
241B ASN* 1.3 75.1 - - - +
243B ARG* 1.3 70.3 + - + +
245B SER* 3.4 3.7 + - - -
246B VAL* 3.1 32.3 + - + +
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Residues in contact with ARG 243 (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 THR* 4.3 9.5 - - - +
239B ASN* 2.6 66.7 + - + +
240B HIS* 3.4 28.5 + - - +
242B LEU* 1.3 79.9 - - + +
244B ALA* 1.3 66.3 + - - +
246B VAL* 3.4 7.4 + - - +
247B SER* 3.1 21.5 + - - -
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Residues in contact with ALA 244 (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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240B HIS 2.7 22.9 + - - +
241B ASN* 3.7 9.6 - - - +
243B ARG* 1.3 71.3 - - - +
245B SER* 1.3 67.4 + - - +
247B SER* 3.0 18.1 + - - -
248B ALA* 3.0 14.7 + - - +
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Residues in contact with SER 245 (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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27B HIS* 4.7 12.2 + - - -
241B ASN 2.8 21.6 + - - -
242B LEU* 3.6 9.2 - - - -
243B ARG 3.4 0.2 - - - -
244B ALA* 1.3 74.0 - - - +
246B VAL* 1.3 57.6 + - - +
248B ALA* 3.2 5.9 + - - +
249B ILE* 2.9 48.2 + - - +
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Residues in contact with VAL 246 (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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242B LEU* 3.1 24.3 + - + +
243B ARG* 3.7 9.2 - - - +
244B ALA 3.2 0.2 - - - -
245B SER* 1.3 78.2 - - - +
247B SER* 1.3 59.2 + - - +
249B ILE* 3.1 7.1 + - + +
250B GLN* 2.7 66.3 + - + +
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Residues in contact with SER 247 (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 ARG 3.1 10.2 + - - -
244B ALA* 3.0 12.0 + - - -
246B VAL* 1.3 79.0 - - - +
248B ALA* 1.3 62.4 + - - +
250B GLN* 3.5 10.0 + - - +
251B GLN* 3.0 52.3 + - - +
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Residues in contact with ALA 248 (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 ALA 3.0 11.1 + - - +
245B SER* 3.7 8.7 - - - +
247B SER* 1.3 75.8 - - - +
249B ILE* 1.3 62.0 + - + +
251B GLN* 4.0 5.9 - - - +
252B THR* 2.8 36.1 + - - +
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Residues in contact with ILE 249 (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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245B SER* 2.9 35.6 + - - +
246B VAL* 3.8 6.5 - - + +
248B ALA* 1.3 76.1 - - + +
250B GLN* 1.3 68.3 + - + +
252B THR* 4.7 2.7 - - - -
253B THR* 2.7 41.6 + - - +
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Residues in contact with GLN 250 (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 VAL* 2.7 46.4 + - + +
247B SER* 3.9 9.2 - - - +
249B ILE* 1.3 76.7 - - + +
251B GLN* 1.3 59.7 + - + +
253B THR* 3.9 4.9 - - - -
254B LYS* 3.0 28.6 + - - +
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Residues in contact with GLN 251 (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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247B SER* 3.0 40.1 + - - +
248B ALA* 4.1 5.5 - - - +
250B GLN* 1.3 78.8 - - + +
252B THR* 1.3 60.5 + - - +
254B LYS* 3.6 6.0 - - - +
255B GLN* 2.8 31.9 + - - +
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Residues in contact with THR 252 (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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248B ALA* 2.8 23.9 + - - +
249B ILE* 4.1 3.6 - - - -
251B GLN* 1.3 76.6 - - - +
253B THR* 1.3 61.4 + - - +
256B ILE* 3.1 51.4 + - + +
265B VAL* 3.8 24.1 - - + +
269B ILE* 4.3 22.2 - - + +
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Residues in contact with THR 253 (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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249B ILE* 2.7 34.3 + - - +
250B GLN* 3.9 4.7 - - - -
252B THR* 1.3 76.1 - - - +
254B LYS* 1.3 65.8 + - - +
256B ILE* 4.1 4.9 - - - +
257B TYR* 3.0 29.6 + - + +
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Residues in contact with LYS 254 (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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250B GLN 3.0 19.8 + - - +
251B GLN* 3.6 7.0 - - - +
253B THR* 1.3 76.5 - - - +
255B GLN* 1.3 65.5 + - - +
257B TYR* 3.1 21.5 + - - +
258B ASP* 2.8 59.4 + - - +
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Residues in contact with GLN 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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251B GLN 2.8 20.3 + - - +
252B THR* 4.6 0.2 - - - -
254B LYS* 1.3 76.1 - - - +
256B ILE* 1.3 57.0 + - - +
258B ASP* 3.5 4.7 + - - +
259B ASP* 2.5 70.5 + - - +
261B SER 6.0 0.2 - - - +
264B ASN* 3.8 22.3 - - + +
265B VAL* 3.7 25.4 - - + -
268B LYS* 5.4 5.4 + - - -
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Residues in contact with ILE 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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252B THR* 3.1 37.8 + - + +
253B THR* 4.1 4.9 - - - +
255B GLN* 1.3 73.2 - - - +
257B TYR* 1.3 68.8 + - - +
260B GLN* 2.9 23.3 + - - -
261B SER 3.8 19.5 + - - +
262B LEU* 3.9 18.2 - - + -
265B VAL* 3.7 26.0 - - + -
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Residues in contact with TYR 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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253B THR* 3.0 23.8 + - + +
254B LYS* 3.1 20.4 + - - +
256B ILE* 1.3 80.6 - - - +
258B ASP* 1.3 74.7 + - - +
260B GLN* 4.0 12.6 + - - +
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Residues in contact with ASP 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 LYS* 2.8 55.8 + - - +
255B GLN* 3.9 6.8 - - - +
257B TYR* 1.3 85.0 - - - +
259B ASP* 1.3 69.5 + - - +
260B GLN* 3.3 5.2 + - - +
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Residues in contact with ASP 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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255B GLN* 2.5 50.8 + - - +
258B ASP* 1.3 80.8 - - - +
260B GLN* 1.3 72.7 + - - +
261B SER* 3.0 26.2 + - - +
264B ASN* 2.9 26.5 + - + +
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Residues in contact with GLN 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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256B ILE* 2.9 14.7 + - - -
257B TYR 4.1 13.0 + - - +
258B ASP 4.5 4.5 - - - +
259B ASP* 1.3 79.8 - - - +
261B SER* 1.3 59.4 + - - +
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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