Contacts of the strand formed by residues 499 - 503 (chain A) in PDB entry 1P0P
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 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A PHE* 4.6 1.0 + - - +
491A PRO* 3.8 35.9 - - + +
492A VAL 4.4 7.2 - - - +
493A PHE* 3.3 30.6 + - - +
494A LYS 4.8 0.6 - - - +
497A GLU* 4.0 38.1 + - + +
498A GLN* 1.3 76.5 - - - +
500A TYR* 1.3 58.8 + - - +
510A ILE* 4.2 11.0 - - + -
511A MET 3.2 9.4 - - - +
512A THR* 3.6 19.5 - - + -
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Residues in contact with TYR 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A LEU* 6.0 0.4 - - + -
418A PHE* 3.3 33.7 - + + +
420A TYR* 3.7 34.4 - + + -
490A TRP* 4.9 2.5 - - - +
491A PRO* 5.2 1.8 - - - -
493A PHE* 5.0 2.9 - + + -
498A GLN 3.9 9.4 - - - +
499A LYS* 1.3 74.3 - - - +
501A LEU* 1.3 64.6 + - - +
502A THR* 3.8 10.1 - - + -
510A ILE* 3.6 8.2 - - - +
511A MET* 2.9 75.4 + - + +
512A THR 3.5 4.9 + - - -
514A LEU* 3.5 50.6 - - + +
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Residues in contact with LEU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A PHE 2.8 8.9 + - - -
419A TYR* 3.1 6.5 - - + +
420A TYR 2.8 25.0 + - - -
470A ARG* 4.0 22.7 - - - +
488A THR* 4.1 4.9 - - + -
489A SER 5.0 0.2 - - - +
490A TRP* 3.5 54.0 - - + +
500A TYR* 1.3 74.7 - - - +
502A THR* 1.3 70.0 + - - +
503A LEU* 4.1 11.4 - - + -
508A THR* 3.7 22.2 - - - +
509A ARG 3.2 16.2 - - - +
510A ILE* 3.6 18.8 - - + -
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Residues in contact with THR 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A TYR* 3.4 8.1 - - + -
422A GLU* 3.8 28.6 + - - +
500A TYR* 3.8 15.9 - - + +
501A LEU* 1.3 77.5 - - - +
503A LEU* 1.3 61.6 + - - +
504A ASN* 3.5 9.2 + - - -
508A THR* 3.5 23.7 - - - -
509A ARG* 2.9 32.0 + - + +
511A MET* 3.7 32.3 - - + -
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Residues in contact with LEU 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A TYR* 3.8 38.6 - - + -
420A TYR 3.0 9.1 + - - +
421A PHE* 4.0 18.2 - - + -
422A GLU* 3.0 24.6 + - - +
423A HIS* 3.9 2.9 + - - +
463A LEU* 4.6 11.7 - - + -
466A SER* 6.0 1.1 - - - +
467A ILE* 4.3 22.2 - - + -
470A ARG* 4.7 13.2 - - - +
471A TRP* 4.2 17.7 - - + -
490A TRP* 5.1 0.7 - - + -
501A LEU* 4.1 21.1 - - + +
502A THR* 1.3 77.4 - - - +
504A ASN* 1.3 63.0 + - - +
508A THR* 5.3 5.8 - - + -
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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