Contacts of the helix formed by residues 312 - 317 (chain R) 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 SER 312 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315Q PHE* 4.0 14.5 - - - -
50R ILE* 3.3 17.5 - - - +
110R GLY* 4.3 1.0 - - - -
111R ASN* 2.8 51.0 + - - -
114R LEU* 3.7 12.1 - - - +
310R GLY 2.9 1.4 + - - -
311R ILE* 1.3 76.0 - - - +
313R GLY* 1.3 52.5 + - - +
314R THR 3.1 0.2 - - - -
315R PHE* 2.6 10.2 + - - +
316R HIS* 2.6 34.4 + - - +
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Residues in contact with GLY 313 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80R HIS* 6.4 1.1 - - - -
82R ASN* 4.9 1.1 - - - +
111R ASN* 4.0 5.6 - - - +
279R ASP* 4.8 1.1 - - - -
280R PRO* 3.9 14.0 - - - +
281R VAL* 5.2 8.3 - - - -
310R GLY 3.2 9.5 + - - -
312R SER* 1.3 78.9 - - - +
314R THR* 1.3 54.3 + - - +
315R PHE 2.9 0.2 - - - -
316R HIS* 2.9 13.0 + - - -
317R TYR* 2.7 41.0 + - - -
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Residues in contact with THR 314 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113Q LEU* 4.4 1.4 - - - +
114Q LEU* 4.5 12.6 - - + +
117Q ILE* 3.5 33.5 - - + +
267R ILE* 4.4 8.7 - - + +
277R ILE* 3.8 21.6 - - + +
278R LEU 2.9 24.8 + - - +
279R ASP* 3.1 12.1 - - - +
280R PRO* 3.3 12.9 - - + +
310R GLY 4.2 0.8 + - - -
311R ILE* 3.5 14.4 + - + +
312R SER 3.1 0.4 - - - -
313R GLY* 1.3 75.1 - - - +
315R PHE* 1.3 59.3 + - + +
318R GLY* 3.7 8.0 - - - +
321R LEU* 5.4 1.8 - - + -
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Residues in contact with PHE 315 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q ILE* 5.4 2.0 - - + -
109Q LYS* 6.2 0.2 - - + -
110Q GLY* 4.2 18.2 - - - -
113Q LEU* 4.2 19.8 - - + +
114Q LEU* 4.2 26.2 - - + -
311Q ILE* 5.4 2.9 - - + -
312Q SER* 2.6 42.8 - - - -
315Q PHE* 3.3 56.8 - + + -
110R GLY* 5.0 1.8 - - - -
311R ILE* 3.4 31.8 + - + -
312R SER 2.6 11.6 + - - +
314R THR* 1.3 83.5 - - - +
316R HIS* 1.3 60.6 + - - +
317R TYR 3.6 0.4 + - - -
318R GLY 4.1 3.9 + - - -
319R ASP* 5.7 0.2 - - - +
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Residues in contact with HIS 316 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79R VAL* 5.1 5.6 - - + +
80R HIS* 3.8 26.5 - - + +
107R GLU* 3.4 17.5 + - - +
109R LYS* 3.1 54.1 + - + +
110R GLY* 3.1 28.0 - - - +
111R ASN* 3.8 7.2 - - - -
112R TYR* 5.1 2.4 - - - +
312R SER 2.6 10.2 + - - +
313R GLY* 2.9 13.8 + - - +
315R PHE* 1.3 75.8 - - - +
317R TYR* 1.3 87.1 + + + +
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Residues in contact with TYR 317 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79R VAL* 6.0 0.3 - - - +
80R HIS* 3.5 33.7 + + - -
105R LYS* 6.1 0.9 - - - +
107R GLU* 5.0 4.3 + - - -
257R GLY* 5.7 4.9 - - - -
259R ILE* 3.4 31.0 - - + -
280R PRO* 4.7 6.5 - - + -
281R VAL* 5.9 5.6 - - + -
313R GLY* 2.7 23.6 + - - +
316R HIS* 1.3 114.0 + + + +
318R GLY* 1.3 50.4 + - - +
319R ASP* 2.4 20.9 + - - -
320R LYS* 2.6 26.6 + - + +
321R LEU* 3.1 8.0 + - - +
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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
------------------------------------------------------------
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