Contacts of the helix formed by residues 282 - 293 (chain E) in PDB entry 6N0M
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 GLU 282 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281E GLU* 1.3 82.6 - - + +
283E MET* 1.3 60.0 + - - +
285E SER* 3.7 15.3 - - - -
286E ARG* 3.4 35.2 + - + +
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Residues in contact with MET 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E GLU* 3.1 25.2 + - - +
282E GLU* 1.3 75.8 - - - +
284E GLU* 1.3 65.3 + - - +
285E SER 3.1 1.0 + - - -
286E ARG* 3.6 14.7 + - - +
287E PHE* 3.8 10.0 + - - +
404E ARG* 5.0 3.8 - - - +
406E ASP 3.3 29.6 - - - +
407E ASP* 3.4 20.2 - - - +
408E TYR 3.4 17.8 - - - +
409E ASP* 3.7 21.5 - - + +
410E TYR* 5.1 4.7 + - - +
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Residues in contact with GLU 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281E GLU 3.5 13.5 + - - +
283E MET* 1.3 77.4 - - - +
285E SER* 1.3 59.3 + - - +
287E PHE* 3.7 3.3 - - - +
288E GLU* 3.2 33.1 + - - +
404E ARG* 4.1 33.0 - - - +
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Residues in contact with SER 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B ASP* 5.0 7.8 + - - -
281E GLU 3.6 4.7 + - - -
282E GLU* 3.7 25.1 - - - +
283E MET 3.1 0.6 - - - -
284E GLU* 1.3 76.8 - - - +
286E ARG* 1.3 63.9 - - - +
287E PHE 3.2 1.8 - - - -
288E GLU* 3.6 8.9 + - - +
289E LEU* 3.4 25.1 + - - +
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Residues in contact with ARG 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B GLN* 4.7 12.3 + - - -
269B GLN 6.3 0.8 - - - -
270B GLU* 5.9 5.7 - - - +
282E GLU* 3.4 23.4 + - + +
283E MET* 3.6 9.9 + - - +
285E SER* 1.3 73.5 - - - +
287E PHE* 1.3 62.9 + - - +
289E LEU* 3.6 16.1 - - + +
290E GLU* 3.3 23.4 + - - +
409E ASP* 2.8 39.3 + - - -
410E TYR* 4.3 9.5 - - + +
411E GLY* 4.3 24.8 - - - +
414E ASN* 5.5 1.6 + - - +
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Residues in contact with PHE 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E MET 3.8 7.3 + - - +
284E GLU 3.7 9.0 - - - +
285E SER 3.2 0.4 - - - -
286E ARG* 1.3 74.3 - - - +
288E GLU* 1.3 65.6 + - - +
289E LEU 3.0 1.6 - - - -
290E GLU* 2.9 7.2 + - - +
291E LYS* 2.8 44.3 + - + +
336E THR* 3.4 28.7 - - - -
399E CYS* 3.4 46.7 - - + -
403E ILE 3.6 22.0 - - - -
404E ARG* 3.6 34.1 - - + -
410E TYR* 3.6 37.5 - + + +
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Residues in contact with GLU 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B ASN* 5.2 1.0 + - - -
284E GLU* 3.2 24.6 + - - +
285E SER* 3.6 8.0 + - - +
287E PHE* 1.3 82.2 - - - +
289E LEU* 1.3 56.7 + - - +
291E LYS* 2.8 38.5 + - - +
292E SER* 3.0 31.4 + - - -
336E THR* 3.1 20.2 + - - +
404E ARG* 4.7 2.6 + - - -
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Residues in contact with LEU 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B ASN* 3.6 31.0 - - + +
383B GLY* 3.3 55.4 - - - +
384B VAL* 3.7 4.9 - - - -
385B ASP* 3.6 32.1 - - + +
285E SER* 3.4 18.4 + - - +
286E ARG* 3.6 17.0 - - + +
288E GLU* 1.3 80.8 - - - +
290E GLU* 1.3 57.5 + - - +
292E SER* 3.2 15.0 + - - -
293E GLU* 3.6 2.6 - - - +
414E ASN* 6.3 0.4 - - - +
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Residues in contact with GLU 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E ARG 3.3 9.7 + - - +
287E PHE* 2.9 10.0 + - - +
289E LEU* 1.3 79.2 - - - +
291E LYS* 1.3 64.6 + - - +
292E SER 3.3 0.4 - - - -
293E GLU* 3.3 28.7 + - - +
396E TYR* 3.8 18.3 - - + -
399E CYS* 3.8 18.1 - - + -
400E VAL* 6.0 1.6 - - - +
410E TYR* 4.0 11.4 - - + +
413E VAL* 3.5 20.4 - - + +
414E ASN* 2.7 29.6 + - - -
422E LYS* 2.7 36.4 + - - -
426E LYS* 5.3 0.9 + - - -
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Residues in contact with LYS 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287E PHE* 2.8 33.6 + - + +
288E GLU* 2.8 30.1 + - - +
290E GLU* 1.3 80.5 - - - +
292E SER* 1.3 60.3 + - - +
293E GLU 4.7 2.3 - - - +
323E TYR* 5.0 5.4 + - - -
332E GLN 4.4 1.9 - - - +
333E ALA* 3.8 23.0 - - + +
334E PRO* 3.0 39.0 + - + +
335E PRO* 3.8 3.2 - - - +
336E THR* 3.1 20.4 + - - +
399E CYS* 3.7 29.4 - - - +
400E VAL* 5.5 3.5 - - - +
402E GLY* 4.9 0.7 - - - -
426E LYS* 5.0 4.2 + - - -
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Residues in contact with SER 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B ASN* 3.5 24.8 + - - +
288E GLU 3.0 14.1 + - - -
289E LEU 3.2 13.2 + - - -
291E LYS* 1.3 78.5 - - - +
293E GLU* 1.3 74.4 + - - +
294E SER* 3.3 9.0 + - - -
331E ALA* 4.5 4.3 - - - +
332E GLN 4.3 8.7 - - - +
333E ALA* 4.2 13.4 - - - +
426E LYS* 5.3 0.2 + - - -
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Residues in contact with GLU 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B SER* 3.4 39.1 - - - +
383B GLY* 3.5 16.3 - - - +
289E LEU 3.6 9.9 - - - +
290E GLU* 3.3 25.1 + - - +
292E SER* 1.3 78.6 + - - +
294E SER* 1.3 60.2 + - - +
295E LEU* 3.5 18.4 - - + +
396E TYR* 4.3 2.4 + - - -
414E ASN* 3.7 6.8 - - - +
422E LYS* 3.1 39.0 + - - -
426E LYS* 2.9 21.0 + - - -
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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
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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