Contacts of the strand formed by residues 470 - 477 (chain K) in PDB entry 3HX0
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 GLN 470 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465K GLU 3.8 1.0 - - - +
466K GLU* 4.0 3.8 - - - +
467K ASN* 3.1 37.2 + - + +
468K GLY 4.0 0.3 - - - +
469K GLN* 1.3 82.3 - - - +
471K GLN* 1.3 65.4 + - - +
472K LYS* 4.2 0.9 - - + -
492K ILE* 4.5 4.7 - - + +
493K VAL 3.3 4.5 - - - -
494K VAL* 3.3 31.6 - - + +
495K PRO* 4.4 0.4 - - + -
498K GLU* 2.9 28.6 + - - +
502K ALA* 4.0 5.7 - - - +
506K PHE* 4.2 10.3 - - - -
529K GLU* 2.9 41.3 + - - +
530K HIS* 3.3 15.8 + - + -
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Residues in contact with GLN 471 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440K HIS* 5.1 3.8 - - - +
441K ARG* 5.7 1.2 - - - -
442K GLY* 5.1 6.4 + - - +
444K PHE* 3.0 59.4 + - + +
445K SER* 5.2 3.2 + - - -
464K GLN* 4.2 10.7 - - - +
465K GLU 3.6 5.4 - - - +
466K GLU* 4.0 17.0 + - - +
469K GLN 5.0 4.5 - - - +
470K GLN* 1.3 78.7 - - - +
472K LYS* 1.3 59.6 + - - +
492K ILE* 3.3 6.0 - - - -
493K VAL* 2.9 43.7 + - + +
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Residues in contact with LYS 472 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444K PHE* 3.3 7.6 - - - -
462K VAL 4.4 0.3 - - - +
464K GLN* 3.7 1.9 - - - -
465K GLU* 2.9 76.1 + - + +
467K ASN* 5.1 7.5 - - + +
470K GLN* 4.2 1.5 - - + -
471K GLN* 1.3 73.7 - - - +
473K TYR* 1.3 63.9 + - - +
474K LEU* 3.5 26.0 - - + +
490K ASP* 5.7 3.1 - - + +
491K ILE 3.5 2.9 - - - +
492K ILE* 4.1 29.2 - - + -
505K TYR* 6.0 0.8 - - - -
506K PHE* 4.7 10.9 - - + -
529K GLU* 5.6 2.4 + - - -
703K D3T 4.0 20.5 + - - +
7L A 6.1 2.4 - - - -
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Residues in contact with TYR 473 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444K PHE* 3.7 18.2 - - + -
448K LEU* 3.6 30.5 - - + -
452K ARG* 4.7 0.9 - - - -
457K LEU* 3.8 26.6 - - + +
459K ASP 3.1 24.3 + - - -
460K ASP* 3.4 29.4 + - - -
462K VAL 3.6 5.4 - - - -
463K SER* 3.2 24.0 - - - -
472K LYS* 1.3 76.4 - - - +
474K LEU* 1.3 74.2 + - - +
475K GLY* 3.2 21.3 - - - -
489K LEU* 4.3 5.6 - - + -
490K ASP* 3.3 6.9 - - - +
491K ILE* 2.8 47.0 + - + +
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Residues in contact with LEU 474 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342K TRP* 4.0 25.4 - - + -
460K ASP* 3.8 0.7 - - - -
461K LEU* 2.8 14.7 + - + +
462K VAL* 2.8 58.4 + - + +
465K GLU* 5.7 1.6 - - + +
472K LYS* 3.5 34.3 - - + -
473K TYR* 1.3 85.3 - - - +
475K GLY* 1.3 58.7 + - - +
489K LEU 3.6 4.5 - - - -
490K ASP* 3.1 19.7 - - - +
703K D3T 5.7 5.6 - - + +
6M T 5.3 8.3 - - + +
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Residues in contact with GLY 475 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459K ASP 3.3 5.8 - - - -
461K LEU* 3.8 10.2 - - - +
473K TYR* 3.2 24.4 - - - -
474K LEU* 1.3 75.1 - - - +
476K VAL* 1.3 67.5 + - - +
488K ARG* 3.7 5.9 - - - +
489K LEU* 3.1 30.8 + - - +
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Residues in contact with VAL 476 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375K ILE* 4.1 8.7 - - + -
379K HIS* 3.6 19.1 - - + +
383K PHE* 3.3 30.1 - - + -
457K LEU* 3.5 7.9 - - - +
458K THR* 2.7 46.6 + - - +
459K ASP* 2.8 29.5 + - + +
461K LEU* 4.6 7.6 - - + -
473K TYR* 4.1 0.6 + - - -
475K GLY* 1.3 80.2 - - - +
477K CYS* 1.3 58.4 + - - +
486K HIS* 3.8 11.2 - - + -
487K ARG 3.5 10.5 - - - +
488K ARG* 5.1 0.2 - - + -
489K LEU* 5.2 0.2 - - - -
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Residues in contact with CYS 477 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395K ILE* 3.8 28.3 - - - -
456K PHE* 3.2 49.1 - - + +
457K LEU* 4.1 7.9 - - + -
458K THR* 4.2 3.8 - - - +
476K VAL* 1.3 75.0 - - - +
478K ARG* 1.3 63.6 + - - +
486K HIS* 3.5 2.1 - - - -
487K ARG* 2.8 42.3 + - - +
489K LEU* 4.0 13.4 - - + +
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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