Contacts of the helix formed by residues 287 - 302 (chain E) in PDB entry 5MGX
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 HIS 287 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282E GLN* 2.8 26.6 + - + +
285E LEU* 3.1 10.3 - - + +
286E ASP* 1.4 73.8 - - - +
288E TYR* 1.3 52.9 + - - +
289E ARG* 4.4 8.5 + - + +
290E ALA* 3.3 30.8 + - + +
291E ALA* 2.9 33.7 + - - +
293E ARG* 5.0 4.5 - - - -
355G ALA* 5.4 2.2 - - + -
356G GLN* 3.5 37.8 - - + +
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Residues in contact with TYR 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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283E LEU* 4.2 10.1 - - + -
286E ASP* 3.0 48.5 + - + -
287E HIS* 1.3 71.9 + - - +
289E ARG* 1.3 60.4 + - + +
291E ALA* 3.8 1.7 - - - +
292E LEU* 3.0 30.0 + - - +
315E VAL* 3.6 27.9 - - + +
318E GLN* 3.0 50.4 + - + +
319E GLN* 3.6 33.7 - - + +
318G GLN 4.6 15.5 + - - -
319G GLN 6.3 0.4 - - - -
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Residues in contact with ARG 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E HIS* 3.5 8.2 + - + +
288E TYR* 1.3 76.8 - - - +
290E ALA* 1.3 60.2 + - - +
292E LEU* 3.6 10.4 - - + +
293E ARG* 3.4 40.1 + - - +
319E GLN* 4.7 12.4 - - - +
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Residues in contact with ALA 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E GLN* 3.4 27.9 - - - +
287E HIS* 3.3 36.4 + - + +
289E ARG* 1.3 75.3 - - - +
291E ALA* 1.4 59.4 + - - +
293E ARG* 3.0 37.7 + - - +
294E SER* 3.1 11.3 + - - -
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Residues in contact with ALA 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E ALA* 4.0 8.8 - - + +
282E GLN* 3.4 23.5 + - + -
283E LEU* 4.0 11.2 - - - +
287E HIS 2.9 18.0 + - - +
288E TYR 3.8 4.5 - - - +
290E ALA* 1.4 74.3 - - - +
292E LEU* 1.3 56.8 + - - +
294E SER* 3.5 2.7 + - - -
295E CYS* 2.9 36.5 + - - +
315E VAL* 4.0 21.1 - - + -
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Residues in contact with LEU 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E TYR 3.0 20.9 + - - +
289E ARG* 3.6 10.8 - - + +
290E ALA 3.2 0.2 - - - -
291E ALA* 1.3 74.5 - - - +
293E ARG* 1.3 58.8 + - + +
295E CYS* 3.4 5.3 + - - +
296E SER* 2.9 36.6 + - - +
312E LYS* 3.8 38.8 - - + +
315E VAL* 3.7 11.4 - - + -
316E LEU* 4.4 15.5 - - + -
319E GLN* 3.4 33.4 - - - +
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Residues in contact with ARG 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287E HIS* 5.0 4.8 + - - -
289E ARG* 3.4 24.0 + - - +
290E ALA* 3.0 31.6 + - - +
292E LEU* 1.3 73.1 - - + +
294E SER* 1.3 58.8 + - - +
296E SER* 3.4 6.2 + - - -
297E LEU* 3.0 42.5 + - + +
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Residues in contact with SER 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E LEU* 3.6 33.4 - - - +
278E LEU* 3.8 12.5 - - - +
279E ALA* 3.9 5.6 - - - -
282E GLN* 2.7 30.7 + - - -
290E ALA 3.1 5.2 + - - -
291E ALA 3.6 5.6 - - - -
293E ARG* 1.3 76.0 - - - +
295E CYS* 1.3 59.6 + - - +
297E LEU* 3.5 4.6 + - - +
298E VAL* 3.2 29.8 + - - +
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Residues in contact with CYS 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279E ALA* 3.8 14.1 - - - -
291E ALA* 2.9 26.2 + - - +
292E LEU* 3.6 6.7 - - - +
294E SER* 1.3 71.8 - - - +
296E SER* 1.3 59.3 + - - +
298E VAL* 3.3 7.7 + - - +
299E LEU* 3.0 35.1 + - - +
308E ALA* 3.7 11.2 - - - +
311E ARG* 3.7 19.3 - - - -
312E LYS* 3.6 42.0 - - + -
315E VAL* 5.5 0.7 - - - -
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Residues in contact with SER 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292E LEU* 2.9 22.2 + - - +
293E ARG* 3.8 6.7 - - - -
295E CYS* 1.3 72.5 - - - +
297E LEU* 1.4 59.1 + - - +
299E LEU* 3.5 7.3 + - - +
300E GLU* 3.1 32.3 + - - +
312E LYS* 3.1 29.3 + - - +
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Residues in contact with LEU 297 (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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271E LYS* 5.6 4.0 - - - +
275E LEU* 4.1 31.4 - - + -
293E ARG* 3.0 28.7 + - + +
294E SER* 3.8 5.2 - - - +
295E CYS 3.3 0.2 - - - -
296E SER* 1.4 72.8 - - - +
298E VAL* 1.3 65.1 + - - +
300E GLU* 3.3 13.4 + - + +
301E HIS* 3.1 32.0 - - + +
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Residues in contact with VAL 298 (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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272E VAL* 3.5 27.1 - - + +
275E LEU* 3.6 12.6 - - + -
276E ASN* 3.5 35.7 - - - +
294E SER 3.2 16.7 + - - +
295E CYS* 3.3 7.8 + - - +
297E LEU* 1.3 75.7 - - - +
299E LEU* 1.3 49.7 + - - +
301E HIS* 3.1 8.1 + - - +
302E GLN* 2.8 31.6 + - + +
305E ASN* 3.8 17.3 - - + +
308E ALA* 3.7 21.8 - - + -
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Residues in contact with LEU 299 (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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295E CYS 3.0 21.5 + - - +
296E SER* 4.0 6.1 - - - +
297E LEU 3.3 0.4 - - - -
298E VAL* 1.3 72.1 - - - +
300E GLU* 1.3 64.2 + - - +
301E HIS 3.3 0.2 - - - -
302E GLN 3.5 16.6 - - - +
303E PRO* 3.2 34.3 - - + +
305E ASN 3.8 3.4 - - - +
308E ALA* 3.8 27.4 - - + +
309E LEU* 3.7 36.3 - - + -
312E LYS* 4.0 28.3 - - + +
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Residues in contact with GLU 300 (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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296E SER* 3.1 18.5 + - - +
297E LEU* 3.5 16.8 - - + +
298E VAL 3.2 0.6 - - - -
299E LEU* 1.3 78.1 - - - +
301E HIS* 1.4 63.8 + - + +
303E PRO* 4.9 2.9 - - - +
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Residues in contact with HIS 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268E LEU* 3.6 33.8 - - + +
271E LYS* 3.7 19.9 + - - -
272E VAL* 3.7 26.4 - - + +
275E LEU* 5.6 0.9 - - + -
297E LEU* 3.1 30.4 - - + +
298E VAL 3.1 6.5 + - - +
300E GLU* 1.4 84.7 - - + +
302E GLN* 1.3 65.2 + - + +
303E PRO* 3.8 6.6 - - - +
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Residues in contact with GLN 302 (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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269E GLN* 3.7 33.9 + - - +
272E VAL* 3.7 24.2 - - + +
298E VAL 2.8 12.2 + - - +
299E LEU* 3.5 12.3 - - - +
301E HIS* 1.3 80.1 - - + +
303E PRO* 1.4 66.7 - - - +
304E ASP 3.2 3.7 + - - +
305E ASN* 3.1 43.9 + - + +
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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