Contacts of the helix formed by residues 304 - 312 (chain E) in PDB entry 5TJ4
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 LEU 304 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E PHE* 6.0 1.8 - - + -
88E LYS* 3.3 34.5 - - + +
89E LEU* 3.5 12.2 - - + +
108E ILE 4.4 0.8 + - - -
285E LEU* 3.4 39.0 - - + +
286E THR* 3.5 18.8 - - - +
287E ASP* 4.0 4.3 - - - +
290E LEU* 3.5 21.8 - - + -
302E VAL* 3.3 2.6 - - + +
303E ALA* 1.3 76.1 - - - +
305E LYS* 1.3 60.4 + - - +
306E SER* 3.4 20.9 - - - +
307E TYR* 3.3 3.2 + - + +
308E GLU* 2.8 30.8 + - - +
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Residues in contact with LYS 305 (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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87E ASP* 3.1 32.4 + - - +
88E LYS* 3.0 19.0 + - - +
89E LEU 4.0 10.4 + - - -
90E TYR* 3.4 49.9 + - + +
91E PRO* 4.9 8.0 - - - +
303E ALA 3.3 1.2 + - - -
304E LEU* 1.3 69.4 - - - +
306E SER* 1.3 65.4 + - - +
308E GLU* 3.2 1.4 + - - +
309E GLU* 3.1 24.1 + - - +
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Residues in contact with SER 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E LYS* 4.6 0.7 + - - +
287E ASP* 3.0 29.4 + - - +
304E LEU* 3.4 18.2 - - - +
305E LYS* 1.3 79.9 - - - +
307E TYR* 1.3 58.6 + - - +
309E GLU* 3.7 14.4 - - - +
310E GLU* 4.1 3.5 + - - +
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Residues in contact with TYR 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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287E ASP* 3.3 35.7 + - + +
290E LEU* 4.0 21.3 - - + -
291E GLU* 3.5 40.8 + - + +
294E ASN* 3.7 13.9 + - + +
302E VAL* 4.0 11.4 - - + -
304E LEU* 3.3 6.9 + - + +
306E SER* 1.3 78.3 + - - +
308E GLU* 1.3 64.9 + - - +
310E GLU* 3.2 18.2 + - + +
311E LEU* 3.2 57.7 + - + +
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Residues in contact with GLU 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E TYR* 3.2 36.3 - - + +
301E ALA* 3.4 23.8 - - - +
302E VAL* 3.1 31.4 + - + +
304E LEU 2.8 18.2 + - - +
305E LYS 3.2 0.6 + - - +
307E TYR* 1.3 74.1 - - - +
309E GLU* 1.3 65.6 + - - +
311E LEU* 3.0 10.1 + - - +
312E ALA* 2.8 41.4 + - + +
317E ILE* 4.2 5.4 - - - +
321E MET* 5.1 3.6 - - - +
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Residues in contact with GLU 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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90E TYR* 4.7 1.0 + - - -
305E LYS 3.1 11.1 + - - +
306E SER* 3.7 12.8 - - - +
307E TYR 3.3 0.4 - - - -
308E GLU* 1.3 76.9 - - - +
310E GLU* 1.3 62.1 + - - +
312E ALA* 3.8 12.5 + - - +
313E LYS* 4.2 4.5 + - - +
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Residues in contact with GLU 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 SER 4.1 2.1 + - - +
307E TYR* 3.2 26.9 + - + +
308E GLU 3.2 0.8 - - - -
309E GLU* 1.3 80.4 - - - +
311E LEU* 1.3 62.3 - - + +
313E LYS* 3.4 17.9 + - - +
314E ASP 4.6 0.5 + - - -
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Residues in contact with LEU 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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294E ASN* 3.6 23.1 - - - +
300E GLY 3.6 16.4 - - - +
302E VAL* 3.6 24.7 - - + -
307E TYR* 3.2 45.2 + - + +
308E GLU* 3.0 19.1 + - - +
310E GLU* 1.3 75.0 - - + +
312E ALA* 1.3 59.4 + - - +
313E LYS 3.1 2.9 - - - -
314E ASP* 2.9 32.9 + - + +
317E ILE* 3.5 16.4 - - + +
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Residues in contact with ALA 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 GLU* 2.8 36.7 + - + +
309E GLU* 4.0 8.1 - - - +
310E GLU 3.4 0.6 - - - -
311E LEU* 1.3 71.9 - - - +
313E LYS* 1.3 60.7 + - - +
314E ASP 3.2 8.4 + - - +
317E ILE* 4.5 7.9 - - + -
318E ALA* 4.9 7.3 + - - +
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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