Contacts of the strand formed by residues 543 - 549 (chain C) in PDB entry 4P3N
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 543 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498C LEU* 3.6 4.8 - - - +
499C SER* 2.9 47.5 + - - +
519C LEU* 5.3 1.3 - - - -
536C ASP 4.2 17.5 - - - -
537C GLY* 4.7 1.8 - - - -
538C ALA* 4.5 14.1 - - - +
540C TYR* 5.6 1.4 + - - -
542C PRO* 1.3 71.8 - - - +
544C ILE* 1.3 64.0 + - - +
545C ASP* 3.3 32.8 + - - +
560C THR* 4.4 2.9 + - - +
561C ILE 3.3 7.4 - - - +
562C GLN* 2.4 40.7 + - - +
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Residues in contact with ILE 544 (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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476C ILE* 4.1 14.4 - - + -
480C LEU* 4.9 1.6 - - + -
496C LEU* 4.6 14.8 - - + -
497C ASN 3.4 7.9 - - - +
498C LEU* 4.3 8.3 - - + -
519C LEU* 3.9 28.7 - - + +
523C LEU* 3.6 38.6 - - + -
543C LYS* 1.3 78.5 - - - +
545C ASP* 1.3 70.6 + - - +
546C ILE* 3.6 14.3 - - + +
560C THR* 3.4 5.4 + - - -
561C ILE* 2.9 49.5 + - + +
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Residues in contact with ASP 545 (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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496C LEU* 3.3 4.7 - - - -
497C ASN* 2.9 57.7 + - - +
499C SER* 4.6 2.4 + - - -
543C LYS* 3.3 27.6 + - - +
544C ILE* 1.3 73.1 - - - +
546C ILE* 1.3 63.2 + - - +
557C GLN* 3.5 29.9 + - - +
559C ALA 3.8 2.1 - - - +
560C THR* 2.9 26.3 + - - -
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Residues in contact with ILE 546 (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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483C LEU* 3.6 22.0 - - + -
487C TYR* 4.0 17.9 - - + -
494C PHE* 3.7 35.9 - - + -
495C LYS 3.4 4.0 - - - +
496C LEU* 3.5 20.9 - - + -
544C ILE* 3.6 19.1 - - + +
545C ASP* 1.3 80.2 - - - +
547C GLN* 1.3 65.4 + - - +
548C ILE* 4.2 0.5 + - - +
557C GLN* 3.9 3.5 - - - +
558C CYS* 3.5 8.0 + - - +
559C ALA* 3.1 46.1 + - + +
561C ILE* 4.1 12.8 - - + -
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Residues in contact with GLN 547 (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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494C PHE* 3.1 4.8 - - - -
495C LYS* 2.9 66.1 + - + +
497C ASN* 5.3 4.8 + - - +
545C ASP 4.3 0.2 - - - -
546C ILE* 1.3 73.0 - - - +
548C ILE* 1.3 62.2 + - - +
555C TYR* 4.2 23.7 + - + +
556C HIS* 3.2 10.9 - - - +
557C GLN* 3.3 38.5 + - - +
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Residues in contact with ILE 548 (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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487C TYR* 3.5 47.1 - - + +
492C PHE* 3.7 36.3 - - + -
493C SER 3.5 4.5 - - - +
494C PHE* 4.3 2.9 - - + -
546C ILE* 5.0 0.9 - - + +
547C GLN* 1.3 77.4 - - - +
549C LYS* 1.3 59.0 + - - +
550C ASP 5.9 0.2 - - - +
554C ARG 3.5 1.2 - - - +
555C TYR* 3.2 8.4 - - - -
556C HIS* 2.9 53.3 + - + +
558C CYS* 3.8 23.3 - - + -
600C MET* 4.1 8.5 - - + -
603C ILE* 4.4 9.0 - - + -
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Residues in contact with LYS 549 (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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491C GLY 5.0 0.7 - - - +
492C PHE* 3.5 17.3 - - - -
493C SER* 2.7 41.1 + - - +
548C ILE* 1.3 71.5 - - - +
550C ASP* 1.3 76.8 + - - +
553C GLY* 3.9 21.5 - - - -
554C ARG 3.5 3.6 - - - -
555C TYR* 3.5 35.7 - - + +
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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