Contacts of the helix formed by residues 336 - 349 (chain B) in PDB entry 1JQO
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 ASN 336 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B CYS* 1.3 77.3 - - - +
337B ASP* 1.3 57.7 + - - +
338B GLU* 3.6 13.3 - - + +
339B LEU* 3.4 21.5 - - + +
340B ARG* 2.7 36.1 + - - +
418B LEU* 4.5 4.5 - - - +
421B LYS* 3.6 14.7 + - - +
422B SER* 3.2 26.9 + - - +
425B ASP* 2.9 43.3 + - - +
426B CYS* 4.9 1.8 - - - -
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Residues in contact with ASP 337 (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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335B CYS 5.6 0.7 - - - -
336B ASN* 1.3 74.2 - - - +
338B GLU* 1.3 55.1 + - - +
340B ARG* 3.8 26.2 + - - +
341B VAL* 2.7 39.7 + - + +
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Residues in contact with GLU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B ASN* 4.0 15.8 - - + +
337B ASP* 1.3 80.9 - - - +
339B LEU* 1.3 58.7 + - - +
341B VAL* 3.4 6.9 + - - +
342B ARG* 3.0 41.6 + - - +
414B GLU* 5.0 3.1 - - - +
418B LEU* 3.5 23.3 - - + +
421B LYS* 4.4 12.3 + - - +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B CYS* 3.9 8.7 - - + -
336B ASN* 3.2 19.8 + - + +
338B GLU* 1.3 75.6 - - - +
340B ARG* 1.3 58.4 + - - +
341B VAL 3.1 0.4 - - - -
342B ARG* 4.1 5.4 - - - -
343B ALA* 2.8 31.1 + - + +
370B PRO* 3.5 35.9 - - + +
371B TYR* 4.2 7.9 - - + +
374B ILE* 3.2 30.5 - - + -
418B LEU* 3.7 21.5 - - + +
419B CYS* 3.9 12.6 - - - -
422B SER* 3.6 22.9 - - - +
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Residues in contact with ARG 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B CYS* 4.0 18.2 - - - -
336B ASN 2.7 22.3 + - - +
337B ASP* 3.8 25.7 + - - +
339B LEU* 1.3 73.4 - - - +
341B VAL* 1.3 80.3 - - - +
343B ALA* 4.3 2.7 - - - +
344B GLU* 2.9 61.2 + - - +
370B PRO* 5.7 0.7 - - - -
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Residues in contact with VAL 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ASP* 2.7 25.7 + - + +
338B GLU* 3.5 7.0 - - - +
340B ARG* 1.3 94.9 - - - +
342B ARG* 1.3 67.6 + - - +
344B GLU* 3.0 20.1 + - - +
345B GLU* 3.0 29.9 + - + +
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Residues in contact with ARG 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLU* 3.0 31.2 + - - +
339B LEU 3.3 4.2 + - - +
341B VAL* 1.3 77.3 - - - +
343B ALA* 1.3 63.1 + - - +
345B GLU* 3.0 25.9 + - - +
346B LEU* 2.9 36.1 + - + +
374B ILE* 4.1 11.5 - - + +
414B GLU* 3.0 36.3 + - - -
415B PRO* 5.1 3.0 - - - +
418B LEU* 3.2 30.9 - - + +
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Residues in contact with ALA 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 2.8 20.7 + - + +
340B ARG* 4.4 2.2 - - - +
342B ARG* 1.3 74.8 - - - +
344B GLU* 1.3 61.5 - - - +
346B LEU* 4.4 1.1 - - - -
347B HIS* 3.0 26.0 + - - +
367B PRO* 5.8 3.6 - - + +
370B PRO* 3.8 33.0 - - + +
373B VAL* 3.6 20.9 - - + +
374B ILE* 4.1 10.3 - - + -
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ARG* 2.9 55.2 + - - +
341B VAL* 3.0 12.7 + - - +
343B ALA* 1.3 77.7 - - - +
345B GLU* 1.3 54.7 + - + +
347B HIS* 3.9 5.2 + - - +
348B SER* 2.9 30.8 + - - -
367B PRO* 5.6 9.2 - - + -
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Residues in contact with GLU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B VAL* 3.0 29.2 + - + +
342B ARG* 3.0 25.0 + - - +
344B GLU* 1.3 74.7 - - + +
346B LEU* 1.3 70.7 - - + +
348B SER* 2.9 8.9 + - - -
349B SER* 2.8 27.7 + - - +
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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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342B ARG* 2.9 46.4 + - + +
343B ALA* 3.9 1.6 - - - +
345B GLU* 1.3 82.5 - - + +
347B HIS* 1.3 61.9 + - - +
349B SER* 3.2 8.0 + - - +
350B SER* 2.8 27.9 + - - +
373B VAL* 3.7 15.7 - - + -
374B ILE* 4.0 21.3 - - + -
377B HIS* 3.3 49.1 - - + +
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Residues in contact with HIS 347 (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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343B ALA 3.0 17.7 + - - +
344B GLU 3.9 2.9 + - - +
346B LEU* 1.3 75.2 - - - +
348B SER* 1.3 67.9 + - - +
349B SER 3.1 9.7 - - - +
350B SER* 4.9 0.7 - - - -
351B GLY 4.1 5.9 - - - +
364B GLN* 3.5 32.7 + - + +
365B ILE 3.1 26.0 + - - -
366B PRO* 4.5 0.4 - - - +
367B PRO* 3.3 39.0 - - + +
373B VAL* 4.1 10.0 - - + +
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Residues in contact with SER 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B GLU 2.9 20.3 + - - -
345B GLU* 3.2 11.7 - - - -
347B HIS* 1.3 83.0 + - - +
349B SER* 1.3 58.8 + - - +
351B GLY* 5.9 0.2 - - - -
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Residues in contact with SER 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B GLU* 2.8 15.8 + - - +
346B LEU* 3.4 2.7 - - - -
347B HIS 3.1 7.4 - - - +
348B SER* 1.3 80.6 + - - +
350B SER* 1.3 67.6 + - - -
351B GLY* 2.7 27.6 + - - +
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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