Contacts of the strand formed by residues 493 - 499 (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 SER 493 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491C GLY 4.0 2.0 + - - -
492C PHE* 1.3 74.0 - - - +
494C PHE* 1.3 61.0 + - - +
548C ILE* 3.5 1.6 - - - -
549C LYS* 2.7 65.3 + - - +
555C TYR* 5.4 0.6 + - - -
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Residues in contact with PHE 494 (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* 5.3 5.2 - - + -
484C ARG* 4.4 29.2 - - + -
487C TYR* 3.9 24.5 - + + -
492C PHE 4.2 7.4 - - - -
493C SER* 1.3 79.8 - - - +
495C LYS* 1.3 63.5 + - - +
496C LEU* 3.8 25.9 - - + +
526C PHE* 4.1 27.6 - + - -
528C GLU* 5.6 1.8 - - + -
546C ILE* 3.7 26.2 - - + -
547C GLN 3.1 15.3 - - - +
548C ILE* 4.3 1.6 - - + -
555C TYR* 5.4 2.0 - - - -
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Residues in contact with LYS 495 (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* 1.3 76.5 - - - +
496C LEU* 1.3 68.3 + - - +
497C ASN* 4.5 5.8 - - + +
529C LYS 5.2 5.6 - - - +
531C GLU* 5.4 9.0 + - - +
545C ASP 3.7 0.5 - - - +
546C ILE* 3.4 4.3 - - - -
547C GLN* 2.9 61.4 + - + +
555C TYR* 3.8 38.7 - - + +
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Residues in contact with LEU 496 (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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480C LEU* 4.0 21.1 - - + -
483C LEU* 4.7 0.4 - - + -
494C PHE* 3.8 22.4 - - + +
495C LYS* 1.3 78.8 - - - +
497C ASN* 1.3 63.0 + - - +
523C LEU* 4.6 9.4 - - + -
526C PHE* 3.9 24.9 - - + -
528C GLU* 4.0 18.4 - - + +
529C LYS 4.3 10.7 + - - +
530C TRP* 3.3 17.1 - - + -
531C GLU* 2.9 24.4 + - - +
544C ILE* 4.6 7.9 - - + -
545C ASP 3.3 6.7 - - - +
546C ILE* 3.5 26.0 - - + -
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Residues in contact with ASN 497 (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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495C LYS* 4.5 6.5 - - + +
496C LEU* 1.3 77.5 - - - +
498C LEU* 1.3 61.9 + - - +
499C SER* 3.7 8.9 + - - -
523C LEU* 5.5 0.7 - - - -
531C GLU* 3.6 18.8 - - + +
533C ASN* 3.5 25.7 + - - +
543C LYS 3.9 0.2 - - - +
544C ILE* 3.4 5.6 - - - +
545C ASP* 2.9 70.8 + - - +
546C ILE* 5.0 0.2 - - - -
547C GLN* 5.3 5.5 + - - +
557C GLN* 4.5 4.0 + - - +
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Residues in contact with LEU 498 (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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497C ASN* 1.3 71.0 - - - +
499C SER* 1.3 71.3 + - - +
500C THR* 3.7 25.5 + - + -
516C GLU* 4.9 2.7 - - + +
519C LEU* 4.3 19.3 - - + -
520C GLU* 3.7 35.4 - - + +
523C LEU* 3.7 29.8 - - + +
530C TRP* 3.7 18.7 - - + -
531C GLU 3.4 7.2 + - - +
532C LEU* 3.8 6.8 - - + +
533C ASN* 2.8 30.5 + - - +
542C PRO* 4.9 1.6 - - + -
543C LYS 3.6 8.1 - - - +
544C ILE* 4.3 7.0 - - + -
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Residues in contact with SER 499 (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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497C ASN* 3.7 12.8 + - - -
498C LEU* 1.3 74.1 - - - +
500C THR* 1.3 62.0 + - - +
533C ASN* 3.2 11.6 - - - +
536C ASP* 3.6 18.3 + - - +
537C GLY* 3.5 17.3 - - - -
542C PRO* 3.4 7.4 - - - +
543C LYS* 2.9 54.9 + - - +
545C ASP* 4.6 2.8 + - - -
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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