Contacts of the helix formed by residues 311 - 319 (chain A) in PDB entry 1RJG
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 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A TYR* 5.5 2.0 - - + +
287A TRP* 4.1 24.8 - - + -
290A PHE* 4.1 12.6 - - + -
299A ARG* 3.9 24.7 - - - +
308A LEU* 3.9 35.2 - - + +
310A GLU* 1.3 72.4 + - - +
312A GLU* 1.3 58.9 + - - +
313A GLU 3.5 0.7 - - - -
314A LEU* 3.6 12.6 + - + +
315A LYS* 3.1 26.7 + - - +
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Residues in contact with GLU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A GLU* 3.2 20.8 + - + +
311A LEU* 1.3 76.4 - - - +
313A GLU* 1.3 64.7 + - - +
314A LEU 3.1 2.0 - - - -
315A LYS* 3.2 21.0 + - - +
316A VAL* 3.1 37.3 + - + +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 3.8 38.0 - - + +
310A GLU* 4.3 8.1 + - + +
312A GLU* 1.3 78.4 - - - +
314A LEU* 1.3 60.3 + - - +
316A VAL* 4.3 5.6 - - + +
317A MET* 3.6 22.3 + - - +
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Residues in contact with LEU 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 4.0 16.0 - - + +
76A TYR* 3.4 47.6 - - + -
77A GLY 4.4 1.1 - - - +
80A LEU* 4.9 2.7 - - + -
287A TRP* 4.2 10.0 - - + -
290A PHE* 4.1 29.8 - - + -
308A LEU* 4.0 20.0 - - + -
310A GLU 4.8 1.0 + - - -
311A LEU* 3.6 13.1 + - + +
312A GLU 3.1 0.4 - - - -
313A GLU* 1.3 78.9 - - - +
315A LYS* 1.3 58.2 + - - +
317A MET* 4.1 2.6 - - + -
318A GLN* 3.1 53.8 + - + +
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Residues in contact with LYS 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A TRP* 3.7 52.9 - - + +
311A LEU 3.1 17.5 + - - +
312A GLU* 3.2 23.4 + - - +
314A LEU* 1.3 74.8 - - - +
316A VAL* 1.3 58.0 + - + +
318A GLN 4.0 0.2 - - - -
319A THR* 2.7 49.1 + - + +
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Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLU* 3.1 28.5 + - + +
313A GLU* 4.5 5.2 - - - +
315A LYS* 1.3 79.3 - - + +
317A MET* 1.3 61.3 + - + +
319A THR* 3.0 15.9 + - - -
320A HIS* 3.2 23.4 + - + +
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Residues in contact with MET 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A VAL* 3.3 46.4 - - + +
74A MET* 4.4 19.3 - - - -
77A GLY* 4.5 3.1 - - - -
313A GLU 3.6 13.4 + - - +
314A LEU* 4.2 3.1 - - + +
315A LYS 3.3 0.4 - - - -
316A VAL* 1.3 83.3 - - + +
318A GLN* 1.3 86.0 + - + +
320A HIS* 3.3 16.8 + - - +
321A TYR* 3.2 29.8 - - + -
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Residues in contact with GLN 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLY* 3.5 35.2 + - - +
80A LEU* 3.6 12.0 - - + +
231A TYR* 4.7 2.2 + - - -
286A MET* 3.1 35.0 + - + +
287A TRP* 3.9 20.4 - - + +
314A LEU* 3.1 38.6 + - + +
315A LYS 3.5 0.4 + - - +
317A MET* 1.3 87.3 - - + +
319A THR* 1.3 59.8 + - - +
320A HIS 3.2 1.6 - - - -
321A TYR* 2.9 43.5 - - - +
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Residues in contact with THR 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ILE* 3.7 14.7 - - - +
285A ASP* 3.7 32.8 - - - +
287A TRP* 3.9 13.0 - - + -
315A LYS* 2.7 37.7 + - + +
316A VAL* 3.0 15.2 + - - -
318A GLN* 1.3 76.0 - - - +
320A HIS* 1.3 69.0 + - - +
321A TYR 3.3 1.6 + - - -
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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