Contacts of the strand formed by residues 479 - 483 (chain E) in PDB entry 3HN3
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 VAL 479 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445E MET* 4.6 0.7 - - - -
446E TRP* 3.4 9.0 - - + +
448E VAL* 3.8 27.6 - - + -
467E ILE* 3.9 29.8 - - + -
470E THR* 3.8 23.1 - - + -
471E LYS* 3.8 28.0 - - + +
474E ASP 5.8 0.2 - - - +
477E ARG 4.1 6.5 - - - +
478E PRO* 1.3 80.2 - - - +
480E THR* 1.3 66.3 + - - +
496E VAL* 3.8 2.9 - - - -
497E ASP* 2.9 35.9 + - - +
498E VAL 4.1 0.2 + - - -
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Residues in contact with THR 480 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404E ILE* 4.6 2.0 - - + -
445E MET* 3.8 28.0 - - + -
446E TRP 2.9 17.2 + - - +
447E SER* 3.2 16.8 - - - -
448E VAL* 2.9 28.9 + - - +
467E ILE* 5.0 0.9 - - - -
479E VAL* 1.3 78.2 - - - +
481E PHE* 1.3 75.6 + - - +
482E VAL* 5.2 0.4 - - + -
496E VAL* 3.9 10.9 - - - +
498E VAL 2.6 26.2 + - - -
500E CYS* 3.5 15.5 - - - -
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Residues in contact with PHE 481 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447E SER* 3.9 4.0 - - - -
448E VAL* 3.9 8.3 - - + -
449E ALA* 3.5 23.1 - - + +
452E PRO* 3.7 28.9 - - + -
454E SER* 3.9 4.7 - - - -
463E LEU* 3.9 18.8 - - + -
467E ILE* 4.5 7.9 - - + -
480E THR* 1.3 84.8 + - - +
482E VAL* 1.3 72.2 + - - +
483E SER* 3.8 22.6 + - - -
490E ASP* 3.6 27.4 - - - -
492E GLY* 3.6 26.0 - - - -
493E ALA* 4.1 1.6 - - - -
496E VAL* 3.4 19.8 - - + +
499E ILE* 5.5 0.2 - - - -
500E CYS* 3.9 9.0 + - - +
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Residues in contact with VAL 482 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382E ARG* 3.4 29.2 - - - +
404E ILE* 5.8 0.4 - - + -
406E GLU* 3.7 9.6 - - - +
447E SER* 3.9 6.1 - - - +
449E ALA 2.9 10.2 + - - +
450E ASN* 3.3 22.9 - - - +
451E GLU* 2.7 31.5 + - - -
480E THR* 5.2 0.2 - - + -
481E PHE* 1.3 79.9 - - - +
483E SER* 1.3 56.1 + - - +
500E CYS* 3.7 19.7 - - + -
502E ASN* 3.1 29.6 - - - +
539E SER* 3.3 12.6 - - - +
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Residues in contact with SER 483 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E MPD 3.6 2.4 - - - +
451E GLU* 4.6 4.7 - - - +
452E PRO* 5.1 0.4 - - - -
454E SER* 3.8 2.5 + - - -
481E PHE* 3.8 14.1 - - - -
482E VAL* 1.3 75.3 - - - +
484E ASN* 1.3 58.6 + - - +
485E SER* 3.0 20.7 + - - -
490E ASP* 2.6 28.1 + - - -
499E ILE* 6.2 0.9 - - - -
500E CYS 2.8 15.6 + - - -
501E LEU* 3.5 13.8 - - - -
502E ASN* 2.9 26.0 + - - +
528E TRP* 4.4 1.6 - - - -
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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