Contacts of the strand formed by residues 403 - 410 (chain C) 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 CYS 403 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336C ALA* 3.4 19.3 - - - -
338C LEU* 4.1 14.6 - - + -
394C ILE* 4.2 20.2 - - - -
401C ILE* 3.3 22.1 + - - -
402C PRO* 1.3 75.3 - - - +
404C ASP* 1.3 64.5 + - - +
405C PHE* 3.5 24.9 - - + -
435C LEU* 5.2 0.7 - - - -
472C PRO 3.7 6.1 + - - -
473C THR* 3.3 11.6 - - + -
474C ASN* 2.8 26.0 + - - +
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Residues in contact with ASP 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C LEU* 5.1 2.6 - - - +
335C HIS* 2.8 32.4 + - - +
336C ALA 2.9 11.6 + - - +
337C MET* 4.5 3.6 - - - -
338C LEU* 2.8 30.3 + - - +
403C CYS* 1.3 73.1 - - - +
405C PHE* 1.3 61.8 + - - +
406C LEU* 3.4 8.7 - - + +
474C ASN* 2.9 38.0 + - + +
476C ILE* 4.8 5.1 - - + +
493C TYR* 2.9 33.5 + - - +
496C LYS* 4.3 1.6 + - - -
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Residues in contact with PHE 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C LEU* 3.5 19.3 - - + -
340C TYR* 3.5 28.3 - + - -
391C TYR* 3.6 24.0 - + - -
394C ILE* 6.4 0.2 - - + -
403C CYS* 3.5 28.5 - - + -
404C ASP* 1.3 76.8 - - - +
406C LEU* 1.3 53.9 + - - +
428C PHE* 3.4 23.6 - + + -
431C GLN* 3.7 15.3 - - + -
432C THR* 3.6 22.9 - - + -
435C LEU* 4.0 17.7 - - + -
473C THR* 3.9 12.8 - - + -
474C ASN 2.8 17.1 + - - +
475C SER* 3.4 0.9 - - - -
476C ILE* 2.7 33.1 + - - +
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Residues in contact with LEU 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C MET* 4.8 3.6 - - + -
338C LEU 3.3 6.3 + - - +
339C PRO* 4.0 26.7 - - + -
340C TYR* 2.7 33.1 + - - +
341C ASP* 6.3 0.4 - - - -
344C LEU* 5.7 2.2 - - + -
347C PHE* 4.2 18.8 - - + -
404C ASP* 3.4 25.4 - - + +
405C PHE* 1.3 76.9 - - - +
407C ILE* 1.3 61.4 + - - +
428C PHE* 3.6 1.9 - - - -
476C ILE* 3.1 27.8 - - + +
478C PHE* 4.1 12.8 - - + -
489C LEU* 5.1 6.3 - - + -
493C TYR* 3.8 29.8 - - + +
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Residues in contact with ILE 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340C TYR* 3.4 26.2 - - + +
341C ASP* 5.7 0.2 - - - -
344C LEU* 6.4 0.2 - - - -
406C LEU* 1.3 76.1 - - - +
408C PRO* 1.3 81.8 - - + +
421C HIS* 4.6 2.7 - - + -
424C LEU* 4.2 10.5 - - + -
425C LEU* 3.5 35.4 - - + -
428C PHE* 3.6 43.3 - - + -
476C ILE 3.0 7.5 + - - -
477C VAL* 3.4 13.9 - - + +
478C PHE* 3.1 28.2 + - - -
548D ILE* 5.7 0.4 - - + -
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Residues in contact with PRO 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340C TYR 4.1 4.9 - - - +
341C ASP* 3.6 29.6 - - + +
407C ILE* 1.3 97.8 - - + +
409C VAL* 1.3 60.5 + - - +
410C GLN 3.7 17.0 - - - +
411C THR* 5.3 2.2 - - - -
421C HIS* 3.0 29.3 + - + -
425C LEU* 4.3 0.5 - - - +
478C PHE* 3.1 33.4 - - + +
480C LYS* 4.1 0.7 - - - -
481C LEU* 3.9 14.6 - - + +
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Residues in contact with VAL 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C PRO* 1.3 71.5 - - - +
410C GLN* 1.3 60.4 + - + +
421C HIS* 2.9 21.9 + - - -
425C LEU* 4.4 8.5 - - + +
477C VAL* 3.5 27.4 - - + -
478C PHE 2.7 16.5 + - - +
479C THR* 3.5 8.5 - - - +
547D PHE* 4.4 2.5 - - + -
548D ILE* 3.5 42.0 - - + +
551D GLN* 4.0 18.2 - - + +
552D ARG* 3.8 24.2 - - + +
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Residues in contact with GLN 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C PRO* 3.7 16.8 - - - +
409C VAL* 1.3 76.5 - - + +
411C THR* 1.3 63.2 + - - +
412C GLN* 4.1 0.9 + - - +
421C HIS* 4.2 1.6 - - - -
479C THR* 2.8 27.9 + - - +
480C LYS* 3.6 40.4 - - + +
481C LEU 4.7 0.3 + - - -
551D GLN 3.1 19.2 - - - +
552D ARG* 3.5 16.5 - - + +
554D ALA 2.6 29.3 + - - +
555D ARG* 4.3 14.9 - - - +
556D VAL 5.3 4.6 - - - +
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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