Contacts of the helix formed by residues 311 - 317 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44M ASP* 6.6 0.2 - - + -
50M ILE* 3.3 41.5 - - + +
82M ASN* 4.5 0.2 - - - +
277M ILE* 4.0 44.0 - - + +
278M LEU 6.1 1.6 - - - -
279M ASP* 5.2 0.7 - - - -
307M HIS* 6.5 0.2 - - - -
309M GLY* 3.4 4.3 - - - -
310M GLY* 1.3 73.6 - - - +
312M SER* 1.3 65.5 + - - +
313M GLY 2.8 7.3 + - - -
314M THR* 2.9 18.0 + - - +
315M PHE* 4.0 24.3 + - + -
50N ILE* 5.4 3.4 - - + -
311N ILE* 5.1 13.7 - - + -
315N PHE* 5.3 1.8 - - + -
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Residues in contact with SER 312 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M ILE* 2.9 25.6 - - - +
82M ASN* 4.2 0.4 - - - -
110M GLY* 4.0 3.9 - - - -
111M ASN* 2.8 46.0 + - - -
310M GLY 3.3 0.2 - - - -
311M ILE* 1.3 78.8 - - - +
313M GLY* 1.3 55.7 + - - +
314M THR 3.3 0.2 - - - -
315M PHE* 3.3 6.9 + - - +
316M HIS* 3.0 27.2 + - - +
315N PHE* 3.6 23.6 - - - -
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Residues in contact with GLY 313 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80M HIS* 5.6 3.8 - - - -
82M ASN* 4.3 5.3 - - - +
111M ASN* 5.4 1.3 - - - -
279M ASP* 4.2 8.5 - - - -
280M PRO* 3.8 10.6 - - - +
281M VAL* 5.6 2.0 - - - -
310M GLY 3.0 10.8 + - - -
311M ILE 2.8 3.6 + - - -
312M SER* 1.3 79.8 - - - +
314M THR* 1.3 58.8 + - - -
316M HIS* 3.5 8.3 - - - +
317M TYR* 3.2 31.7 + - - -
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Residues in contact with THR 314 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267M ILE* 4.8 6.7 - - + -
277M ILE* 4.0 17.1 - - + +
278M LEU 2.6 30.3 + - - +
279M ASP* 3.3 8.4 - - - +
280M PRO* 4.1 5.8 - - - -
311M ILE* 2.9 12.8 + - - +
313M GLY* 1.3 75.5 - - - +
315M PHE* 1.3 61.5 + - - +
317M TYR 4.3 0.8 - - - -
318M GLY* 3.6 19.2 + - - -
321M LEU* 4.1 11.6 - - + +
113N LEU* 3.8 5.4 - - - +
114N LEU* 4.9 8.7 - - + -
117N ILE* 3.9 21.3 - - + +
118N MET* 5.9 1.1 - - + -
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Residues in contact with PHE 315 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M LYS* 5.2 2.6 - - - +
110M GLY* 5.1 1.8 - - - +
311M ILE* 4.1 28.7 - - + -
312M SER* 3.3 6.0 + - - +
313M GLY 3.2 0.6 - - - -
314M THR* 1.3 76.0 - - - +
316M HIS* 1.3 69.9 + - - +
318M GLY* 3.6 5.9 + - - -
50N ILE* 4.7 1.3 - - + -
110N GLY* 3.8 19.3 - - - -
113N LEU* 3.9 15.3 - - + +
114N LEU* 3.3 32.5 - - + -
311N ILE* 4.3 4.0 - - + -
312N SER* 2.9 41.7 - - - -
315N PHE* 3.7 51.6 - + + -
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Residues in contact with HIS 316 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79M VAL* 4.7 8.8 - - - +
80M HIS* 3.6 28.5 + - + +
107M GLU* 3.4 25.8 + - - +
109M LYS* 3.1 53.8 + - + +
110M GLY* 3.7 15.4 - - - +
111M ASN 4.4 0.7 - - - +
312M SER 3.0 14.3 + - - +
313M GLY* 3.5 11.2 - - - +
315M PHE* 1.3 81.9 - - - +
317M TYR* 1.3 97.2 + + + +
318M GLY 3.3 2.3 + - - -
319M ASP* 5.1 1.6 + - - +
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Residues in contact with TYR 317 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M HIS* 2.7 47.3 + + + +
107M GLU* 5.3 1.1 - - - -
109M LYS* 6.4 0.2 - - - -
257M GLY 5.4 6.1 - - - -
259M ILE* 3.1 31.9 - - + -
280M PRO* 4.3 1.8 - - + -
281M VAL* 4.3 12.8 - - + -
313M GLY* 3.2 15.7 + - - +
314M THR 4.3 2.0 - - - -
316M HIS* 1.3 111.9 + + + +
318M GLY* 1.3 63.9 + - - +
319M ASP 3.5 2.0 - - - -
320M LYS* 3.4 12.8 - - + +
321M LEU* 3.3 23.7 + - - +
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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