Contacts of the helix formed by residues 338 - 345 (chain B) in PDB entry 5JG8
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 338 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321B SER* 4.2 8.7 + - - -
326B SER 3.8 9.0 + - - -
327B PHE* 3.8 6.9 - - - -
328B PRO* 3.2 32.9 + - - +
337B SER* 1.3 73.0 - - - +
339B ARG* 1.3 63.4 + - - +
340B TRP* 3.1 10.3 + - - +
341B LEU* 3.0 17.0 + - - +
342B TYR* 3.1 41.2 + - - -
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Residues in contact with ARG 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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334B GLY* 4.7 17.0 - - - +
335B ASN* 5.3 5.7 + - - +
337B SER* 3.2 15.7 + - - +
338B SER* 1.3 77.4 - - - +
340B TRP* 1.3 69.9 + - - +
342B TYR* 4.5 9.4 - - - +
343B GLU* 2.9 65.2 + - + +
362B ARG 4.8 7.9 - - - +
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Residues in contact with TRP 340 (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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289B ARG* 3.0 70.9 - - + +
292B GLN* 4.5 3.4 - - + -
293B LEU* 3.9 28.7 - - + +
320B GLU 4.4 3.8 - - - -
321B SER* 3.9 35.5 + - - -
322B THR* 4.1 7.2 + - + -
335B ASN 4.5 1.1 - - - -
337B SER* 3.0 29.1 + - - -
338B SER* 3.9 7.5 + - - +
339B ARG* 1.3 88.2 - - - +
341B LEU* 1.3 92.4 + - + +
343B GLU* 3.9 1.8 - - - +
344B ALA* 2.9 30.3 + - - +
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Residues in contact with LEU 341 (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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292B GLN* 5.4 2.7 - - + +
293B LEU* 4.0 13.0 - - + -
296B LEU* 4.3 7.0 - - + -
320B GLU* 3.5 21.1 - - + +
321B SER* 3.5 36.6 - - - +
327B PHE* 4.2 10.5 - - + -
338B SER* 3.0 10.7 + - - +
340B TRP* 1.3 107.3 - - + +
342B TYR* 1.3 68.2 + - + +
344B ALA* 3.2 2.8 + - - +
345B MET* 2.9 54.8 + - + +
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Residues in contact with TYR 342 (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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316B VAL* 4.8 5.8 - - + -
327B PHE* 3.6 21.7 - + - +
328B PRO 4.8 3.9 + - - -
330B PRO* 6.5 0.4 - - + -
338B SER* 3.1 35.4 + - - +
339B ARG* 4.1 3.6 - - - +
341B LEU* 1.3 86.7 - - + +
343B GLU* 1.3 53.3 + - - +
345B MET* 2.6 40.3 - - - +
346B ALA* 4.2 4.7 - - - +
361B LEU* 3.3 17.5 - - - +
362B ARG* 3.5 18.5 - - - +
363B ILE 3.3 29.6 - - - -
364B GLY* 3.7 14.3 + - - -
365B GLY* 3.9 10.1 - - - -
381B ASN* 3.1 24.6 + - - -
384B PHE* 3.8 12.4 - + - -
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Residues in contact with GLU 343 (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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339B ARG* 2.9 57.0 + - + +
340B TRP* 4.3 2.5 - - - +
342B TYR* 1.3 73.0 - - - +
344B ALA* 1.3 58.4 + - - +
345B MET 2.8 16.2 - - - +
346B ALA* 4.6 0.3 - - - +
347B LYS* 3.5 12.6 + - - +
362B ARG* 4.1 34.8 + - + +
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Residues in contact with ALA 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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293B LEU* 3.3 39.0 - - + -
296B LEU* 4.5 6.7 - - + +
297B THR* 5.7 3.6 - - + +
340B TRP 2.9 19.8 + - - +
341B LEU 3.6 2.9 - - - +
343B GLU* 1.3 73.4 - - - +
345B MET* 1.3 59.8 + - - +
347B LYS* 3.1 22.7 - - - +
348B ALA* 3.2 11.8 + - - +
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Residues in contact with MET 345 (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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279B ILE* 6.2 0.4 - - + -
296B LEU* 3.4 22.4 - - + +
316B VAL* 4.1 23.6 - - + -
320B GLU* 3.9 20.9 - - + -
341B LEU* 2.9 46.9 + - + +
342B TYR* 2.6 30.4 - - - +
343B GLU 2.8 14.2 - - - +
344B ALA* 1.3 70.2 - - - +
346B ALA* 1.3 65.0 + - - +
347B LYS 2.8 5.2 - - - -
348B ALA* 4.4 3.4 - - - +
349B TRP* 3.6 41.1 - - + -
361B LEU* 4.1 10.5 - - + -
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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