Contacts of the helix formed by residues 281 - 295 (chain A) in PDB entry 3MPM
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 281 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A LEU* 4.4 0.4 - - - -
280A MET* 1.3 79.7 - - - +
282A PRO* 1.3 73.4 - - - +
283A ASP* 3.6 9.0 + - - +
284A ALA* 3.1 21.9 + - - +
285A PHE* 3.1 17.8 + - - +
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Residues in contact with PRO 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A LEU* 4.2 13.2 - - + -
280A MET 4.2 2.7 - - - +
281A SER* 1.3 86.8 - - - +
283A ASP* 1.3 59.8 + - - +
285A PHE* 3.3 1.6 + - + +
286A LEU* 2.8 41.3 + - + +
308A THR 5.8 0.2 - - - +
312A ILE* 3.7 30.7 - - + -
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Residues in contact with ASP 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A SER* 3.2 8.9 + - - +
282A PRO* 1.3 82.0 - - - +
284A ALA* 1.3 59.4 + - - +
286A LEU* 3.4 9.7 + - - +
287A ALA* 3.1 23.6 + - - +
290A ASN* 5.7 0.9 + - - -
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A MET* 3.8 24.6 - - + +
281A SER* 3.1 21.7 + - - +
283A ASP* 1.3 72.8 - - - +
285A PHE* 1.3 66.1 + - - +
287A ALA* 3.5 16.4 - - - +
288A GLU* 4.5 0.9 + - - +
385A LEU* 5.8 1.7 - - - +
387A ARG* 5.5 8.2 - - - -
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Residues in contact with PHE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A LYS* 3.5 43.7 - - + -
275A LEU* 3.6 41.1 - - + -
280A MET* 3.5 11.4 - - - -
281A SER 3.1 6.0 + - - +
282A PRO 3.5 6.3 - - - +
284A ALA* 1.3 79.0 - - - +
286A LEU* 1.3 61.1 + - + +
287A ALA 3.1 1.8 + - - -
288A GLU* 3.4 15.8 + - - +
312A ILE* 3.6 43.7 - - + -
314A ILE* 3.6 35.0 - - + +
394A TYR* 3.5 26.7 - + - -
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A PRO* 2.8 29.6 + - + +
283A ASP* 3.4 11.4 + - - +
284A ALA 3.4 0.2 - - - -
285A PHE* 1.3 74.0 - - - +
287A ALA* 1.3 64.3 + - - +
288A GLU 3.2 0.2 - - - -
289A ALA* 3.0 7.7 + - + +
290A ASN* 3.0 29.2 + - - +
306A VAL* 4.0 33.2 - - + -
308A THR* 3.7 25.4 - - + -
312A ILE* 3.8 27.4 - - + -
313A TYR 4.5 0.4 - - - +
314A ILE* 4.3 11.4 - - + -
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ASP 3.1 12.1 + - - +
284A ALA* 3.5 15.9 - - - +
285A PHE 3.1 0.8 - - - -
286A LEU* 1.3 77.1 - - - +
288A GLU* 1.3 62.4 + - - +
290A ASN* 3.2 13.8 + - - +
291A LEU* 3.0 33.9 + - + +
385A LEU* 5.2 3.6 - - + -
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Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A 5LK 2.6 40.8 + - - -
273A LYS* 3.3 21.8 + - - +
284A ALA 4.5 0.4 + - - -
285A PHE* 3.4 13.7 + - - +
287A ALA* 1.3 78.1 - - - +
289A ALA* 1.3 60.0 + - - +
291A LEU* 3.4 6.0 + - - +
292A MET* 3.2 29.7 + - + +
314A ILE* 3.9 6.7 - - + +
382A ASP* 3.4 31.8 + - - +
383A PHE 5.8 0.7 - - - +
385A LEU* 3.7 27.5 - - + +
394A TYR* 5.8 0.2 - - - -
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A LEU* 3.0 12.9 + - + +
288A GLU* 1.3 76.7 - - - +
290A ASN* 1.3 60.1 + - - +
292A MET* 3.0 16.4 + - - +
293A LYS* 2.9 33.0 + - - +
303A LEU* 3.7 12.9 - - + +
306A VAL* 3.6 30.7 - - + -
314A ILE* 3.9 15.9 - - + +
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Residues in contact with ASN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A ASP 5.7 0.6 + - - -
286A LEU* 3.0 21.0 + - - +
287A ALA* 3.5 15.0 - - - +
289A ALA* 1.3 76.5 - - - +
291A LEU* 1.3 57.1 + - + +
293A LYS* 3.1 37.7 + - + +
294A GLN* 3.1 41.1 + - - +
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ALA* 3.0 24.3 + - + +
288A GLU 3.7 5.8 - - - +
289A ALA 3.3 0.4 - - - -
290A ASN* 1.3 72.6 - - + +
292A MET* 1.3 61.0 + - + +
294A GLN* 3.2 14.8 + - - +
295A LEU* 3.0 25.5 + - + +
360A TYR* 3.8 30.1 - - + -
383A PHE* 3.5 28.9 - - + +
384A GLY* 3.2 42.0 - - - +
385A LEU* 3.8 15.9 - - + +
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Residues in contact with MET 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A 5LK 3.7 23.6 - - - +
238A TRP* 5.9 0.2 - - - -
288A GLU* 3.2 29.1 + - + +
289A ALA* 3.0 11.2 + - - +
291A LEU* 1.3 73.7 - - - +
293A LYS* 1.3 65.1 + - - +
295A LEU 3.3 14.3 - - - +
296A GLN* 3.5 11.6 - - - +
301A VAL* 3.6 29.3 - - - +
303A LEU* 3.8 23.7 + - + +
314A ILE* 3.8 18.4 - - + -
316A THR* 4.0 17.3 - - + -
381A ALA* 6.4 0.4 - - - -
382A ASP 6.0 3.6 - - - +
383A PHE* 3.7 26.9 - - + -
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Residues in contact with LYS 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A TRP* 3.6 55.6 - - + +
289A ALA* 2.9 20.1 + - - +
290A ASN* 3.1 37.0 + - - +
292A MET* 1.3 76.4 - - - +
294A GLN* 1.3 60.7 + - + +
296A GLN* 2.9 27.3 + - - +
303A LEU* 3.7 14.1 - - + +
306A VAL* 5.1 8.4 - - - +
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Residues in contact with GLN 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A ASN* 3.1 34.2 + - - +
291A LEU* 3.2 17.2 + - - +
293A LYS* 1.3 79.1 - - + +
295A LEU* 1.3 66.6 + - + +
296A GLN* 4.1 1.3 + - - -
358A ARG* 4.8 7.6 + - - -
360A TYR* 2.5 42.9 + - + +
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A LEU* 3.0 12.4 + - + +
292A MET* 3.3 10.6 - - - +
294A GLN* 1.3 83.7 - - - +
296A GLN* 1.3 62.2 + - - +
300A LEU* 3.6 23.2 - - + +
301A VAL 5.3 1.7 - - - +
354A PHE* 3.8 8.7 - - + -
355A ILE* 4.0 19.7 - - + -
358A ARG* 3.7 39.3 - - + +
360A TYR* 3.8 42.2 - - + -
383A PHE* 3.9 28.9 - - + -
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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