Contacts of the helix formed by residues 284 - 295 (chain E) in PDB entry 4GDF
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 284 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282E CYS* 3.4 9.9 - - - -
283E ASP* 1.3 84.1 - - - +
285E VAL* 1.3 66.9 + - - +
286E LEU* 2.7 39.0 + - - +
287E LEU* 3.1 23.9 + - + +
288E LEU* 2.9 19.2 + - - +
341E VAL* 4.3 1.3 - - - -
349F ARG* 3.0 32.4 + - - +
353F LEU* 4.9 4.7 - - + +
517F ARG* 4.4 4.2 + - - -
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Residues in contact with VAL 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E ASP 4.2 0.8 - - - -
284E ASP* 1.3 71.2 + - - +
286E LEU* 1.3 74.1 + - + +
288E LEU* 3.2 6.9 + - - +
289E LEU* 2.8 34.0 + - - +
334E LYS* 5.1 7.6 - - + +
337E CYS* 3.9 6.4 - - + +
338E GLN* 3.3 58.6 - - + +
341E VAL* 3.5 13.6 - - + +
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Residues in contact with LEU 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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284E ASP* 2.7 17.8 + - - +
285E VAL* 1.3 92.0 - - + +
287E LEU* 1.3 61.3 + - - +
289E LEU* 4.6 6.1 - - + -
290E GLY* 3.1 18.9 + - - -
342F ASP* 4.1 9.4 - - + +
345F LEU* 4.0 18.8 - - + +
346F ALA* 3.5 36.6 - - + +
349F ARG* 3.6 40.4 - - + +
514F LEU* 6.3 3.4 - - + -
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Residues in contact with LEU 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E CYS* 4.7 12.3 - - + -
283E ASP* 5.8 2.2 - - - +
284E ASP* 3.1 27.8 + - + +
286E LEU* 1.3 79.5 - - - +
288E LEU* 1.3 59.6 + - - +
290E GLY* 3.7 0.3 - - - -
291E MET* 2.8 57.8 + - + +
349F ARG* 4.2 3.3 - - + +
350F VAL* 4.1 20.6 - - + +
353F LEU* 3.8 32.8 - - + -
354F GLN* 4.5 8.3 - - - +
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Residues in contact with LEU 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273E VAL* 4.3 11.7 - - + -
276E TYR* 3.6 33.7 - - + -
277E ALA* 4.0 19.3 - - + +
282E CYS* 3.9 13.0 - - - -
284E ASP 2.9 16.3 + - - +
285E VAL* 3.6 4.5 - - - +
287E LEU* 1.3 76.4 - - - +
289E LEU* 1.3 65.7 + - - +
291E MET* 3.0 4.8 + - - +
292E TYR* 2.9 29.9 + - + +
337E CYS* 3.7 37.7 - - + +
340E ALA* 3.8 18.2 - - + -
341E VAL* 4.4 4.7 - - + +
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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
----------------------------------------------------------
285E VAL 2.8 21.4 + - - +
286E LEU* 3.9 7.6 - - + +
288E LEU* 1.3 72.8 - - - +
290E GLY* 1.3 62.5 + - - +
292E TYR* 4.0 2.4 - - - +
293E LEU* 3.1 53.7 + - + +
327E PHE* 4.1 18.4 - - + -
333E GLN* 4.3 14.1 - - + +
334E LYS* 5.0 17.7 - - + +
337E CYS* 3.6 15.4 - - + -
339F GLN* 6.1 1.3 - - + -
342F ASP* 4.0 35.2 - - + +
343F THR* 4.6 2.2 - - - +
346F ALA* 3.9 9.4 - - + -
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Residues in contact with GLY 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 LEU 3.1 10.3 + - - -
287E LEU 3.8 1.6 - - - -
289E LEU* 1.3 76.7 - - - +
291E MET* 1.3 66.7 + - - +
293E LEU* 3.5 8.3 + - - +
294E GLU* 3.4 22.2 + - - +
346F ALA* 3.6 19.1 - - - +
347F LYS* 4.9 2.2 - - - -
350F VAL* 4.0 14.8 - - - -
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Residues in contact with MET 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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276E TYR* 3.6 20.6 - - + +
287E LEU* 2.8 41.8 + - + +
288E LEU* 3.7 2.9 - - - +
290E GLY* 1.3 73.6 - - - +
292E TYR* 1.3 62.5 + - - +
294E GLU* 3.0 47.4 + - - +
295E PHE* 3.6 10.5 + - + -
310E GLN* 5.8 0.7 - - + -
312E SER* 3.5 29.4 - - - +
313E HIS* 3.9 16.2 - - + +
350F VAL* 4.1 11.4 - - + +
354F GLN* 3.6 27.6 - - - +
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Residues in contact with TYR 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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272E LEU 4.1 0.7 + - - -
273E VAL* 3.6 33.0 - - + +
276E TYR* 4.1 21.3 - + + -
288E LEU* 2.9 20.5 + - + +
289E LEU* 4.1 2.5 - - - +
291E MET* 1.3 71.5 - - - +
293E LEU* 1.3 63.1 + - - +
294E GLU 2.9 5.4 - - - -
295E PHE* 2.9 34.8 + + - +
296E GLN 3.7 2.4 + - - -
320E HIS* 3.1 47.4 + + + +
323E ASN* 2.9 26.2 + - - +
324E ALA* 3.7 22.4 - - + +
327E PHE* 3.8 32.2 - + + -
337E CYS* 5.7 0.7 - - - -
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Residues in contact with LEU 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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289E LEU* 3.1 47.4 + - + +
290E GLY* 3.8 8.5 - - - +
291E MET 3.3 0.2 - - - -
292E TYR* 1.3 75.2 - - - +
294E GLU* 1.3 61.0 + - - +
296E GLN* 3.3 42.0 + - + +
297E TYR* 4.0 4.6 - - - -
327E PHE* 3.7 13.2 - - + -
328E ALA* 4.7 5.6 - - + -
333E GLN* 3.4 27.4 - - - +
274F THR* 5.9 0.9 - - + -
343F THR* 3.7 35.4 - - + +
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Residues in contact with GLU 294 (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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290E GLY 3.5 13.9 - - - +
291E MET* 3.0 28.4 + - - +
292E TYR 2.9 0.6 - - - -
293E LEU* 1.3 75.6 - - - +
295E PHE* 1.3 60.0 + - - +
296E GLN 3.0 6.1 + - - -
297E TYR* 3.4 25.1 + - + +
304E LYS* 3.4 31.2 + - + +
313E HIS* 3.2 32.0 + - + +
317E HIS* 4.0 8.0 - - - -
347F LYS* 5.5 2.9 + - - -
350F VAL* 4.0 17.4 - - - +
354F GLN* 4.8 2.8 - - - +
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Residues in contact with PHE 295 (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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276E TYR* 3.5 44.6 - + - -
291E MET* 4.0 5.8 - - + -
292E TYR* 2.9 48.8 + + - +
294E GLU* 1.3 76.0 - - - +
296E GLN* 1.3 64.3 + - - +
297E TYR 3.1 1.5 - - - +
312E SER 4.3 2.5 - - - -
313E HIS* 3.2 32.3 - + - -
316E TYR* 4.1 5.8 - - + -
317E HIS* 2.9 53.2 + + + -
320E HIS* 3.9 12.6 - - + +
321E TYR* 3.3 10.0 - - - -
324E ALA* 3.4 15.2 - - + +
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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