Contacts of the helix formed by residues 269 - 289 (chain M) in PDB entry 3J8B
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 LEU 269 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209M VAL* 6.5 0.9 - - + -
213M LYS* 5.4 5.8 - - + +
264M ASP* 3.3 11.1 + - + +
267M GLY* 3.1 8.6 + - - -
268M LEU* 1.3 77.8 - - - +
270M HIS* 1.3 64.1 + - - +
272M GLN* 3.2 12.5 + - - +
273M ASN* 3.0 18.7 + - + +
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Residues in contact with HIS 270 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261M ASP* 5.0 1.1 - - - +
264M ASP* 2.9 37.4 + - + +
265M SER* 4.4 2.2 - - - +
268M LEU 3.3 1.0 - - - -
269M LEU* 1.3 79.1 - - - +
271M GLU* 1.3 50.1 + - - +
273M ASN* 2.8 11.1 + - + -
274M MET* 1.9 48.1 + - + -
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Residues in contact with GLU 271 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268M LEU* 3.8 12.1 + - + +
269M LEU 3.3 0.8 - - - -
270M HIS* 1.3 78.2 - - - +
272M GLN* 1.3 54.8 + - - +
274M MET* 3.7 10.0 - - - +
275M ALA* 2.7 34.0 + - - +
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Residues in contact with GLN 272 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212M LEU 4.5 3.3 - - - +
213M LYS* 4.6 22.9 - - + +
268M LEU 4.4 2.3 + - - +
269M LEU* 3.2 12.1 + - - +
271M GLU* 1.3 77.2 - - - +
273M ASN* 1.3 58.2 + - - +
275M ALA* 3.8 5.7 - - - +
276M LYS* 3.2 24.8 + - - +
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Residues in contact with ASN 273 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212M LEU* 4.0 23.6 - - + +
213M LYS* 5.1 2.4 - - + +
264M ASP* 6.0 0.2 - - + -
269M LEU* 3.0 14.2 + - + +
270M HIS* 2.8 15.6 + - + +
272M GLN* 1.3 76.4 - - - +
274M MET* 1.3 57.2 + - - -
276M LYS* 3.3 1.6 + - - +
277M MET* 2.9 30.0 + - - +
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Residues in contact with MET 274 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270M HIS* 1.9 33.9 + - + +
271M GLU* 3.7 11.4 - - - -
273M ASN* 1.3 64.7 - - - +
275M ALA* 1.3 66.3 + - - +
277M MET* 3.3 5.9 + - - +
278M ARG* 3.1 24.0 + - - +
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Residues in contact with ALA 275 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271M GLU 2.7 22.1 + - - +
272M GLN* 3.8 6.5 - - - +
274M MET* 1.3 72.6 - - - +
276M LYS* 1.3 56.6 + - - +
278M ARG* 3.2 7.0 + - - +
279M LEU* 2.9 28.3 + - - +
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Residues in contact with LYS 276 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212M LEU 4.1 15.3 - - - +
213M LYS 6.3 0.4 - - - -
214M ASP 6.0 2.2 - - - +
217M ALA 5.6 5.8 - - - +
272M GLN 3.2 16.0 + - - +
273M ASN 3.7 4.7 - - - +
274M MET 3.3 0.2 - - - -
275M ALA* 1.3 79.6 - - - +
277M MET* 1.3 57.8 + - - +
279M LEU* 3.1 8.7 + - - +
280M LEU* 2.8 30.5 + - - +
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Residues in contact with MET 277 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243M ILE 5.8 4.0 - - - +
244M PHE* 6.5 1.1 - - - -
247M ALA 5.4 0.4 - - - +
248M LYS* 5.0 3.5 - - - +
249M LEU* 4.3 20.9 + - + +
273M ASN 2.9 17.3 + - - +
274M MET* 3.3 6.2 + - - +
276M LYS* 1.3 76.5 - - - +
278M ARG* 1.3 58.0 + - - +
280M LEU* 3.4 8.2 + - - +
281M THR* 2.9 27.4 + - - -
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Residues in contact with ARG 278 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249M LEU* 4.9 10.2 - - + +
274M MET 3.1 13.2 + - - +
275M ALA* 3.7 8.7 - - - +
277M MET* 1.3 73.9 - - - +
279M LEU* 1.3 64.1 - - - +
281M THR* 3.2 10.0 + - - -
282M PHE* 3.1 20.3 + - - +
301M LEU* 5.4 12.1 - - - +
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Residues in contact with LEU 279 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275M ALA 2.9 13.9 + - - +
276M LYS* 3.1 11.4 + - - +
278M ARG* 1.3 75.4 - - - +
280M LEU* 1.3 64.6 + - - +
282M PHE* 3.1 18.8 + - - +
283M MET* 3.1 11.8 + - - +
316M VAL* 5.9 6.3 - - + +
317M ARG* 5.7 12.8 - - + +
320M MET* 6.0 6.5 - - + +
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Residues in contact with LEU 280 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218M PHE* 5.6 8.7 - - + +
244M PHE* 5.1 11.2 - - - +
247M ALA 5.1 10.5 - - - +
276M LYS 2.8 19.7 + - - +
277M MET* 3.6 8.5 - - - +
279M LEU* 1.3 74.0 - - - +
281M THR* 1.3 57.5 + - - +
283M MET* 3.1 10.5 + - - +
284M GLY* 2.9 24.8 + - - -
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Residues in contact with THR 281 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247M ALA 5.6 0.2 - - - -
248M LYS* 4.4 14.3 - - - +
249M LEU* 4.2 20.0 - - - -
277M MET 2.9 14.7 + - - -
278M ARG* 3.2 13.6 + - - -
280M LEU* 1.3 74.2 - - - +
282M PHE* 1.3 64.9 + - - +
284M GLY* 3.2 2.6 + - - -
285M MET* 3.0 23.8 + - - +
300M GLU* 5.3 15.0 - - - -
301M LEU* 6.5 0.2 - - - -
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Residues in contact with PHE 282 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278M ARG 3.1 10.1 + - - +
279M LEU* 3.1 12.9 + - - +
281M THR* 1.3 75.2 - - - +
283M MET* 1.3 57.4 + - - +
285M MET* 3.2 7.3 + - - +
286M ALA* 2.9 30.2 + - - +
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Residues in contact with MET 283 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279M LEU 3.1 12.1 + - - +
280M LEU* 3.1 12.5 + - - +
282M PHE* 1.3 76.9 - - - +
284M GLY* 1.3 62.8 + - - +
286M ALA* 3.3 7.1 + - - +
287M VAL* 3.1 21.8 + - - +
320M MET* 6.2 4.9 - - + -
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Residues in contact with GLY 284 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280M LEU 2.9 13.7 + - - -
281M THR* 3.2 4.4 + - - -
283M MET* 1.3 75.7 - - - +
285M MET* 1.3 63.7 + - - +
287M VAL* 3.2 19.2 + - - +
288M GLU* 3.5 8.0 + - - +
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Residues in contact with MET 285 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281M THR 3.0 12.7 + - - +
282M PHE* 3.6 10.3 - - - +
284M GLY* 1.3 76.9 - - - +
286M ALA* 1.3 57.9 + - - +
288M GLU* 3.2 9.3 + - - +
289M ASN* 3.1 27.6 + - - +
292M ILE* 5.4 11.0 - - + -
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Residues in contact with ALA 286 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282M PHE 2.9 17.1 + - - +
283M MET* 3.8 7.4 - - - +
284M GLY 3.2 0.4 - - - -
285M MET* 1.3 72.7 - - - +
287M VAL* 1.3 65.1 + - - +
288M GLU 3.3 0.2 - - - -
289M ASN 3.2 21.8 + - - +
290M LYS* 4.4 2.6 + - - +
334M VAL* 4.6 25.5 - - + +
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Residues in contact with VAL 287 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283M MET 3.1 12.4 + - - +
284M GLY* 3.4 13.7 - - - +
286M ALA* 1.3 79.7 - - - +
288M GLU* 1.3 58.7 + - - +
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Residues in contact with GLU 288 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284M GLY 3.5 6.8 + - - +
285M MET* 3.2 10.1 + - - +
287M VAL* 1.3 80.9 - - - +
289M ASN* 1.3 60.3 + - + +
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Residues in contact with ASN 289 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285M MET 3.1 8.8 + - - +
286M ALA* 3.2 23.8 - - - +
287M VAL 3.5 1.2 - - - -
288M GLU* 1.3 82.6 - - + +
290M LYS* 1.3 59.9 + - - +
291M GLU 3.3 21.7 + - - +
292M ILE* 5.0 4.6 + - + +
334M VAL* 5.5 1.0 - - - +
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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