Contacts of the helix formed by residues 343 - 352 (chain A) in PDB entry 1JRX
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 GLY 343 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A GLY 5.6 1.6 - - - -
315A GLY 3.5 11.8 + - - -
316A PHE* 3.5 17.0 - - - -
322A ARG* 3.5 12.8 + - - -
342A VAL* 1.3 76.9 - - - +
344A ASP* 1.3 65.4 + - - +
345A GLY 3.1 3.6 - - - -
346A LEU* 2.9 22.3 + - - +
347A ASP* 3.1 11.4 + - - -
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Residues in contact with ASP 344 (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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104A THR* 5.6 1.1 - - - -
105A ILE* 3.7 12.0 - - + +
157A LYS* 3.2 22.4 - - - -
277A ARG* 3.0 43.8 + - - +
340A GLY 3.8 2.3 - - - +
342A VAL* 3.3 21.8 + - + +
343A GLY* 1.3 72.9 + - - +
345A GLY* 1.3 55.5 + - - +
347A ASP* 3.0 15.9 + - - +
348A VAL* 2.9 31.0 + - - +
1805A FAD 3.1 20.4 + - - -
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Residues in contact with GLY 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A LEU* 4.3 4.4 - - - +
313A THR* 3.1 39.5 + - - -
314A GLY 5.8 0.2 - - - -
343A GLY* 3.1 1.2 - - - -
344A ASP* 1.3 81.9 + - - +
346A LEU* 1.4 55.6 + - - +
348A VAL* 3.2 10.3 + - - +
349A ALA* 2.9 27.4 + - - +
535A VAL* 4.1 2.3 - - - +
1805A FAD 3.9 4.3 + - - -
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Residues in contact with LEU 346 (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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313A THR* 4.2 0.2 + - - -
314A GLY 5.4 2.4 + - - +
315A GLY* 5.9 1.3 - - - -
316A PHE* 3.6 31.9 - - + -
322A ARG* 4.0 12.3 - - - +
343A GLY* 2.9 14.5 + - - +
345A GLY* 1.4 72.4 - - - +
347A ASP* 1.3 58.0 + - - +
349A ALA* 3.3 3.0 + - - +
350A GLU* 2.7 37.7 + - - +
356A LEU* 3.5 10.5 - - + +
359A MET* 3.6 25.6 - - + -
508A GLY 4.9 0.7 - - - +
509A GLY* 3.5 4.9 - - - -
510A VAL* 3.3 36.6 - - + +
534A GLU 6.1 0.2 - - - +
535A VAL* 3.3 23.5 - - + +
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Residues in contact with ASP 347 (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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104A THR* 4.9 6.2 - - - -
105A ILE* 4.0 26.7 + - + +
106A ALA* 5.3 2.7 + - - +
322A ARG* 3.2 25.5 + - - -
342A VAL 5.5 0.2 - - - +
343A GLY 3.1 11.1 + - - +
344A ASP* 3.0 14.5 + - - +
346A LEU* 1.3 76.5 - - - +
348A VAL* 1.3 57.4 + - - +
350A GLU* 3.7 8.5 - - - +
351A ASN* 2.8 41.5 + - - +
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Residues in contact with VAL 348 (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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105A ILE* 4.2 6.7 - - + -
132A VAL* 6.4 0.2 - - + -
278A GLY 3.6 20.0 - - - +
279A ILE* 3.2 28.9 - - - +
280A GLU* 4.3 2.2 - - - +
281A VAL* 3.7 32.3 + - + +
292A ILE* 5.1 4.3 - - + -
311A LEU* 4.1 14.1 - - + -
344A ASP 2.9 20.9 + - - +
345A GLY* 3.6 8.3 - - - +
346A LEU 3.2 0.2 - - - -
347A ASP* 1.3 73.1 - - - +
349A ALA* 1.3 64.6 + - - +
351A ASN* 3.4 5.9 + - - +
352A ALA* 3.1 22.0 + - - +
1805A FAD 4.4 3.4 - - - +
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Residues in contact with ALA 349 (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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311A LEU* 3.4 25.3 - - + +
345A GLY 2.9 13.2 + - - +
346A LEU 3.7 1.3 - - - +
348A VAL* 1.3 75.3 - - - +
350A GLU* 1.3 58.5 + - - +
352A ALA* 3.3 13.1 + - - +
354A GLY* 2.8 25.6 + - - -
510A VAL* 3.2 41.7 - - + -
529A LEU* 4.5 3.5 - - + +
535A VAL* 5.3 0.2 - - + -
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Residues in contact with GLU 350 (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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322A ARG* 4.4 7.4 + - - -
346A LEU 2.7 19.5 + - - +
347A ASP* 3.7 9.7 - - - +
349A ALA* 1.3 70.8 - - - +
351A ASN* 1.3 62.6 - - - +
353A GLY* 2.9 20.6 + - - -
354A GLY 3.4 17.7 + - - +
355A ALA* 5.2 0.6 - - - -
356A LEU* 3.6 39.8 - - + +
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Residues in contact with ASN 351 (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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105A ILE* 3.6 27.9 - - - +
106A ALA* 5.5 1.8 - - - +
279A ILE 5.0 1.9 + - - +
280A GLU* 5.5 12.2 - - + +
281A VAL 6.4 0.2 - - - +
283A LYS* 5.4 0.5 - - - -
347A ASP* 2.8 28.0 + - - +
348A VAL* 3.4 5.7 + - - +
350A GLU* 1.3 77.9 - - - +
352A ALA* 1.3 58.7 + - - +
353A GLY 3.2 1.0 + - - -
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Residues in contact with ALA 352 (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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281A VAL* 3.9 25.5 - - + +
283A LYS* 2.4 40.3 + - - +
348A VAL 3.1 12.6 + - - +
349A ALA* 3.3 13.2 - - - +
350A GLU 3.1 0.4 - - - -
351A ASN* 1.3 77.4 - - - +
353A GLY* 1.3 52.5 + - - +
354A GLY 3.5 0.2 - - - -
526A ILE* 3.2 9.7 - - + +
529A LEU* 3.9 20.9 - - + -
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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