Contacts of the helix formed by residues 311 - 317 (chain E) in PDB entry 1J0B
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 ILE 311 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E ILE* 3.7 37.9 - - + +
277E ILE* 4.0 42.6 + - + +
278E LEU 5.8 0.9 - - - -
279E ASP* 5.1 0.6 - - - +
307E HIS* 5.5 0.6 - - - -
309E GLY 3.4 4.6 + - - -
310E GLY* 1.3 74.1 - - - +
312E SER* 1.3 70.3 + - - +
313E GLY 3.0 6.1 + - - -
314E THR* 3.1 16.9 + - - +
315E PHE* 3.3 37.7 - - + -
49F GLY 5.7 0.7 - - - +
50F ILE* 5.0 4.5 - - + -
114F LEU* 5.5 0.9 - - + -
311F ILE* 5.0 15.0 - - + -
315F PHE* 5.0 1.6 - - + -
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Residues in contact with SER 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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50E ILE* 3.6 11.1 - - - +
82E ASN* 4.2 2.5 - - - -
110E GLY* 3.8 6.9 - - - -
111E ASN* 3.2 40.2 + - - -
114E LEU* 3.6 6.8 - - - +
310E GLY 2.8 5.1 + - - -
311E ILE* 1.3 74.5 - - - +
313E GLY* 1.3 56.2 + - - -
314E THR 3.4 0.4 - - - -
315E PHE* 4.0 4.3 + - - +
316E HIS* 3.2 24.7 + - - +
315F PHE* 3.2 33.8 - - - -
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Residues in contact with GLY 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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80E HIS* 6.1 1.8 - - - -
82E ASN* 5.0 2.0 - - - +
111E ASN* 5.7 1.3 - - - -
279E ASP* 4.9 1.6 - - - -
280E PRO* 3.5 21.6 - - - +
281E VAL* 5.0 7.6 - - - -
310E GLY 2.8 16.7 + - - -
312E SER* 1.3 72.6 - - - +
314E THR* 1.3 64.7 + - - +
315E PHE 3.3 0.2 - - - -
316E HIS* 3.7 8.0 - - - +
317E TYR* 3.1 25.8 + - - +
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Residues in contact with THR 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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267E ILE* 4.6 5.6 - - + -
277E ILE* 4.3 8.9 - - + +
278E LEU 2.8 27.3 + - - +
279E ASP* 3.5 3.1 - - - +
280E PRO* 3.5 13.3 - - - +
310E GLY 4.2 0.4 + - - -
311E ILE* 3.1 11.5 + - - -
313E GLY* 1.3 78.9 - - - +
315E PHE* 1.3 63.3 + - - +
317E TYR 3.7 0.5 - - - -
318E GLY* 3.1 23.0 + - - -
321E LEU* 4.4 11.0 - - + +
113F LEU* 4.0 2.2 - - - +
114F LEU* 3.6 28.9 - - + -
117F ILE* 3.9 15.0 - - + +
118F MET* 5.3 0.2 - - + -
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Residues in contact with PHE 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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109E LYS* 5.1 1.9 + - - -
110E GLY* 5.7 1.1 - - - +
311E ILE* 3.3 49.4 - - + -
312E SER* 4.0 4.5 - - - +
313E GLY 3.3 0.2 - - - -
314E THR* 1.3 79.6 - - - +
316E HIS* 1.3 62.8 + - - +
318E GLY 3.4 8.1 + - - -
50F ILE* 4.6 2.9 - - + -
110F GLY* 4.0 23.6 - - - +
113F LEU* 3.4 20.1 - - + +
114F LEU* 4.2 17.3 - - + -
311F ILE* 4.9 1.1 - - + -
312F SER* 3.6 38.6 - - - -
315F PHE* 3.5 53.2 - + + -
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Residues in contact with HIS 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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79E VAL* 4.9 8.6 - - + +
80E HIS* 3.9 28.1 - - + +
107E GLU* 3.5 24.5 - - + +
109E LYS* 3.1 46.3 + - + +
110E GLY* 3.5 29.4 - - - +
111E ASN* 4.3 2.9 - - - -
312E SER 3.2 16.3 + - - +
313E GLY* 3.7 9.4 - - - +
315E PHE* 1.3 82.0 - - - +
317E TYR* 1.3 87.6 + + + +
318E GLY 3.7 1.0 + - - -
319E ASP* 5.4 0.9 - - - +
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Residues in contact with TYR 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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80E HIS* 2.9 40.2 + + + +
107E GLU* 5.1 2.0 - - - -
109E LYS* 5.7 0.4 - - - -
257E GLY* 5.6 4.7 - - - -
259E ILE* 3.5 33.2 - - + -
280E PRO* 4.3 9.4 - - + -
281E VAL* 5.0 11.9 - - + -
313E GLY* 3.1 22.4 + - - +
314E THR 3.7 3.8 - - - -
316E HIS* 1.3 109.7 - + + +
318E GLY* 1.3 64.0 + - - +
319E ASP 3.5 2.0 - - - -
320E LYS* 3.3 10.5 + - + +
321E LEU* 3.2 23.5 + - - +
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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