Contacts of the helix formed by residues 305 - 320 (chain E) in PDB entry 3J8B
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 PHE 305 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300E TYR* 5.3 3.6 - - - +
303E PHE* 3.4 7.4 + - - +
304E ASP* 1.3 72.3 - - - +
306E ASP* 1.3 60.0 + - - +
308E ALA* 3.5 8.6 - - - +
309E GLN* 2.9 31.7 + - - +
340E ILE* 3.5 31.9 - - + +
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Residues in contact with ASP 306 (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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304E ASP* 3.3 1.1 - - + -
305E PHE* 1.3 76.0 - - - +
307E GLY* 1.3 60.9 + - - +
309E GLN* 3.2 6.1 + - - +
310E LYS* 2.9 29.5 + - - +
360E LEU 3.4 25.6 - - - +
361E ASN* 4.1 12.3 - - + -
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Residues in contact with GLY 307 (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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299E LEU* 4.6 4.7 - - - -
304E ASP* 3.6 10.6 + - - +
305E PHE 3.4 0.2 - - - -
306E ASP* 1.3 78.5 - - - +
308E ALA* 1.3 62.8 + - - +
310E LYS* 3.2 8.1 + - - +
311E LYS* 3.0 23.2 + - - +
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Residues in contact with ALA 308 (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 VAL* 3.8 24.2 - - + +
299E LEU* 3.9 10.5 - - + +
300E TYR* 4.1 11.7 - - + +
304E ASP 3.3 13.8 + - - +
305E PHE* 3.5 13.5 - - - +
306E ASP 3.3 0.2 - - - -
307E GLY* 1.3 74.5 - - - +
309E GLN* 1.3 58.7 + - - +
311E LYS* 3.2 9.4 + - - +
312E LEU* 3.0 26.6 + - - +
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Residues in contact with GLN 309 (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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305E PHE 2.9 18.6 + - - +
306E ASP* 3.8 4.9 - - - +
308E ALA* 1.3 77.4 - - - +
310E LYS* 1.3 56.4 - - - +
312E LEU* 3.6 8.8 - - - +
313E ARG* 2.9 27.2 + - - +
337E ARG* 6.3 3.8 - - + -
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Residues in contact with LYS 310 (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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306E ASP 2.9 16.9 + - - +
307E GLY* 3.6 7.0 - - - +
309E GLN* 1.3 74.8 - - - +
311E LYS* 1.3 66.2 + - - +
313E ARG* 3.2 8.3 + - - +
314E GLU* 2.9 22.9 + - - +
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Residues in contact with LYS 311 (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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292E ILE* 4.8 7.6 - - + +
296E VAL* 4.4 22.0 - - + +
307E GLY 3.0 12.4 + - - +
308E ALA* 3.2 10.1 + - - +
310E LYS* 1.3 75.0 - - - +
312E LEU* 1.3 64.7 + - - +
314E GLU* 3.0 9.8 + - - +
315E CYS* 2.9 24.6 + - - +
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Residues in contact with LEU 312 (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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308E ALA 3.0 13.8 + - - +
309E GLN* 3.6 12.1 - - - +
311E LYS* 1.3 77.5 - - - +
313E ARG* 1.3 63.4 + - - +
315E CYS* 3.3 6.0 + - - +
316E GLU* 2.9 25.7 + - - +
333E ILE* 5.3 12.8 - - + -
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Residues in contact with ARG 313 (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 GLN 2.9 17.3 + - - +
310E LYS* 3.2 8.7 + - - +
312E LEU* 1.3 76.7 - - - +
314E GLU* 1.3 63.1 + - - +
316E GLU* 3.5 16.3 + - - +
317E SER* 4.7 1.0 + - - -
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Residues in contact with GLU 314 (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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310E LYS 2.9 13.2 + - - +
311E LYS* 3.0 13.2 + - - +
313E ARG* 1.3 81.5 - - - +
315E CYS* 1.3 59.7 + - - +
316E GLU 3.4 0.3 + - - -
317E SER* 4.2 8.7 + - - -
318E VAL* 5.0 0.7 + - - +
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Residues in contact with CYS 315 (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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292E ILE* 6.4 2.2 - - + -
311E LYS 2.9 13.8 + - - +
312E LEU* 4.0 5.8 - - - +
314E GLU* 1.3 73.9 - - - +
316E GLU* 1.3 66.1 + - - +
317E SER 3.2 3.1 - - - -
318E VAL* 3.0 13.8 + - + +
319E LEU* 2.9 25.8 + - + +
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Residues in contact with GLU 316 (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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312E LEU 2.9 16.7 + - - +
313E ARG* 3.6 13.0 - - - +
314E GLU 3.2 1.6 - - - -
315E CYS* 1.3 75.8 - - - +
317E SER* 1.3 58.7 + - - +
319E LEU* 3.2 7.1 + - - +
320E VAL* 2.9 31.0 + - - +
329E LEU* 5.7 3.3 - - + +
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Residues in contact with SER 317 (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 ARG 4.7 0.8 + - - -
314E GLU 4.2 6.8 + - - -
315E CYS 3.2 0.8 - - - -
316E GLU* 1.3 79.8 - - - +
318E VAL* 1.3 61.7 + - - +
320E VAL* 3.5 13.3 + - - +
321E ASN* 3.6 9.4 + - - +
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Residues in contact with VAL 318 (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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4E TYR* 5.8 8.7 - - + +
314E GLU 5.0 1.0 + - - +
315E CYS* 3.0 14.8 + - + +
317E SER* 1.3 78.2 - - - +
319E LEU* 1.3 56.5 + - - +
321E ASN* 2.9 28.4 + - - +
322E ASP* 3.5 4.2 + - - +
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Residues in contact with LEU 319 (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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315E CYS* 2.9 22.7 + - + +
316E GLU* 3.8 8.3 - - - +
318E VAL* 1.3 68.8 - - - +
320E VAL* 1.3 59.7 + - - +
321E ASN 3.0 5.6 - - - -
322E ASP* 3.2 23.0 + - + +
325E LEU* 4.1 7.7 - - + +
326E VAL* 4.0 11.6 + - - -
329E LEU* 4.9 13.2 - - + +
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Residues in contact with VAL 320 (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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29E LYS* 4.3 13.5 - - - +
316E GLU 2.9 16.6 + - - +
317E SER* 3.7 9.2 - - - +
318E VAL 3.1 0.4 - - - -
319E LEU* 1.3 77.5 - - - +
321E ASN* 1.3 59.1 + - - +
322E ASP 3.3 0.4 - - - -
326E VAL* 3.8 23.2 - - - +
329E LEU* 5.3 5.1 - - + +
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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