Contacts of the helix formed by residues 286 - 298 (chain M) in PDB entry 3EXG
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 286 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43M ARG* 3.0 25.9 + - - -
260M TYR* 2.8 25.9 + - - +
282M ARG* 3.2 27.2 + - + +
285M SER* 1.3 77.0 - - - +
287M PRO* 1.3 68.9 - - - +
288M ILE* 2.7 30.8 + - - +
289M MET* 2.8 23.8 + - + +
290M LEU* 3.0 22.2 + - - +
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Residues in contact with PRO 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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39M MET* 3.7 13.6 - - - +
43M ARG* 3.9 4.0 - - - +
67M GLY 4.3 11.9 - - - +
69M GLU* 3.5 24.7 - - + +
70M ALA* 3.6 24.2 - - + +
228M MET* 3.2 31.7 - - + +
230M ILE* 4.8 2.0 - - - +
260M TYR* 3.8 6.3 - - - +
285M SER 3.4 3.7 - - - +
286M ASP* 1.3 95.5 - - - +
288M ILE* 1.3 64.4 + - + +
290M LEU* 3.5 2.2 + - + +
291M LEU* 3.1 18.0 + - - +
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Residues in contact with ILE 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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36M TYR* 3.7 27.7 - - + +
39M MET* 3.6 46.4 - - + +
40M GLN* 3.3 36.3 - - + +
43M ARG* 3.6 28.5 - - + +
69M GLU* 4.7 2.2 - - - +
286M ASP* 2.7 13.4 + - - +
287M PRO* 1.3 74.3 - - + +
289M MET* 1.3 59.1 + - - +
291M LEU* 3.5 2.4 + - - +
292M LYS* 3.1 26.0 + - + +
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Residues in contact with MET 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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282M ARG 4.4 8.1 - - - +
283M SER* 3.8 20.4 - - - +
284M LYS 4.3 9.4 - - - +
286M ASP* 2.8 21.4 + - + +
288M ILE* 1.3 76.4 - - - +
290M LEU* 1.3 101.0 + - + +
292M LYS* 3.2 10.2 + - + +
293M ASP* 2.8 53.0 + - - +
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Residues in contact with LEU 290 (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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226M ASP* 5.7 2.2 - - - +
228M MET* 3.6 29.6 - - + +
229M ASP* 4.7 10.8 - - + +
230M ILE* 6.5 0.2 - - + -
284M LYS 4.0 5.4 - - - +
285M SER* 3.8 26.9 - - - +
286M ASP 3.0 21.4 + - - +
287M PRO 4.1 2.0 - - - +
289M MET* 1.3 103.9 - - + +
291M LEU* 1.3 65.1 + - - +
293M ASP* 3.7 5.0 + - + +
294M ARG* 3.2 30.3 + - - +
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Residues in contact with LEU 291 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M LEU* 4.5 15.3 - - + -
32M GLY* 3.9 9.9 - - - +
35M TYR* 4.1 8.5 - - + -
36M TYR* 3.7 30.3 - - + +
39M MET* 3.3 36.8 - - + -
230M ILE* 4.2 17.4 - - + +
231M LEU* 5.4 6.1 - - + -
287M PRO 3.1 8.1 + - - +
288M ILE 3.9 2.0 - - - +
289M MET 3.1 0.6 - - - -
290M LEU* 1.3 73.7 - - - +
292M LYS* 1.3 68.1 + - - +
294M ARG* 2.9 17.0 + - + +
295M MET* 2.8 41.9 + - + +
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Residues in contact with LYS 292 (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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36M TYR* 4.1 15.1 - - + +
288M ILE* 3.1 16.4 + - + +
289M MET* 3.4 13.0 - - + +
291M LEU* 1.3 74.2 - - - +
293M ASP* 1.3 72.2 + - - +
295M MET* 3.0 5.4 + - - +
296M VAL* 2.8 27.9 + - + +
303M VAL* 3.3 39.3 + - - +
306M LEU* 3.4 35.2 - - + -
307M LYS* 5.6 4.3 - - - +
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Residues in contact with ASP 293 (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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289M MET* 2.8 49.0 + - + +
290M LEU* 4.0 6.3 - - + +
292M LYS* 1.3 80.3 - - - +
294M ARG* 1.3 57.5 + - + +
296M VAL* 4.9 3.4 - - - -
297M ASN* 3.0 44.0 + - - +
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Residues in contact with ARG 294 (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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7M PHE* 3.5 38.1 - - + +
8M GLU 3.0 27.5 + - - -
9M ILE* 3.8 8.5 - - - +
27M LEU* 6.0 0.9 - - + -
229M ASP* 2.8 42.5 + - - -
230M ILE* 5.3 3.0 - - - +
231M LEU* 3.4 25.7 - - - +
290M LEU* 3.2 18.4 + - - +
291M LEU* 2.9 17.2 + - + +
293M ASP* 1.3 78.2 - - + +
295M MET* 1.3 60.6 + - + +
297M ASN* 3.7 3.3 + - - +
298M SER* 2.9 29.8 + - - -
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Residues in contact with MET 295 (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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27M LEU* 4.1 11.9 - - + -
29M ARG 5.0 1.6 - - - +
32M GLY* 3.2 45.1 - - - +
33M LEU* 3.5 23.1 - - + +
36M TYR* 4.1 7.0 - - + -
291M LEU* 2.8 31.2 + - + +
292M LYS* 3.4 8.5 - - - +
294M ARG* 1.3 79.7 - - - +
296M VAL* 1.3 61.4 + - - +
299M ASN 3.5 0.9 + - - -
300M LEU* 2.9 46.0 + - - -
301M ALA* 3.3 14.3 + - + -
306M LEU* 3.9 19.5 - - + -
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Residues in contact with VAL 296 (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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292M LYS* 2.8 25.5 + - + +
293M ASP* 4.2 4.3 - - - +
295M MET* 1.3 68.8 - - - +
297M ASN* 1.3 72.2 + - - +
298M SER 2.9 9.9 + - - -
299M ASN* 3.1 12.5 + - - -
301M ALA 3.3 19.0 - - - +
302M SER* 4.0 0.9 - - - -
303M VAL* 3.5 35.0 - - + +
306M LEU* 4.5 8.1 - - + -
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Residues in contact with ASN 297 (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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293M ASP* 3.0 26.5 + - - +
294M ARG* 4.4 3.4 - - - +
295M MET 3.4 0.2 - - - -
296M VAL* 1.3 89.0 - - - +
298M SER* 1.3 57.7 + - - +
299M ASN 3.4 0.2 - - - -
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Residues in contact with SER 298 (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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2M ALA* 3.8 11.3 - - - +
5M ALA* 4.0 12.3 - - - +
7M PHE* 3.5 17.0 - - - -
294M ARG 2.9 18.7 + - - -
295M MET 3.5 0.9 + - - -
296M VAL 3.1 1.0 - - - -
297M ASN* 1.3 78.6 - - - +
299M ASN* 1.3 68.5 + - - +
300M LEU* 3.2 23.4 + - - +
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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