Contacts of the strand formed by residues 448 - 455 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445F ALA* 5.6 2.2 - - - +
446F PRO* 3.2 42.1 + - - +
447F GLN* 1.3 82.5 + - - +
449F LYS* 1.3 61.5 + - - +
478F PRO* 3.4 23.8 + - - +
479F ASN* 3.7 13.9 - - - +
480F HIS 3.9 13.7 - - - +
481F ILE* 3.7 16.6 - - + -
571F TYR* 3.4 5.5 - - - -
572F GLY 2.7 39.2 + - - +
573F THR* 4.1 7.4 - - - -
574F ALA* 4.4 12.2 - - - +
4057F SO4 3.2 37.9 + - - -
245G ASN* 5.5 0.6 + - - -
276G ARG* 3.9 0.7 - - - -
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Residues in contact with LYS 449 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275F PHE* 6.1 0.6 - - - -
448F ARG* 1.3 75.2 - - - +
450F CYS* 1.3 59.7 + - - +
451F ILE* 3.9 24.0 + - + +
479F ASN* 3.0 28.4 + - - +
569F VAL* 4.0 18.4 - - + -
570F LEU 3.3 3.1 - - - -
571F TYR* 3.4 33.3 + - + -
269G LEU* 4.3 8.0 + - - +
272G GLU* 2.6 46.4 + - - +
273G ALA* 4.9 1.0 - - - +
276G ARG* 3.7 36.7 - - - +
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Residues in contact with CYS 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449F LYS* 1.3 73.0 - - - +
451F ILE* 1.3 65.0 + - - +
452F VAL* 3.9 6.9 + - - +
473F ALA* 3.4 11.0 - - - -
474F CYS* 2.1 59.7 - - - -
479F ASN 3.8 11.9 - - - +
481F ILE* 4.1 8.0 - - + +
568F LEU 3.6 1.6 - - - +
569F VAL* 3.5 2.5 - - - -
570F LEU* 2.7 53.1 + - + +
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Residues in contact with ILE 451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449F LYS* 3.9 32.9 + - + +
450F CYS* 1.3 81.2 - - - +
452F VAL* 1.3 65.1 + - - +
474F CYS* 4.3 1.9 - - - -
567F THR* 3.9 14.1 - - + -
568F LEU 3.8 3.1 - - - -
569F VAL* 4.5 8.5 - - + +
234G ALA* 3.8 28.3 - - + -
237G ALA* 3.7 32.5 - - + +
238G ARG* 3.5 40.1 + - + +
269G LEU* 4.0 11.0 - - + -
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Residues in contact with VAL 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450F CYS* 4.3 14.4 - - - +
451F ILE* 1.3 76.9 - - - +
453F GLU* 1.3 68.2 + - - +
454F ILE* 3.4 21.3 + - + -
469F LYS* 5.5 4.3 - - + -
471F VAL* 4.5 22.9 - - + -
567F THR* 3.6 3.3 - - - -
568F LEU* 2.9 65.4 + - + +
570F LEU* 4.8 3.1 - - + -
238G ARG* 5.6 0.2 - - - +
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Residues in contact with GLU 453 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451F ILE* 5.3 0.2 - - + -
452F VAL* 1.3 75.6 - - - +
454F ILE* 1.3 64.0 - - - +
455F LEU 4.5 7.6 - - - +
469F LYS* 5.0 6.2 - - - -
566F PHE 4.2 3.1 - - - -
567F THR* 4.6 7.9 - - - +
175G VAL* 5.1 4.3 - - - +
178G GLN* 4.3 21.6 + - - +
232G THR* 2.8 32.1 + - - +
234G ALA* 3.4 29.7 - - + +
235G VAL* 3.8 15.9 + - - +
238G ARG* 4.9 11.1 + - - +
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Residues in contact with ILE 454 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452F VAL* 3.6 29.6 - - + +
453F GLU* 1.3 72.8 - - - +
455F LEU* 1.3 64.1 + - - +
456F VAL* 3.8 2.8 + - - +
467F VAL* 3.7 19.0 - - + +
469F LYS* 3.7 44.2 + - + +
471F VAL* 4.4 7.9 - - + -
547F TRP* 5.8 1.8 - - + -
566F PHE* 2.9 62.7 + - + +
568F LEU* 4.0 14.8 - - + -
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Residues in contact with LEU 455 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453F GLU* 4.5 9.7 - - - +
454F ILE* 1.3 81.9 - - - +
456F VAL* 1.3 63.1 + - - +
457F GLU 3.8 14.4 - - - +
459F LYS* 4.1 23.8 - - + -
467F VAL* 4.2 28.0 - - + -
563F LEU* 3.6 34.3 - - + +
564F THR 3.7 6.7 - - - +
565F LYS* 3.7 21.8 - - - +
566F PHE* 3.7 21.7 + - + +
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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