Contacts of the helix formed by residues 247 - 265 (chain B) in PDB entry 3NAV
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 247 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B HIS* 3.5 8.5 + - + +
245B LEU 3.3 0.8 - - - -
246B ASP* 1.3 83.4 - - + +
248B PRO* 1.3 63.2 - - - +
249B ALA* 3.6 8.5 + - - +
250B LYS* 3.4 35.6 + - + +
251B GLN* 3.0 26.9 + - - +
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Residues in contact with PRO 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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32B GLN* 3.2 38.9 + - + +
245B LEU 4.5 5.8 - - - +
246B ASP 3.8 4.7 - - - +
247B ASN* 1.3 91.1 - - - +
249B ALA* 1.3 63.0 + - - +
251B GLN* 3.2 8.4 + - + +
252B LEU* 3.1 20.1 + - - +
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ASN* 3.3 7.8 + - - +
248B PRO* 1.3 77.7 - - - +
250B LYS* 1.3 57.9 + - - +
252B LEU* 3.3 12.0 + - - +
253B THR* 3.1 28.2 + - - -
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Residues in contact with LYS 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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244B HIS* 3.9 28.0 - - + +
247B ASN* 3.4 32.7 + - + +
248B PRO 3.3 0.4 - - - -
249B ALA* 1.3 73.2 - - - +
251B GLN* 1.3 68.3 + - - +
252B LEU 3.1 1.8 - - - -
253B THR* 3.7 10.0 - - + -
254B GLU* 2.9 49.9 + - + +
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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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28B PRO* 4.2 13.0 - - - +
32B GLN* 2.8 36.9 + - - +
36B ILE* 3.4 12.3 - - - +
240B ILE* 4.5 1.5 - - - +
241B ILE* 3.8 25.0 + - - +
244B HIS* 3.1 40.1 + - + +
245B LEU* 4.0 8.5 + - - +
247B ASN 3.0 10.8 + - - +
248B PRO* 3.3 12.4 - - - +
250B LYS* 1.3 77.7 - - - +
252B LEU* 1.3 61.8 + - - +
254B GLU* 3.6 3.0 + - - +
255B LEU* 3.1 36.7 + - + +
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Residues in contact with LEU 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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32B GLN* 3.6 21.1 - - - +
35B ALA* 3.9 17.5 - - + -
36B ILE* 3.8 31.4 - - + +
39B THR* 3.4 35.3 - - + +
248B PRO 3.1 14.0 + - - +
249B ALA* 3.6 10.5 - - - +
250B LYS 3.1 0.6 - - - -
251B GLN* 1.3 78.8 - - - +
253B THR* 1.3 57.7 + - - +
255B LEU* 3.2 2.9 + - + +
256B ALA* 3.0 25.8 + - - +
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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 ALA 3.1 15.0 + - - -
250B LYS* 3.2 14.2 + - + -
252B LEU* 1.3 76.1 - - - +
254B GLU* 1.3 60.2 + - + +
256B ALA* 3.4 5.8 + - - +
257B ASN* 2.9 50.9 + - - +
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Residues in contact with GLU 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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240B ILE* 3.7 22.9 - - + +
244B HIS* 3.5 27.0 - - + +
250B LYS* 2.9 54.0 + - + +
251B GLN 3.8 0.9 - - - +
253B THR* 1.3 74.1 - - - +
255B LEU* 1.3 57.2 + - - +
257B ASN* 3.9 13.7 + - - +
258B PHE* 3.0 30.0 + - - +
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Residues in contact with LEU 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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36B ILE* 3.8 42.4 - - + -
39B THR* 4.4 8.3 - - + -
40B LEU* 4.4 9.0 - - + -
43B ALA* 5.1 0.2 - - - -
237B VAL* 3.6 30.3 - - + +
240B ILE* 3.6 31.9 - - + -
241B ILE* 4.0 13.5 - - + -
251B GLN* 3.1 27.4 + - + +
252B LEU* 3.2 6.5 + - + +
254B GLU* 1.3 73.6 - - - +
256B ALA* 1.3 67.3 + - - +
258B PHE* 3.8 2.9 - - + +
259B THR* 2.8 30.9 + - - -
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Residues in contact with ALA 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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39B THR* 3.8 12.4 - - + +
43B ALA* 3.6 21.0 - - + +
252B LEU 3.0 16.7 + - - +
253B THR* 3.7 7.2 - - - +
255B LEU* 1.3 77.4 - - - +
257B ASN* 1.3 67.5 + - - +
259B THR 3.2 0.2 + - - -
260B GLN* 2.9 27.3 + - + +
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Residues in contact with ASN 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* 2.9 37.6 + - - +
254B GLU* 3.9 14.6 + - - +
255B LEU 3.2 0.2 - - - -
256B ALA* 1.3 79.5 - - - +
258B PHE* 1.3 65.0 + - - +
260B GLN* 3.4 11.8 + - - +
261B ALA* 3.0 24.7 + - - +
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Residues in contact with PHE 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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19B PHE* 4.4 4.3 - + - -
215B SER 3.4 22.0 - - - -
216B GLU* 5.3 1.8 - - - -
217B PRO* 4.9 7.4 - - + -
233B SER* 4.4 1.3 - - - -
236B ALA* 3.8 16.4 - - + -
237B VAL* 3.7 29.2 - - + -
240B ILE* 3.5 25.8 - - + -
254B GLU 3.0 18.6 + - - +
255B LEU* 3.8 3.4 - - + +
257B ASN* 1.3 76.0 - - - +
259B THR* 1.3 64.7 + - - +
261B ALA* 3.2 5.4 + - + +
262B MET* 2.9 72.0 + - + +
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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
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19B PHE* 4.2 19.3 - - + -
21B PRO* 5.4 0.2 - - - +
40B LEU* 3.2 42.9 - - + +
43B ALA* 3.4 24.5 - - - +
44B GLY 4.2 0.9 - - - -
45B ALA* 3.6 17.3 - - + +
237B VAL* 5.5 0.2 - - - +
255B LEU 2.8 20.5 + - - -
258B PHE* 1.3 80.8 - - - +
260B GLN* 1.3 55.9 + - - +
262B MET* 3.3 2.1 + - - +
263B LYS* 2.9 28.6 + - - +
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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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43B ALA* 3.5 21.2 + - + +
256B ALA* 2.9 17.8 + - + +
257B ASN* 3.6 12.6 - - - +
259B THR* 1.3 77.3 - - - +
261B ALA* 1.3 63.3 + - - +
263B LYS* 3.4 4.2 + - - +
264B LYS* 3.0 36.3 + - + +
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Residues in contact with ALA 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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217B PRO* 3.7 27.6 - - + +
257B ASN 3.0 17.6 + - - +
258B PHE* 3.8 5.2 - - + +
260B GLN* 1.3 77.9 - - - +
262B MET* 1.3 62.3 + - - +
264B LYS* 3.6 12.7 + - - +
265B ALA* 3.4 15.2 + - - +
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Residues in contact with MET 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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19B PHE* 3.6 36.6 - - + -
214B ILE* 3.8 21.8 - - + +
215B SER 3.9 1.1 - - - -
216B GLU 3.4 12.6 - - - +
217B PRO* 3.3 36.6 - - + -
220B VAL* 3.5 35.5 - - + +
233B SER* 4.2 0.7 - - - -
258B PHE* 2.9 57.0 + - + +
259B THR 3.8 0.2 - - - +
261B ALA* 1.3 74.8 - - - +
263B LYS* 1.3 63.7 + - - +
265B ALA* 3.3 17.6 + - - +
266B THR* 3.7 0.9 - - - +
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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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11B LEU* 3.8 1.4 - - - +
16B GLN* 2.8 33.5 + - - +
17B GLY 2.9 19.0 + - - -
19B PHE* 4.3 8.0 - - + -
43B ALA 4.6 1.6 - - - +
44B GLY* 3.5 31.4 - - - +
46B ASP* 3.0 26.6 + - - +
259B THR 2.9 17.7 + - - +
260B GLN* 3.8 5.6 - - - +
262B MET* 1.3 73.2 - - - +
264B LYS* 1.3 61.3 + - - +
266B THR* 2.4 57.7 + - + +
267B LYS* 4.1 4.0 + - - +
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Residues in contact with LYS 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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260B GLN* 3.0 26.8 + - + +
261B ALA* 3.7 10.5 - - - +
263B LYS* 1.3 78.6 - - - +
265B ALA* 1.3 58.1 + - - +
266B THR 3.1 1.7 + - - -
267B LYS* 2.8 52.2 + - - +
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Residues in contact with ALA 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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217B PRO* 3.1 34.5 - - + +
220B VAL* 3.7 7.6 - - + +
221B LYS* 3.4 35.6 + - + +
224B ILE* 3.8 1.7 - - - +
261B ALA 3.4 10.2 + - - +
262B MET 3.3 11.6 + - - +
263B LYS 3.2 0.6 - - - -
264B LYS* 1.3 76.7 - - - +
266B THR* 1.3 57.8 + - - +
267B LYS 3.4 2.6 + - - +
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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
------------------------------------------------------------
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