Contacts of the strand formed by residues 443 - 449 (chain B) in PDB entry 1JS6
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 GLN 443 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399B GLU* 4.2 3.8 - - - +
401B CYS* 5.3 5.3 - - - +
412B ARG* 3.2 46.7 + - - +
417B ASP* 3.5 12.1 - - - +
439B ARG* 3.2 5.9 - - - -
440B LEU* 3.1 37.3 + - - +
441B ARG* 3.0 6.8 + - - +
442B GLY* 1.3 76.2 - - - +
444B PHE* 1.3 63.1 + - - +
445B VAL* 3.4 7.6 + - + +
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Residues in contact with PHE 444 (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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412B ARG* 3.1 26.5 + - - +
417B ASP* 2.8 34.8 + - + +
420B ASN* 3.6 25.3 - - + +
421B GLU* 3.5 44.4 - - + -
424B LEU* 3.5 15.5 - - + -
437B PRO* 3.5 31.2 - - + -
438B CYS 4.0 4.5 - - - -
439B ARG* 4.7 10.3 - - + -
442B GLY 3.7 1.0 + - - -
443B GLN* 1.3 69.6 - - - +
445B VAL* 1.3 58.9 + - - +
446B LEU* 3.7 14.8 - - + -
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Residues in contact with VAL 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B CYS* 3.9 19.3 - - + -
410B CYS* 3.6 27.6 - - + -
411B PHE 3.5 14.4 - - - +
412B ARG* 4.4 3.6 - - - -
437B PRO* 3.1 7.3 - - - +
438B CYS* 2.9 44.0 + - - +
440B LEU* 3.8 20.4 - - + -
443B GLN* 3.6 17.5 - - + +
444B PHE* 1.3 80.9 - - - +
446B LEU* 1.3 76.4 + - - +
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Residues in contact with LEU 446 (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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410B CYS* 3.4 4.7 - - - -
411B PHE* 2.9 73.3 + - + +
412B ARG* 5.3 0.4 - - - -
420B ASN* 4.0 23.6 - - + +
423B LEU* 4.3 13.0 - - + -
424B LEU* 4.4 20.9 - - + +
427B ILE* 4.0 23.3 - - + -
435B LEU* 4.5 5.2 - - + -
436B VAL 4.3 2.7 - - - +
437B PRO* 4.3 0.2 - - - -
444B PHE* 3.7 25.4 - - + -
445B VAL* 1.3 81.3 - - - +
447B ARG* 1.3 61.4 + - - +
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Residues in contact with ARG 447 (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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77B PHE 3.9 4.9 + - - +
78B ALA* 4.2 2.4 - - - +
79B TYR* 2.8 50.2 + - - +
80B PHE* 3.9 11.5 - - - -
246B THR* 3.1 27.0 + - - -
247B SER 3.4 13.5 + - - +
408B LEU* 3.7 22.2 - - + +
409B VAL 3.6 3.6 - - - -
410B CYS* 4.2 7.6 - - - -
411B PHE* 4.4 1.6 - - - -
435B LEU* 3.5 22.7 - - - +
436B VAL* 3.0 31.9 + - - +
437B PRO 4.2 3.6 - - - -
438B CYS* 3.8 34.1 - - + -
446B LEU* 1.3 74.3 - - - +
448B PHE* 1.3 61.0 + - - +
449B ALA* 4.1 2.0 - - - +
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Residues in contact with PHE 448 (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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77B PHE* 3.2 56.3 - + + -
388B PHE* 3.5 69.5 - + + -
407B GLY 3.7 1.2 - - - +
408B LEU* 3.3 3.2 - - - +
409B VAL* 2.8 41.7 + - + +
411B PHE* 4.3 2.9 - - + -
435B LEU* 4.2 13.2 - - + -
447B ARG* 1.3 72.9 - - - +
449B ALA* 1.3 59.6 + - - +
450B ILE* 3.8 22.7 - - + -
460B VAL* 4.4 9.0 - - + -
463B ALA* 4.2 12.8 - - + -
467B ILE* 4.6 4.7 - - + -
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Residues in contact with ALA 449 (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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77B PHE* 3.1 41.7 + - - +
78B ALA 4.2 3.8 - - - +
79B TYR 3.3 26.2 - - - +
80B PHE* 4.8 6.7 - - + -
81B PRO* 5.3 0.2 - - + -
407B GLY 3.5 6.1 - - - +
408B LEU* 3.9 12.1 - - + -
447B ARG* 4.5 0.7 - - - +
448B PHE* 1.3 75.9 - - - +
450B ILE* 1.3 67.5 + - - +
451B CYS* 3.3 7.2 + - - -
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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