Contacts of the strand formed by residues 334 - 339 (chain B) in PDB entry 1JLH
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 THR 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A GLU* 4.3 2.8 + - - +
334A THR* 3.6 31.4 - - + -
377A ILE* 3.5 22.0 - - + +
327B ILE* 5.8 1.0 - - - +
332B CYS* 4.4 4.1 - - - +
333B GLU* 1.3 87.5 - - + +
335B HIS* 1.3 61.3 + - - +
376B PRO* 4.3 3.9 - - - +
377B ILE* 3.2 19.1 - - + +
379B TRP* 3.2 21.3 + - + +
400B MET 5.0 0.5 + - - -
401B ILE* 3.7 11.8 - - - +
402B PRO* 3.3 24.1 - - - +
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Residues in contact with HIS 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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323B GLY* 6.0 4.3 - - - -
327B ILE* 6.2 0.2 - - + -
334B THR* 1.3 75.3 - - - +
336B ALA* 1.3 62.4 + - - +
337B MET* 3.7 23.8 - - + +
355B ASP* 5.3 1.8 - - - -
376B PRO* 4.2 20.2 - - + -
377B ILE 2.9 7.0 + - - +
378B VAL* 3.3 13.2 - - + +
379B TRP* 3.2 23.1 + - - +
402B PRO* 3.7 22.4 + - + +
404B ASP* 2.9 42.3 + - - -
474B ASN* 5.1 3.6 - - - -
493B TYR* 4.6 0.2 - - - -
496B LYS* 3.3 26.5 + - - -
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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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334B THR 4.3 0.2 - - - -
335B HIS* 1.3 75.7 + - - +
337B MET* 1.3 61.4 + - - +
338B LEU* 3.9 14.6 - - + -
379B TRP* 3.2 32.4 - - + +
401B ILE* 4.0 4.0 - - + +
402B PRO 3.0 8.2 + - - +
403B CYS* 3.4 25.2 - - - -
404B ASP* 2.8 28.6 + - - +
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Residues in contact with MET 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 HIS* 3.7 27.4 - - + +
336B ALA* 1.3 70.1 - - - +
338B LEU* 1.3 61.0 + - - +
339B PRO* 3.4 10.1 - - - +
347B PHE* 3.6 27.8 - - + -
348B ALA* 3.6 18.9 - - + +
351B PHE* 3.7 28.3 - - + -
355B ASP* 5.9 1.1 - - - +
378B VAL* 3.6 25.8 - - + -
379B TRP 2.9 7.8 + - - +
380B GLY* 3.6 19.4 - - - -
404B ASP* 3.8 7.6 - - + +
406B LEU* 5.1 2.2 - - + -
493B TYR* 3.4 35.4 - - + +
496B LYS* 6.0 0.2 - - - -
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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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336B ALA* 4.2 9.4 - - + -
337B MET* 1.3 80.8 - - - +
339B PRO* 1.3 63.6 - - - +
340B TYR* 3.6 10.3 + - + -
380B GLY* 3.9 4.5 - - - -
381B GLU 3.4 29.4 - - - +
383B GLY 5.1 0.4 - - - +
390B PHE* 3.8 20.0 - - + -
391B TYR* 3.4 32.3 - - + +
394B ILE* 4.6 4.5 - - + -
403B CYS* 4.1 18.8 - - + -
404B ASP 2.8 14.7 + - - +
405B PHE* 3.4 29.1 - - + -
406B LEU* 3.2 17.7 + - - +
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Residues in contact with PRO 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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337B MET 3.4 11.4 - - - +
338B LEU* 1.3 85.0 - - - +
340B TYR* 1.3 58.4 + - - +
341B ASP 2.9 9.0 + - - +
344B LEU* 3.7 50.0 - - + +
347B PHE* 4.3 14.1 - - + -
348B ALA* 5.2 3.4 - - + +
381B GLU 4.4 0.7 - - - +
382B PRO* 3.1 15.7 - - + +
383B GLY 2.9 18.0 + - - -
406B LEU* 3.4 23.3 - - + +
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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