Contacts of the strand formed by residues 463 - 471 (chain C) 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 LYS 463 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461C ILE* 3.2 0.9 + - - -
462C GLY* 1.3 73.5 - - - -
464C ARG* 1.3 64.9 + - + +
552C GLU* 3.6 2.0 - - - +
553C ASN* 2.9 54.9 + - + +
554C THR 4.8 0.6 - - - -
555C SER 2.6 30.7 + - - +
556C GLU* 3.7 15.7 + - - +
557C ALA 5.3 0.6 + - - +
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Residues in contact with ARG 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C ASP 4.9 0.9 - - - +
461C ILE 3.1 10.7 + - - +
463C LYS* 1.3 87.1 + - + +
465C LEU* 1.3 66.4 + - - +
466C GLU* 3.8 32.5 + - - +
550C GLU* 3.5 34.5 + - - +
551C ILE 3.4 11.9 - - - +
552C GLU* 4.3 16.0 + - + +
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Residues in contact with LEU 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459C LYS* 4.0 32.5 - - + -
460C ASP 4.1 13.5 - - - +
461C ILE* 4.0 20.0 - - + +
464C ARG* 1.3 82.0 + - - +
466C GLU* 1.3 80.3 + - - +
467C VAL* 4.2 12.1 - - + -
549C LEU 3.8 0.6 - - - +
550C GLU* 3.6 3.3 - - - +
551C ILE* 2.8 46.2 + - + +
563C LEU* 4.1 29.2 - - + -
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Residues in contact with GLU 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459C LYS* 5.8 0.5 - - - +
464C ARG* 3.8 27.7 + - - +
465C LEU* 1.3 85.9 - - - +
467C VAL* 1.3 64.3 + - - +
468C ARG* 2.7 47.8 + - + +
548C VAL* 3.7 19.5 - - + +
549C LEU 3.3 3.8 - - - +
550C GLU* 4.5 7.6 - - + +
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Residues in contact with VAL 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454C ILE* 3.7 30.5 - - + +
455C LEU* 3.9 28.7 - - + -
459C LYS* 4.3 10.5 - - + +
465C LEU* 4.2 20.2 - - + -
466C GLU* 1.3 76.5 - - - +
468C ARG* 1.3 66.6 + - - +
547C TRP 3.7 1.0 - - - +
548C VAL* 3.3 3.6 - - - -
549C LEU* 2.8 51.2 + - + +
563C LEU* 4.3 9.2 - - + -
566C PHE* 4.3 4.1 - - + -
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Residues in contact with ARG 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466C GLU* 2.7 39.2 + - - +
467C VAL* 1.3 78.2 - - - +
469C LYS* 1.3 67.0 + - - +
506C ILE* 6.3 0.6 - - - +
546C GLU* 2.4 46.1 + - - +
547C TRP 3.4 3.8 - - - -
548C VAL* 3.4 27.5 - - + +
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Residues in contact with LYS 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452C VAL* 4.6 5.8 - - + +
453C GLU 3.1 26.3 + - - -
454C ILE* 3.6 49.0 + - + +
467C VAL 4.3 0.2 + - - -
468C ARG* 1.3 77.8 - - - +
470C ALA* 1.3 76.5 + - - +
471C VAL* 3.5 6.6 + - + +
546C GLU* 4.2 5.3 - - - +
547C TRP* 2.8 34.1 + - + +
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Residues in contact with ALA 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469C LYS* 1.3 88.4 - - - +
471C VAL* 1.3 60.7 + - - +
472C THR* 4.3 2.9 + - + +
545C GLY 3.6 7.2 - - - +
546C GLU* 4.1 9.7 + - + +
509E MET* 5.1 16.2 - - + -
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Residues in contact with VAL 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452C VAL* 4.4 23.8 - - + -
454C ILE* 4.4 14.8 - - + -
469C LYS* 3.7 9.0 - - + +
470C ALA* 1.3 78.1 - - - +
472C THR* 1.3 64.3 + - - +
473C ALA* 3.3 20.4 - - + +
543C PRO 4.4 0.9 - - - +
544C ALA* 3.5 3.5 - - - +
545C GLY* 2.7 38.8 + - - +
547C TRP* 3.4 28.9 - - + +
568C LEU* 4.2 10.1 - - + -
570C LEU* 4.4 9.9 - - + -
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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