Contacts of the strand formed by residues 462 - 467 (chain A) 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 ASP 462 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A TYR* 4.1 2.9 + - - -
412A ASN* 3.3 36.4 + - - +
413A CYS* 5.0 1.5 - - - -
416A HIS* 4.6 0.4 - - - -
434A LEU 4.0 0.2 - - - +
435A ALA* 3.2 3.6 - - - +
436A ASP* 2.6 47.7 + - - +
437A PHE* 5.4 0.2 - - - -
460A GLN* 3.8 26.1 + - + +
461A ASP* 1.3 74.5 - - - +
463A ALA* 1.3 68.3 + - - +
464A HIS* 3.3 24.2 + - - -
590A HIS* 5.4 1.6 - - - +
591A ARG* 3.8 9.5 + - - +
592A ALA* 4.9 1.5 - - - +
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Residues in contact with ALA 463 (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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364A TYR* 4.2 3.1 - - - +
369A PHE* 3.6 29.2 - - + -
434A LEU 3.2 9.4 - - - +
435A ALA* 4.1 3.1 - - - -
462A ASP* 1.3 76.3 + - - +
464A HIS* 1.3 67.7 + - - +
589A VAL 3.3 0.2 - - - +
590A HIS* 3.8 0.3 - - - -
591A ARG* 2.8 61.3 + - + +
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Residues in contact with HIS 464 (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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413A CYS* 3.0 35.6 - - + -
416A HIS* 3.0 29.3 + - + +
417A CYS* 6.6 0.2 - - - -
432A LEU 3.4 4.5 - - - +
433A ARG* 4.5 0.2 - - - -
434A LEU* 2.9 32.3 + - - +
462A ASP* 3.3 30.4 + - - -
463A ALA* 1.3 72.8 - - - +
465A ILE* 1.3 62.9 + - - +
466A PHE* 3.9 21.0 + + + -
588A ILE* 4.0 12.1 - - + -
589A VAL 3.2 3.8 - - - +
590A HIS* 2.9 44.9 + + - -
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Residues in contact with ILE 465 (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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369A PHE* 4.5 8.7 - - + -
431A PRO* 4.0 12.6 - - + -
432A LEU 3.6 2.5 - - - -
433A ARG* 3.8 18.4 - - + +
464A HIS* 1.3 74.7 - - - +
466A PHE* 1.3 63.5 + - - +
467A CYS* 3.8 6.4 + - + -
475A GLU* 3.3 39.9 - - + +
479A CYS* 3.8 29.6 - - - -
587A VAL 3.2 7.1 - - - +
588A ILE* 3.6 1.6 - - - -
589A VAL* 2.9 46.9 + - + +
591A ARG* 3.9 20.0 - - - -
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Residues in contact with PHE 466 (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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416A HIS* 3.9 24.9 - - + -
417A CYS* 4.5 2.9 - - - -
420A PHE* 3.5 45.8 - + + -
430A LEU* 3.4 8.0 - - + +
431A PRO* 3.2 3.2 - - - +
432A LEU* 2.9 60.8 + - + +
434A LEU* 4.1 20.6 - - + -
464A HIS* 4.0 26.5 - + + -
465A ILE* 1.3 70.8 - - - +
467A CYS* 1.3 58.7 + - - +
573A LEU* 4.1 9.6 - - + -
586A PRO* 4.7 8.1 - - + -
587A VAL 3.7 2.9 - - - -
588A ILE* 3.7 37.0 - - + -
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Residues in contact with CYS 467 (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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430A LEU* 4.4 4.3 - - - -
431A PRO* 3.9 16.2 - - + -
465A ILE* 4.4 2.5 - - + -
466A PHE* 1.3 74.1 - - - +
468A ALA* 1.3 73.4 + - - +
471A GLN* 3.3 16.8 - - + +
472A ILE* 3.9 28.0 - - - -
475A GLU* 4.4 9.6 - - + -
586A PRO* 3.5 8.1 - - - +
587A VAL* 2.8 36.9 + - - -
589A VAL* 4.5 15.0 - - - -
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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