Contacts of the strand formed by residues 448 - 455 (chain E) in PDB entry 1P8J
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 ARG 448 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445E ALA* 5.8 0.6 - - - +
446E PRO* 3.1 41.6 + - - +
447E GLN* 1.3 81.4 - - - +
449E LYS* 1.3 61.6 + - - +
478E PRO 3.3 24.5 + - - -
479E ASN* 3.7 24.9 - - - +
480E HIS 4.0 11.9 - - - +
481E ILE* 3.8 7.0 - - + -
571E TYR* 3.4 5.4 - - - -
572E GLY 2.7 38.7 + - - +
573E THR* 4.2 6.7 - - - -
574E ALA* 4.5 13.5 + - - +
4046E SO4 3.3 42.2 + - - -
276H ARG* 3.9 0.7 - - - -
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Residues in contact with LYS 449 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275E PHE* 6.0 1.4 - - - -
448E ARG* 1.3 73.7 - - - +
450E CYS* 1.3 60.4 + - - +
451E ILE* 3.9 24.2 + - + +
479E ASN* 3.0 29.2 + - - +
569E VAL* 4.0 17.7 - - + -
570E LEU 3.4 3.4 - - - -
571E TYR* 3.3 34.8 + - + -
269H LEU* 4.4 6.2 + - - +
272H GLU* 2.6 43.8 + - - +
273H ALA* 5.0 1.2 - - - +
276H ARG* 3.5 40.6 - - - +
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Residues in contact with CYS 450 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449E LYS* 1.3 74.0 - - - +
451E ILE* 1.3 65.4 + - - +
452E VAL* 4.3 9.6 - - - +
473E ALA* 3.6 9.2 - - - -
474E CYS* 2.1 58.1 - - + -
479E ASN 3.9 11.2 - - - +
481E ILE* 4.0 9.3 - - + +
568E LEU 3.6 2.3 - - - +
569E VAL* 3.4 2.8 - - - -
570E LEU* 2.7 49.6 + - + +
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Residues in contact with ILE 451 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449E LYS* 3.9 31.7 + - + +
450E CYS* 1.3 80.0 - - - +
452E VAL* 1.3 63.8 + - - +
453E GLU 5.1 0.2 - - - +
474E CYS* 4.4 2.6 - - - -
567E THR* 3.8 22.4 - - + -
568E LEU 3.8 2.5 - - - -
569E VAL* 4.5 8.3 - - + +
234H ALA* 4.2 13.5 - - + -
237H ALA* 3.7 32.5 - - + +
238H ARG* 3.7 38.3 + - + +
269H LEU* 4.1 16.4 - - + -
273H ALA* 6.3 0.2 - - + -
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Residues in contact with VAL 452 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450E CYS* 4.3 11.9 - - - +
451E ILE* 1.3 77.1 - - - +
453E GLU* 1.3 68.0 + - - +
454E ILE* 3.4 23.0 + - + +
469E LYS* 5.5 2.2 - - + -
470E ALA 6.0 0.4 - - - +
471E VAL* 4.4 22.4 - - + -
567E THR* 4.2 2.7 - - - -
568E LEU* 2.8 66.5 + - + +
570E LEU* 4.7 5.8 - - + -
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Residues in contact with GLU 453 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451E ILE* 5.2 1.1 - - + -
452E VAL* 1.3 76.7 - - - +
454E ILE* 1.3 64.1 + - - +
455E LEU 5.7 0.2 - - - +
456E VAL* 4.2 24.3 - - + +
469E LYS* 5.5 3.6 - - - +
566E PHE 4.2 3.8 - - - -
567E THR* 4.6 7.4 - - - +
175H VAL* 4.9 3.5 - - - +
178H GLN* 6.1 0.5 - - - +
232H THR* 3.1 27.1 + - - +
234H ALA* 3.4 29.3 - - + +
235H VAL* 3.9 14.8 - - - +
238H ARG* 4.5 18.2 + - - +
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Residues in contact with ILE 454 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452E VAL* 3.5 30.7 - - + +
453E GLU* 1.3 74.2 - - - +
455E LEU* 1.3 60.5 + - - +
456E VAL* 5.4 0.7 - - - -
467E VAL* 3.8 15.3 - - + +
469E LYS* 3.7 46.3 - - + +
471E VAL* 4.3 8.3 - - + -
547E TRP* 5.8 1.6 - - + -
566E PHE* 2.9 55.7 + - + +
568E LEU* 4.0 13.9 - - + -
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Residues in contact with LEU 455 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453E GLU* 5.7 0.2 - - - +
454E ILE* 1.3 84.5 + - + +
456E VAL* 1.3 64.3 + - - +
457E GLU 3.6 18.2 - - - +
459E LYS* 3.6 37.0 - - + -
467E VAL* 4.2 11.9 - - + -
563E LEU* 3.8 29.6 - - + +
564E THR 3.7 6.5 - - - +
565E LYS* 3.5 33.2 - - - +
566E PHE* 3.2 25.9 + - + +
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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