Contacts of the strand formed by residues 403 - 410 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335D HIS* 5.0 0.2 - - - -
336D ALA* 3.5 22.7 - - - -
338D LEU* 4.0 13.2 - - + -
394D ILE* 4.3 20.6 - - - -
401D ILE* 3.2 22.4 + - - -
402D PRO* 1.3 73.3 - - - +
404D ASP* 1.3 64.0 + - - +
405D PHE* 3.4 24.9 - - + -
435D LEU* 5.9 0.4 - - - -
472D PRO 3.5 6.3 + - - -
473D THR* 3.2 11.9 - - + +
474D ASN* 2.8 26.2 + - - +
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Residues in contact with ASP 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319D LEU* 5.0 5.2 - - - +
335D HIS* 2.9 30.7 + - - +
336D ALA 2.8 14.1 + - - +
337D MET* 4.4 4.0 - - - +
338D LEU* 2.8 31.7 + - - +
403D CYS* 1.3 72.6 - - - +
405D PHE* 1.3 61.2 + - - +
406D LEU* 3.4 9.1 - - + +
474D ASN* 2.9 37.2 + - + +
476D ILE* 5.4 2.5 - - + -
493D TYR* 2.7 35.8 + - - +
496D LYS* 4.5 0.9 + - - -
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Residues in contact with PHE 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D LEU* 3.5 18.8 - - + -
340D TYR* 3.7 19.5 - + - -
391D TYR* 3.7 21.3 - + - -
394D ILE* 6.2 0.9 - - + -
403D CYS* 3.4 26.9 - - + -
404D ASP* 1.3 77.2 - - - +
406D LEU* 1.3 54.2 + - - +
428D PHE* 3.4 25.7 - - + -
431D GLN* 3.8 21.1 - - + -
432D THR* 3.5 21.5 - - + -
435D LEU* 3.9 20.9 - - + -
473D THR* 3.8 17.0 - - + -
474D ASN 2.8 12.7 + - - +
475D SER* 3.3 1.8 - - - +
476D ILE* 2.7 32.2 + - - +
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Residues in contact with LEU 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D MET* 4.8 2.9 - - + -
338D LEU 3.2 6.9 + - - +
339D PRO* 4.0 26.5 - - + -
340D TYR 2.7 31.2 + - - -
344D LEU* 5.6 1.1 - - + -
347D PHE* 4.2 18.2 - - + -
404D ASP* 3.4 26.7 - - + +
405D PHE* 1.3 76.5 - - - +
407D ILE* 1.3 62.4 + - - +
428D PHE* 3.5 4.9 - - - -
476D ILE* 3.2 29.6 - - + +
478D PHE* 4.1 13.9 - - + -
489D LEU* 5.1 5.8 - - + -
493D TYR* 3.8 28.9 - - + +
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Residues in contact with ILE 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548C ILE* 5.6 0.2 - - + -
340D TYR* 3.5 27.1 - - + +
341D ASP* 5.6 0.2 - - - -
406D LEU* 1.3 77.0 - - - +
408D PRO* 1.3 82.3 - - + +
421D HIS* 4.4 2.2 - - + -
424D LEU* 4.2 10.8 - - + -
425D LEU* 3.6 36.6 - - + -
428D PHE* 3.6 42.6 - - + -
476D ILE 3.1 6.3 + - - -
477D VAL* 3.4 14.0 - - + +
478D PHE* 3.2 29.5 + - - -
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Residues in contact with PRO 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340D TYR 4.1 4.7 - - - +
341D ASP* 3.6 28.5 - - + +
407D ILE* 1.3 98.5 - - + +
409D VAL* 1.3 61.2 + - - +
410D GLN 3.8 17.5 - - - +
411D THR* 5.3 2.0 - - - -
421D HIS* 2.8 31.3 + - + -
425D LEU* 4.5 0.2 - - - +
478D PHE* 3.1 33.7 - - + +
480D LYS* 4.1 0.7 - - - -
481D LEU* 3.8 16.6 - - + +
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Residues in contact with VAL 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547C PHE* 4.3 2.2 - - + -
548C ILE* 3.4 42.2 - - + +
551C GLN* 3.9 18.4 - - + +
552C ARG* 3.7 24.1 - - + +
408D PRO* 1.3 72.7 - - - +
410D GLN* 1.3 59.4 + - + +
421D HIS* 2.9 21.8 + - - -
425D LEU* 4.5 9.0 - - - +
477D VAL* 3.5 27.8 - - + -
478D PHE 2.7 15.9 + - - +
479D THR* 3.5 9.0 - - - +
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Residues in contact with GLN 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551C GLN 3.0 22.3 - - - +
552C ARG* 3.6 13.9 - - + +
554C ALA 2.6 28.9 + - - +
555C ARG* 4.5 17.1 - - - +
556C VAL* 5.1 4.0 - - - +
408D PRO* 3.8 17.3 - - - +
409D VAL* 1.3 77.3 - - + +
411D THR* 1.3 64.8 + - - +
412D GLN* 4.1 1.0 + - - +
421D HIS* 4.1 2.2 - - - -
479D THR* 2.7 27.7 + - - +
480D LYS* 3.7 36.4 - - + +
481D LEU 4.5 0.7 + - - -
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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