Contacts of the strand formed by residues 443 - 450 (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 443 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327E ARG* 3.0 13.7 + - - -
393E MET* 4.2 10.3 - - - -
403E VAL* 3.5 15.5 - - + +
405E ASP* 3.7 40.4 - - + +
437E ASP* 4.4 4.7 - - + +
440E HIS* 3.1 27.3 + - + +
442E ALA* 1.3 74.7 - - + +
444E VAL* 1.3 58.8 + - - +
445E MET 4.1 7.9 - - - +
446E TRP* 4.0 11.2 - - + -
477E ARG* 2.8 42.4 + - - +
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Residues in contact with VAL 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288E TRP* 5.4 0.4 - - + -
327E ARG* 4.5 2.0 - - - +
329E VAL* 3.6 28.1 - - + +
336E PHE* 3.7 9.0 - - + -
338E ILE* 4.3 9.9 - - + -
345E PHE* 3.8 33.4 - - + -
402E VAL* 3.8 22.7 - - + -
403E VAL 2.9 15.5 + - - +
441E PRO 4.1 6.5 - - - +
442E ALA 3.4 14.8 - - - +
443E VAL* 1.3 75.8 - - - +
445E MET* 1.3 63.1 + - + +
477E ARG* 4.2 5.3 - - - +
478E PRO* 3.1 25.2 - - - +
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Residues in contact with MET 445 (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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336E PHE* 4.2 8.7 - - + -
345E PHE* 4.7 0.7 - - + -
403E VAL 3.6 1.1 + - - +
404E ILE* 3.4 37.6 - - + -
405E ASP* 2.9 25.1 + - - -
443E VAL* 3.7 6.4 - - - +
444E VAL* 1.3 83.6 - - + +
446E TRP* 1.3 75.3 + - - +
477E ARG* 4.4 2.2 - - - +
478E PRO* 3.4 26.9 - - + +
479E VAL 4.6 0.4 - - - -
480E THR* 3.8 23.3 - - + -
498E VAL* 3.9 31.9 - - + -
500E CYS* 4.4 2.2 - - - -
537E ILE* 4.1 17.3 - - + -
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Residues in contact with TRP 446 (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* 4.7 0.2 - - - -
405E ASP* 3.5 41.3 - - + +
430E MET* 4.3 8.7 - - + -
433E VAL* 3.9 21.1 - - + -
434E VAL* 3.9 34.5 - - + -
437E ASP* 4.0 22.7 - - + -
438E LYS* 4.3 0.9 - - - -
443E VAL* 4.0 6.1 - - + -
445E MET* 1.3 73.3 - - - +
447E SER* 1.3 60.7 + - - +
448E VAL 4.2 0.2 - - - -
470E THR* 3.6 30.0 - - + +
474E ASP* 2.9 34.9 + - + +
477E ARG* 3.6 25.7 - - + +
478E PRO 3.0 15.5 + - - +
479E VAL* 3.4 9.5 - - + -
480E THR* 2.9 28.8 + - - +
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Residues in contact with SER 447 (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* 3.8 20.2 - - - -
405E ASP 2.9 8.6 + - - +
406E GLU* 2.7 33.1 + - - +
407E CYS* 3.1 26.3 + - - +
430E MET* 4.6 2.1 - - - +
445E MET 4.1 0.6 + - - -
446E TRP* 1.3 74.6 - - - +
448E VAL* 1.3 61.8 + - - +
449E ALA 3.3 13.5 + - - -
480E THR* 3.2 11.7 - - - -
481E PHE* 3.9 5.0 - - - -
482E VAL* 3.9 3.9 - - - +
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Residues in contact with VAL 448 (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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407E CYS* 3.1 14.0 - - - -
409E GLY* 4.0 0.2 - - - -
426E HIS* 2.8 28.9 + - - +
430E MET* 4.1 9.2 - - + -
447E SER* 1.3 74.8 - - - +
449E ALA* 1.3 59.8 + - - +
463E LEU* 4.2 13.9 - - + -
466E VAL* 3.6 24.9 - - + +
467E ILE* 4.0 17.5 - - + -
470E THR* 3.6 24.0 - - + +
479E VAL* 3.8 19.5 - - + -
480E THR 2.9 15.3 + - - +
481E PHE* 3.9 10.8 - - + -
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Residues in contact with ALA 449 (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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406E GLU* 3.8 4.3 - - - +
407E CYS 5.0 1.6 - - - -
409E GLY* 3.1 19.1 - - - +
412E LEU* 4.8 1.8 - - + -
426E HIS* 4.6 4.0 - - + -
447E SER* 3.3 10.6 + - - -
448E VAL* 1.3 84.5 - - - +
450E ASN* 1.3 61.2 + - - +
451E GLU 4.3 0.2 - - - -
452E PRO* 4.2 13.2 - - + -
463E LEU* 4.1 23.3 - - + -
481E PHE* 3.8 5.1 - - + +
482E VAL 2.9 24.5 + - - -
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Residues in contact with ASN 450 (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* 2.9 20.6 + - - +
385E HIS* 3.2 28.5 + - - +
406E GLU* 3.5 17.7 - - - +
409E GLY 2.9 8.4 + - - +
410E VAL* 3.8 31.2 - - + +
411E GLY 4.1 2.4 + - - -
449E ALA* 1.3 74.9 - - - +
451E GLU* 1.3 89.2 + - - +
452E PRO* 3.2 3.2 - - - +
482E VAL* 3.3 16.2 - - - +
502E ASN* 3.5 1.6 + - - -
540E GLU* 3.5 6.3 + - - +
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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