Contacts of the helix formed by residues 327 - 339 (chain B) in PDB entry 1JGG
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 327 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323B GLU* 5.1 1.0 + - - -
325B TYR* 3.6 23.5 - - - -
326B VAL* 1.3 73.6 - - - +
328B ARG* 1.3 70.2 + - - +
329B PRO* 3.8 17.6 - - - +
330B ARG* 2.8 23.6 + - - +
331B ARG* 3.0 11.6 + - - +
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Residues in contact with ARG 328 (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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325B TYR* 2.3 47.9 + - - +
327B SER* 1.3 71.1 - - - +
329B PRO* 1.3 69.3 - - + +
331B ARG* 2.8 46.8 - - - +
332B CYS* 3.3 26.4 + - - -
342B GLU* 5.8 0.5 - - - +
346B LYS* 6.0 1.0 - - - +
213D T 5.0 0.4 - - - -
214D T 2.4 48.0 + - - -
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Residues in contact with PRO 329 (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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327B SER* 2.9 16.1 - - - +
328B ARG* 1.3 94.5 - - + +
330B ARG* 1.3 64.7 + - - +
331B ARG 3.2 1.1 - - - -
332B CYS* 3.2 16.6 + - + +
333B GLU* 3.2 20.4 + - - +
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Residues in contact with ARG 330 (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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315B ARG* 3.9 8.7 - - - +
319B GLU* 3.0 39.9 + - - -
322B LYS* 4.1 9.6 - - - +
323B GLU* 5.4 5.6 - - - +
326B VAL* 4.2 14.6 - - + -
327B SER* 2.8 21.1 + - - +
329B PRO* 1.3 74.3 - - - +
331B ARG* 1.3 58.3 + - - +
333B GLU* 2.9 47.9 + - - +
334B LEU* 2.8 43.3 + - - +
337B GLN* 4.1 21.6 + - - +
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Residues in contact with ARG 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B TYR* 5.0 1.2 - - - -
326B VAL* 2.9 44.3 + - + -
327B SER 3.3 11.4 - - - +
328B ARG* 2.8 62.5 - - - +
330B ARG* 1.3 79.0 - - - +
332B CYS* 1.3 56.8 + - - +
334B LEU* 3.9 4.3 - - - +
335B ALA* 3.0 29.2 + - - +
342B GLU* 4.6 16.2 + - + +
345B ILE* 4.1 17.4 - - + +
346B LYS* 3.5 56.8 - - - +
349B PHE* 5.7 0.7 - - - -
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Residues in contact with CYS 332 (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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328B ARG 3.3 13.4 + - - -
329B PRO* 3.2 11.8 + - + +
330B ARG 3.2 1.0 - - - -
331B ARG* 1.3 74.9 - - - +
333B GLU* 1.3 65.5 + - - +
335B ALA* 3.6 7.7 + - - +
336B ALA* 3.1 23.9 + - - +
342B GLU* 3.7 30.3 - - - -
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Residues in contact with GLU 333 (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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329B PRO* 3.2 21.3 + - - +
330B ARG* 2.9 43.9 + - - +
332B CYS* 1.3 75.7 - - - +
334B LEU* 1.3 63.9 + - - +
336B ALA* 3.4 6.6 + - - +
337B GLN* 3.1 31.1 + - - +
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Residues in contact with LEU 334 (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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315B ARG* 3.8 40.4 - - + +
316B LEU* 5.4 4.9 - - + -
319B GLU* 3.9 22.4 - - + +
326B VAL* 4.5 6.3 - - + -
330B ARG* 2.8 45.3 + - - +
331B ARG* 4.0 7.0 - - - +
333B GLU* 1.3 76.8 - - - +
335B ALA* 1.3 50.5 + - - +
337B GLN* 3.2 16.5 + - - +
338B LEU* 2.8 49.7 + - + +
345B ILE* 4.4 18.6 - - + -
349B PHE* 4.9 2.5 - - + -
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Residues in contact with ALA 335 (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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331B ARG 3.0 18.8 + - - +
332B CYS* 3.7 7.4 - - - +
334B LEU* 1.3 73.2 - - - +
336B ALA* 1.3 59.5 + - - +
339B ASN* 2.9 24.4 + - - -
340B LEU 3.1 29.3 + - - +
342B GLU* 4.1 15.9 - - + +
345B ILE* 3.6 15.7 - - + +
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Residues in contact with ALA 336 (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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332B CYS 3.1 18.6 + - - +
333B GLU* 3.6 6.5 - - - +
335B ALA* 1.3 75.5 - - - +
337B GLN* 1.3 63.1 + - + +
338B LEU 3.6 0.2 + - - -
339B ASN* 3.7 15.6 + - - +
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Residues in contact with GLN 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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315B ARG* 5.1 10.7 - - - +
330B ARG* 4.1 20.3 + - - +
333B GLU* 3.1 16.9 + - - +
334B LEU* 3.2 21.5 + - - +
336B ALA* 1.3 80.5 - - + +
338B LEU* 1.3 66.2 + - + +
339B ASN* 3.5 3.6 + - - -
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Residues in contact with LEU 338 (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 ASP* 4.9 5.2 - - - +
312B GLN* 2.9 57.4 + - + +
315B ARG* 4.0 31.0 - - + -
316B LEU* 4.4 15.7 - - + -
334B LEU* 2.8 30.8 + - + +
337B GLN* 1.3 83.5 - - + +
339B ASN* 1.3 70.7 + - - +
340B LEU* 3.2 24.9 + - + -
345B ILE* 5.0 1.6 - - + -
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Residues in contact with ASN 339 (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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312B GLN* 4.5 3.3 + - - +
335B ALA 2.9 10.2 + - - -
336B ALA 3.7 11.2 + - - +
337B GLN 3.5 4.6 + - - -
338B LEU* 1.3 81.2 - - - +
340B LEU* 1.3 60.4 + - - +
341B PRO* 4.5 2.0 - - - +
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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
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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