Contacts of the helix formed by residues 343 - 352 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314B GLY 5.5 1.6 - - - -
315B GLY 3.6 8.3 + - - -
316B PHE* 3.4 19.5 - - - +
322B ARG* 3.6 12.5 + - - -
342B VAL* 1.3 78.5 - - - +
344B ASP* 1.3 60.3 + - - +
345B GLY 3.2 3.6 - - - -
346B LEU* 2.8 29.3 + - - +
347B ASP* 3.1 11.4 + - - -
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Residues in contact with ASP 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLU* 4.3 2.0 - - - -
104B THR* 5.7 0.9 - - - -
105B ILE* 3.6 15.9 - - + +
157B LYS* 3.2 28.0 - - - +
277B ARG* 3.1 42.2 + - - +
340B GLY 3.8 2.1 - - - +
342B VAL* 3.5 14.4 + - + +
343B GLY* 1.3 72.9 + - - +
345B GLY* 1.3 54.1 + - - +
347B ASP* 3.0 11.8 + - - +
348B VAL* 2.9 31.8 + - - +
2805B FAD 3.2 24.3 + - - -
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Residues in contact with GLY 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LEU* 4.4 4.4 - - - +
313B THR* 3.1 38.4 + - - -
343B GLY* 3.2 1.0 - - - -
344B ASP* 1.3 82.9 + - - +
346B LEU* 1.4 55.2 + - - +
348B VAL* 3.3 7.3 + - - +
349B ALA* 3.0 26.0 + - - +
535B VAL* 4.1 4.1 - - - +
2805B FAD 3.8 7.9 + - - -
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B THR* 4.3 0.2 + - - -
314B GLY 5.4 2.8 + - - +
315B GLY* 6.2 0.7 - - - -
316B PHE* 3.6 22.9 - - + -
322B ARG* 3.9 13.9 - - - +
343B GLY* 2.8 17.3 + - - +
345B GLY* 1.4 68.4 - - - +
347B ASP* 1.3 63.9 + - - +
349B ALA* 3.6 2.8 - - - +
350B GLU* 2.8 32.6 + - - +
356B LEU* 3.6 8.5 - - + -
359B MET* 3.4 36.3 - - + -
508B GLY 5.1 0.7 - - - +
509B GLY* 3.4 13.2 - - - -
510B VAL* 3.5 14.4 - - + +
535B VAL* 3.1 35.7 - - + +
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Residues in contact with ASP 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B THR* 5.0 6.4 - - - +
105B ILE* 3.9 26.2 + - + +
106B ALA* 5.2 1.9 + - - +
322B ARG* 3.0 27.6 + - - -
342B VAL 5.4 0.3 - - - +
343B GLY 3.6 10.6 - - - +
344B ASP* 3.0 14.8 + - - +
346B LEU* 1.3 74.2 - - - +
348B VAL* 1.3 61.5 + - - +
350B GLU* 3.3 9.2 + - - +
351B ASN* 2.8 42.4 + - - +
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Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ILE* 4.1 7.0 - - + -
132B VAL* 6.4 0.9 - - + -
278B GLY 3.7 18.4 - - - +
279B ILE 3.3 26.0 - - - +
280B GLU* 4.4 0.8 - - - +
281B VAL* 3.8 36.2 + - + +
292B ILE* 5.1 4.0 - - + -
311B LEU* 4.1 13.5 - - + -
344B ASP 2.9 21.6 + - - +
345B GLY* 3.5 8.7 - - - +
346B LEU 3.2 0.2 - - - -
347B ASP* 1.3 78.2 - - - +
349B ALA* 1.3 62.0 + - - +
351B ASN* 3.3 6.1 + - - +
352B ALA* 3.1 22.7 + - - +
2805B FAD 4.2 4.0 - - - +
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Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B LEU* 3.9 19.5 - - + +
345B GLY 3.0 12.0 + - - +
346B LEU 3.6 4.7 - - - +
347B ASP 3.2 0.2 - - - -
348B VAL* 1.3 76.3 - - - +
350B GLU* 1.3 60.6 + - - +
352B ALA* 3.2 13.3 + - - +
353B GLY 3.3 0.5 + - - -
354B GLY* 2.9 22.9 + - - -
356B LEU* 5.2 0.7 - - + -
510B VAL* 3.2 43.1 - - + -
529B LEU* 4.7 3.0 - - + +
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Residues in contact with GLU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B ARG* 4.3 9.4 + - - -
346B LEU 2.8 20.3 + - - +
347B ASP* 3.8 9.1 - - - +
349B ALA* 1.3 70.4 - - - +
351B ASN* 1.4 66.7 - - - +
353B GLY* 2.9 19.2 + - - -
354B GLY 3.5 15.5 - - - +
356B LEU* 3.5 40.6 - - + +
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Residues in contact with ASN 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ILE* 3.4 31.7 - - - +
106B ALA* 5.4 1.8 - - - +
279B ILE 5.1 1.6 + - - +
280B GLU* 5.6 12.1 - - + +
347B ASP* 2.8 25.7 + - - +
348B VAL* 3.8 5.6 - - - +
350B GLU* 1.4 78.1 - - - +
352B ALA* 1.3 58.1 + - - +
353B GLY 3.2 1.1 + - - -
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Residues in contact with ALA 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B VAL* 3.8 32.9 - - + +
283B LYS* 2.7 36.2 + - + +
348B VAL 3.1 13.1 + - - +
349B ALA* 3.4 9.6 - - - +
350B GLU 3.1 0.4 - - - -
351B ASN* 1.3 75.0 - - - +
353B GLY* 1.3 53.8 + - - +
354B GLY 3.6 0.2 - - - -
526B ILE* 2.9 22.6 - - + +
529B LEU* 4.1 9.4 - - + -
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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