Contacts of the strand formed by residues 403 - 410 (chain B) in PDB entry 1N8T
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B GLN* 4.2 0.4 - - - -
336B ALA* 3.5 19.3 - - + -
338B LEU* 4.1 9.6 - - + -
394B ILE* 4.0 30.5 - - - -
401B ILE* 3.1 22.8 + - - -
402B PRO* 1.3 75.9 - - - +
404B ASP* 1.3 65.4 + - - +
405B PHE* 3.4 24.9 - - + -
435B LEU* 5.1 0.7 - - - -
472B PRO 3.6 6.1 + - - -
473B THR* 3.3 10.0 - - + +
474B ASN* 2.9 26.3 + - - +
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Residues in contact with ASP 404 (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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319B LEU* 4.8 3.1 - - - +
335B GLN* 4.1 13.7 + - - +
336B ALA 2.9 14.7 + - - +
337B VAL* 4.5 6.6 - - + +
338B LEU* 2.8 29.8 + - - +
403B CYS* 1.3 75.4 - - - +
405B PHE* 1.3 61.5 + - - +
406B LEU* 3.4 7.5 - - + +
474B ASN* 2.8 36.5 - - + +
476B ILE* 4.4 5.6 - - + +
493B TYR* 2.7 39.3 + - - +
496B LYS* 4.7 6.9 + - - -
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Residues in contact with PHE 405 (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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338B LEU* 3.5 18.4 - - + -
340B TYR* 3.7 26.7 - + - -
391B TYR* 3.6 22.9 - + - -
394B ILE* 6.0 0.9 - - + -
403B CYS* 3.4 30.1 - - + -
404B ASP* 1.3 72.6 - - - +
406B LEU* 1.3 61.0 + - - +
428B PHE* 3.4 23.7 - + + -
431B GLN* 3.7 15.3 - - + -
432B THR* 3.6 22.2 - - + -
435B LEU* 3.8 18.6 - - + -
473B THR* 3.7 19.7 - - + -
474B ASN 2.8 14.4 + - - +
475B SER* 3.4 0.8 - - - +
476B ILE* 2.8 26.7 + - - +
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Residues in contact with LEU 406 (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 VAL* 4.2 13.0 - - + -
338B LEU 3.1 19.5 + - - +
339B PRO* 4.1 11.9 - - + -
340B TYR* 2.6 34.0 + - - +
341B ASP* 5.4 0.4 - - - +
344B LEU* 5.9 1.8 - - + -
347B PHE* 4.2 20.0 - - + -
404B ASP* 3.4 22.9 - - + +
405B PHE* 1.3 77.2 - - - +
407B ILE* 1.3 62.0 + - - +
428B PHE* 3.6 2.5 - - - -
476B ILE* 3.3 29.2 - - + +
478B PHE* 4.1 12.6 - - + -
489B LEU* 4.9 9.2 - - + -
492B MET* 5.6 0.2 - - + -
493B TYR* 3.9 23.3 - - + +
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Residues in contact with ILE 407 (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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340B TYR* 3.5 29.2 - - + +
341B ASP* 5.6 0.4 - - - -
406B LEU* 1.3 76.2 - - - +
408B PRO* 1.3 88.7 - - + +
421B HIS* 4.6 1.6 - - + -
424B LEU* 4.1 15.9 - - + -
425B LEU* 3.9 26.5 - - + -
428B PHE* 3.5 42.8 - - + -
476B ILE 3.0 4.8 + - - -
477B VAL* 3.3 15.6 - - + +
478B PHE* 3.1 31.5 + - - -
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Residues in contact with PRO 408 (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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340B TYR 4.0 9.6 - - - +
341B ASP* 3.5 25.1 - - + +
407B ILE* 1.3 105.0 - - + +
409B VAL* 1.3 63.6 + - - +
410B GLN 3.6 17.9 - - - +
411B THR* 5.7 1.1 - - - -
421B HIS* 3.1 20.8 + - + -
425B LEU* 4.2 0.9 - - - +
478B PHE* 3.2 27.8 - - + +
480B LYS* 4.0 0.7 - - - -
481B LEU* 3.9 17.9 - - + +
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Residues in contact with VAL 409 (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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547A PHE* 4.1 7.2 - - + -
548A ILE* 3.7 37.0 - - + +
551A GLN* 4.0 19.5 - - + +
552A ARG* 3.7 25.8 - - + +
407B ILE 3.9 0.6 + - - -
408B PRO* 1.3 71.6 - - - +
410B GLN* 1.3 58.2 + - + +
421B HIS* 2.8 23.0 + - - -
425B LEU* 4.3 11.1 - - + +
477B VAL* 3.7 20.4 - - + -
478B PHE 2.8 19.1 + - - +
479B THR* 3.5 8.1 - - - +
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Residues in contact with GLN 410 (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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551A GLN 3.1 23.4 + - - +
552A ARG* 3.7 13.7 + - - +
554A ALA 2.9 31.6 + - - +
556A ILE* 5.2 3.1 - - - +
408B PRO* 3.6 16.9 - - - +
409B VAL* 1.3 79.9 - - + +
411B THR* 1.3 64.7 + - - +
412B GLN* 4.1 1.4 + - - +
421B HIS* 4.1 1.8 - - - -
479B THR* 2.9 27.8 + - - +
480B LYS* 3.5 39.7 + - + +
481B 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