Contacts of the strand formed by residues 467 - 475 (chain A) in PDB entry 3HN8
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 PRO 467 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456A LEU* 3.8 17.0 - - + -
465A SER* 2.9 18.4 - - - +
466A ASP* 1.3 84.7 - - - +
468A TYR* 1.3 56.9 + - - +
487A ILE 3.4 1.1 - - - -
488A LYS 2.9 37.7 + - - +
491A THR* 3.5 22.4 - - + +
494A PRO* 3.6 17.9 - - + -
496A TYR* 2.8 23.5 + - - +
518A VAL* 4.1 9.0 - - + -
519A VAL 3.2 9.0 - - - +
520A ASP* 4.4 0.9 - - - -
530A ILE* 4.6 0.9 - - + -
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Residues in contact with TYR 468 (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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467A PRO* 1.3 74.3 - - - +
469A VAL* 1.3 71.9 + - - +
470A LYS* 4.6 9.5 + - + -
484A LYS* 4.0 44.1 + - + -
485A THR* 3.9 3.8 - - - +
486A SER 3.0 24.9 - - - +
487A ILE* 3.9 25.4 - - + -
496A TYR* 3.5 4.0 - - - -
518A VAL* 3.5 4.5 - - - +
519A VAL* 2.8 85.4 + - + +
521A TYR* 4.1 11.4 - + + -
527A ASN* 3.2 29.4 + - - +
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Residues in contact with VAL 469 (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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433A LEU* 4.4 12.8 - - + -
450A ILE* 3.6 33.0 - - + -
468A TYR* 1.3 86.1 - - - +
470A LYS* 1.3 60.0 + - - +
471A ALA 3.8 1.0 + - - +
483A ARG 3.7 1.2 - - - +
484A LYS* 3.4 2.8 - - - -
485A THR* 3.1 41.9 + - + +
496A TYR* 3.7 20.6 - - + +
516A ILE* 3.4 33.7 - - + -
517A ALA 3.7 7.2 - - - +
518A VAL* 4.4 7.2 - - + +
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Residues in contact with LYS 470 (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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468A TYR* 4.2 15.1 + - + -
469A VAL* 1.3 71.8 - - - +
471A ALA* 1.3 61.4 + - - +
472A SER* 4.3 13.9 - - - +
482A LYS* 3.6 40.4 - - + +
483A ARG 3.6 7.4 - - - +
484A LYS* 3.8 17.6 - - + +
515A SER 3.3 7.1 - - - +
516A ILE* 4.4 0.2 - - - -
517A ALA* 2.9 44.2 + - + +
519A VAL* 4.6 13.8 - - + +
529A VAL* 5.7 5.3 - - - +
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Residues in contact with ALA 471 (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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448A VAL* 4.5 4.0 - - + -
450A ILE* 5.2 0.2 - - + -
469A VAL 3.8 2.2 + - - -
470A LYS* 1.3 73.4 - - - +
472A SER* 1.3 59.3 + - - +
482A LYS* 3.4 1.6 - - - +
483A ARG* 2.8 36.5 + - - -
500A LEU* 3.7 24.0 - - + -
502A PHE* 3.7 15.2 - - + -
514A LEU* 4.4 6.1 - - + -
515A SER 3.8 3.6 - - - -
516A ILE* 3.6 27.1 - - + -
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Residues in contact with SER 472 (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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470A LYS* 4.1 12.7 + - - +
471A ALA* 1.3 76.3 - - - +
473A LEU* 1.3 65.0 + - - +
474A ILE* 3.5 4.1 + - - +
479A ARG* 4.2 18.6 - - - -
481A LYS 3.2 9.2 - - - -
482A LYS* 3.9 13.9 - - - -
502A PHE* 4.7 0.4 - - - -
514A LEU* 3.3 4.5 - - - +
515A SER* 2.9 49.2 + - - +
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Residues in contact with LEU 473 (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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446A LEU* 4.5 16.4 - - + -
472A SER* 1.3 71.3 - - - +
474A ILE* 1.3 57.8 + - - +
479A ARG* 3.6 5.5 - - - +
480A LEU* 2.9 38.8 + - + -
481A LYS* 2.7 26.0 + - + +
502A PHE* 4.3 21.2 - - + -
503A ASP 4.8 3.6 - - - +
504A VAL* 3.6 28.7 - - + -
512A VAL* 3.4 28.0 - - + -
513A GLY 3.3 18.6 - - - +
514A LEU* 4.2 8.0 - - + +
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Residues in contact with ILE 474 (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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472A SER* 3.7 8.7 - - - +
473A LEU* 1.3 79.2 - - - +
475A SER* 1.3 65.3 + - - +
476A GLU 4.6 0.7 - - - +
477A GLY* 4.3 17.5 - - - +
478A ARG 3.5 9.6 - - - +
479A ARG* 4.9 7.6 - - + -
512A VAL* 3.3 3.2 - - - +
513A GLY* 2.5 46.6 + - - +
514A LEU* 4.6 1.1 - - - -
515A SER* 3.4 31.6 - - - +
534A ARG* 4.2 11.4 - - + +
573A SER* 3.4 24.0 - - - +
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Residues in contact with SER 475 (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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474A ILE* 1.3 75.5 - - - +
476A GLU* 1.3 80.8 + - - +
477A GLY 3.4 0.9 - - - -
478A ARG* 3.1 22.7 + - - +
480A LEU* 3.4 22.9 - - - +
511A ASN* 2.9 28.5 + - - +
512A VAL* 3.7 7.8 - - - +
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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