Contacts of the strand formed by residues 425 - 431 (chain B) in PDB entry 3P08
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 TYR 425 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420B LYS* 3.2 7.4 - - - +
421B TRP* 2.7 66.5 + + + +
422B ARG* 3.9 29.5 + - + -
424B GLN* 1.3 91.9 - - + +
426B ASP* 1.3 61.9 + - - +
427B VAL* 3.5 5.6 + - + -
461B TYR* 4.2 30.5 - + + +
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Residues in contact with ASP 426 (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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418B TYR* 2.8 36.8 + - + -
419B GLY 3.8 4.5 - - - -
420B LYS* 2.8 24.0 + - - -
424B GLN 4.1 0.6 + - - -
425B TYR* 1.3 70.2 - - - +
427B VAL* 1.3 62.0 + - - +
461B TYR* 4.1 8.3 + - - -
474B THR 4.0 0.3 - - - +
475B GLU* 4.1 0.7 - - - +
476B TYR* 3.2 34.8 + - + +
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Residues in contact with VAL 427 (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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402B LEU* 4.1 20.0 - - + -
418B TYR* 3.5 8.7 - - - -
419B GLY* 2.9 54.0 + - - +
421B TRP* 3.9 20.9 - - + -
425B TYR* 3.9 2.9 - - + +
426B ASP* 1.3 76.6 - - - +
428B ALA* 1.3 62.7 + - - +
429B ILE* 4.5 4.0 - - + -
461B TYR* 3.4 33.0 - - + -
473B ILE* 4.1 15.9 - - + -
474B THR 3.1 6.5 - - - +
476B TYR* 3.8 5.5 - - - +
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Residues in contact with ALA 428 (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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416B VAL* 4.0 21.1 - - + -
417B LYS 3.3 4.9 - - - -
427B VAL* 1.3 74.4 - - - +
429B ILE* 1.3 63.8 + - - +
430B LYS* 4.7 10.8 - - + -
472B ILE 3.7 0.7 - - - +
473B ILE* 3.4 6.1 - - - -
474B THR* 2.9 44.4 + - - +
475B GLU 4.9 1.3 - - - +
476B TYR* 4.0 14.1 - - + +
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Residues in contact with ILE 429 (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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413A PHE* 3.8 43.7 - - + +
402B LEU* 3.9 9.2 - - + -
405B LEU* 3.6 30.7 - - + -
417B LYS* 2.9 40.9 + - + +
418B TYR 4.3 6.1 - - - +
419B GLY* 4.3 5.6 - - - +
427B VAL* 4.5 6.1 - - + -
428B ALA* 1.3 77.3 - - - +
430B LYS* 1.3 65.9 + - - +
431B MET* 6.2 0.2 - - - +
471B PHE* 3.9 25.4 - - + -
472B ILE 3.6 2.5 - - - +
473B ILE* 4.1 12.1 - - + -
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Residues in contact with LYS 430 (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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428B ALA* 4.7 9.2 - - + +
429B ILE* 1.3 81.0 - - - +
431B MET* 1.3 65.0 + - - +
471B PHE* 3.2 5.5 - - - +
472B ILE* 2.8 56.1 + - + +
474B THR* 3.6 28.5 - - + +
528B LEU* 5.8 9.4 - - - +
539B ASP* 4.6 14.1 + - - +
546B VAL* 4.1 26.4 - - + +
547B LEU 5.7 0.4 - - - +
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Residues in contact with MET 431 (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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413A PHE* 4.4 19.1 - - + +
414A GLY* 4.1 31.9 - - - +
484A ASN* 6.0 4.5 - - - -
429B ILE 5.8 0.7 - - - +
430B LYS* 1.3 77.9 - - - +
432B ILE* 1.3 62.9 + - - +
469B PRO* 4.1 25.8 - - + -
470B ILE 3.6 5.4 - - - +
471B PHE* 4.4 11.0 - - + -
546B VAL* 3.3 8.4 - - - +
547B LEU* 2.8 52.5 + - + +
548B ASP* 5.3 9.4 - - + +
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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