Contacts of the helix formed by residues 320 - 331 (chain E) in PDB entry 6DWZ
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 ASN 320 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E SER* 4.4 8.5 + - - +
274E LEU* 3.1 43.3 - - + +
275E GLU* 5.5 0.9 + - - -
278E PHE* 4.6 9.7 - - - -
314E GLU* 5.8 0.4 - - - -
318E ARG 3.0 6.8 + - - -
319E TRP* 1.3 79.3 - - + +
321E SER* 1.3 57.5 + - - +
322E THR* 2.6 35.3 + - - +
323E TYR* 2.8 31.2 + - + +
324E THR* 3.8 2.8 + - - +
364E LEU* 4.3 11.3 - - + +
368E GLU* 5.4 1.9 - - - +
371E PHE* 4.8 5.2 - - + -
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Residues in contact with SER 321 (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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313E SER 3.9 6.1 - - - -
314E GLU* 3.5 5.7 - - - +
315E CYS* 2.9 43.2 + - - +
318E ARG* 3.8 9.7 + - - +
319E TRP 3.0 5.2 + - - -
320E ASN* 1.3 73.5 - - - +
322E THR* 1.3 50.5 + - - -
323E TYR 3.1 0.2 - - - -
324E THR* 2.8 21.8 + - - -
325E MET* 2.3 39.7 + - - +
16G T 4.6 8.1 - - - -
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Residues in contact with THR 322 (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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278E PHE* 5.7 0.9 - - + -
288E ILE* 4.0 27.8 - - + -
314E GLU* 2.9 27.2 + - - +
320E ASN* 2.6 32.2 + - - +
321E SER* 1.3 72.5 + - - +
323E TYR* 1.3 56.8 + - - +
325E MET* 3.7 19.3 - - + -
326E LEU* 2.6 49.5 + - + +
364E LEU* 4.7 4.0 - - + -
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Residues in contact with TYR 323 (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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320E ASN* 2.8 17.6 + - + +
322E THR* 1.3 81.9 - - - +
324E THR* 1.3 59.7 + - + +
326E LEU* 2.8 3.8 + - - +
327E ARG* 2.7 64.4 + - + -
361E VAL* 4.0 18.5 + - + +
362E ASN* 5.8 0.2 + - - -
364E LEU* 4.0 26.7 - - + +
365E ASP* 2.7 57.5 + - + +
368E GLU* 4.2 27.4 - - + +
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Residues in contact with THR 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312E LYS* 3.9 17.2 + - - +
313E SER 4.7 1.2 + - - -
319E TRP 5.7 0.4 - - - +
320E ASN 4.1 3.6 - - - +
321E SER* 2.8 28.9 + - - +
323E TYR* 1.3 79.4 - - + +
325E MET* 1.3 59.1 + - - +
327E ARG* 3.9 3.7 - - - +
328E SER* 2.8 30.5 + - - -
368E GLU* 5.4 7.2 - - - +
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Residues in contact with MET 325 (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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288E ILE* 4.6 2.9 - - + +
291E CYS* 4.0 6.3 - - + -
292E LYS* 3.9 37.0 - - + -
295E VAL* 4.1 4.3 - - + -
312E LYS 3.0 23.3 - - - +
314E GLU* 3.7 22.9 - - + +
321E SER 2.3 26.9 + - - +
322E THR* 3.7 29.2 - - + +
324E THR* 1.3 66.5 + - - +
326E LEU* 1.3 68.6 + - + +
328E SER* 2.6 24.2 + - - +
329E ILE* 2.7 33.6 + - + +
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Residues in contact with LEU 326 (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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288E ILE* 4.4 13.7 - - + -
291E CYS* 3.7 29.6 - - + -
322E THR* 2.6 33.8 + - + +
323E TYR 2.8 2.3 + - - +
325E MET* 1.3 84.7 - - + +
327E ARG* 1.3 50.4 + - - +
329E ILE* 3.3 5.8 + - - +
330E LEU* 2.6 39.5 + - - +
357E ILE* 4.6 13.2 - - + +
360E MET* 3.7 38.6 - - + -
361E VAL* 4.0 14.8 - - + +
364E LEU* 3.8 17.3 - - + -
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Residues in contact with ARG 327 (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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323E TYR* 2.7 50.9 + - + +
324E THR* 4.1 4.7 - - - +
326E LEU* 1.3 74.6 - - - +
328E SER* 1.3 58.3 + - - +
330E LEU* 2.9 9.4 + - + -
331E ASP* 2.7 67.6 + - - +
361E VAL* 4.0 14.8 - - + +
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Residues in contact with SER 328 (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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309E SER* 5.8 2.5 - - - -
310E SER 3.9 6.7 - - - -
311E LEU* 3.5 7.1 - - - +
312E LYS* 2.8 45.6 + - - +
324E THR 2.8 17.1 + - - -
325E MET* 2.6 17.6 + - - +
327E ARG* 1.3 74.3 - - - +
329E ILE* 1.3 60.9 + - - +
331E ASP* 3.6 6.4 + - - +
332E ASN* 3.0 28.5 + - - +
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Residues in contact with ILE 329 (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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291E CYS* 3.5 49.4 - - + +
294E ILE* 4.7 9.0 - - + -
295E VAL* 3.5 26.7 - - + -
311E LEU* 4.2 23.3 - - + -
325E MET* 2.7 23.6 + - + +
326E LEU* 3.8 5.6 - - - +
328E SER* 1.3 73.3 + - - +
330E LEU* 1.3 65.1 + - + +
332E ASN* 3.5 9.4 + - - +
333E TRP* 3.5 31.2 + - + -
336E VAL* 4.9 9.3 - - + +
357E ILE* 5.2 5.6 - - + -
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Residues in contact with LEU 330 (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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326E LEU 2.6 21.3 + - - +
327E ARG* 2.9 11.2 + - + +
329E ILE* 1.3 73.2 - - - +
331E ASP* 1.3 67.8 + - - +
332E ASN 3.1 3.1 + - - -
333E TRP* 3.1 23.5 + - + +
334E GLU* 5.2 0.3 - - - +
354E LYS* 4.1 22.8 + - - +
357E ILE* 3.4 25.8 - - + -
358E GLN* 3.6 40.6 - - + +
361E VAL* 3.5 29.6 - - + -
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Residues in contact with ASP 331 (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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309E SER* 5.3 8.6 + - - +
327E ARG* 2.7 74.3 + - - +
328E SER* 3.6 7.5 + - - +
329E ILE 3.4 0.2 - - - -
330E LEU* 1.3 78.7 - - - +
332E ASN* 1.3 64.1 + - - +
333E TRP 3.4 0.2 - - - -
334E GLU* 5.3 4.0 - - - +
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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