Contacts of the strand formed by residues 487 - 493 (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 ARG 487 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382K ASP 4.7 2.1 + - - -
383K PHE* 4.5 2.2 - - - -
385K GLU* 2.9 32.6 + - - +
386K ARG 3.5 3.2 + - - -
387K MET* 3.2 49.7 - - + +
388K PRO* 4.5 2.2 - - - +
391K GLU* 2.8 41.2 + - - +
395K ILE* 4.0 15.5 - - + -
426K GLY 5.9 0.7 - - - -
476K VAL* 3.5 5.5 - - - -
477K CYS* 2.8 37.7 + - - +
478K ARG* 5.8 0.7 - - - -
479K LEU* 6.1 0.7 - - + +
485K ARG* 3.4 39.5 + - - +
486K HIS* 1.3 78.7 - - - +
488K ARG* 1.3 63.2 + - - +
489K LEU 3.7 0.2 + - - -
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Residues in contact with ARG 488 (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* 3.6 38.7 - - - +
383K PHE* 3.6 46.5 + - + +
387K MET* 4.3 2.9 - - - +
426K GLY* 3.7 27.2 + - - +
427K ASP* 3.1 38.0 + - + +
428K VAL* 3.1 23.2 + - - +
461K LEU* 4.7 6.5 - - + -
475K GLY 3.7 9.2 - - - +
476K VAL* 4.7 0.2 - - - +
477K CYS* 5.2 0.4 - - - -
487K ARG* 1.3 74.9 - - - +
489K LEU* 1.3 59.3 + - - +
490K ASP* 4.7 4.0 + - - +
703K D3T 4.6 6.1 + - - -
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Residues in contact with LEU 489 (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* 4.0 7.2 - - + -
399K VAL* 4.1 4.0 - - + -
428K VAL* 3.4 25.8 - - + +
430K VAL* 3.8 24.5 - - + -
451K LEU* 5.2 0.4 - - + -
456K PHE* 4.0 27.1 - - + -
457K LEU* 4.0 16.2 - - + -
473K TYR* 3.8 3.8 - - + +
474K LEU* 3.6 0.7 - - - -
475K GLY 3.1 38.0 + - - +
476K VAL 5.2 0.2 - - - -
477K CYS* 4.0 17.0 - - + -
487K ARG 3.7 0.2 + - - -
488K ARG* 1.3 74.7 - - - +
490K ASP* 1.3 69.1 + - - +
491K ILE* 4.0 25.8 - - + -
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Residues in contact with ASP 490 (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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427K ASP* 2.9 10.8 - - - +
428K VAL 2.7 9.3 + - - +
429K ASP* 2.8 17.2 - - + +
430K VAL* 2.7 34.8 + - - +
472K LYS* 5.8 2.2 - - + -
473K TYR 3.3 3.8 - - - +
474K LEU* 3.1 33.6 - - + +
488K ARG* 4.7 3.1 + - - -
489K LEU* 1.3 78.6 - - - +
491K ILE* 1.3 57.9 + - - +
492K ILE* 4.7 11.2 - - + +
808K NA 2.6 28.2 - - - -
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Residues in contact with ILE 491 (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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399K VAL* 4.1 13.0 - - + -
430K VAL* 3.4 7.6 - - + +
432K ILE* 4.3 21.1 - - + -
444K PHE* 4.3 8.0 - - + -
447K LEU* 4.3 9.6 - - + -
448K LEU* 4.1 17.9 - - + -
451K LEU* 3.8 28.7 - - + -
471K GLN 3.7 1.3 - - - +
472K LYS* 3.5 0.9 - - - -
473K TYR* 2.8 49.2 + - + +
489K LEU* 4.0 26.9 - - + -
490K ASP* 1.3 77.0 - - - +
492K ILE* 1.3 70.4 + - - +
493K VAL* 4.8 5.6 - - + -
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Residues in contact with ILE 492 (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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429K ASP* 5.6 5.4 - - + +
430K VAL 2.9 14.6 + - - +
431K LEU* 3.5 10.0 - - + +
432K ILE* 2.7 33.3 + - - +
470K GLN* 4.5 5.2 - - + +
471K GLN 3.3 14.4 - - - +
472K LYS* 4.1 19.3 - - + -
490K ASP* 4.7 10.1 - - + +
491K ILE* 1.3 85.1 - - - +
493K VAL* 1.3 61.5 + - - +
494K VAL* 3.8 20.4 - - + -
506K PHE* 3.3 55.6 - - + -
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Residues in contact with VAL 493 (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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432K ILE* 3.3 32.5 - - + +
440K HIS* 3.9 38.4 - - + +
443K ILE* 5.0 6.3 - - + -
444K PHE* 4.1 28.9 - - + +
447K LEU* 5.2 0.9 - - + -
469K GLN 4.0 1.9 - - - +
470K GLN* 3.3 2.3 - - - -
471K GLN* 2.9 48.7 + - - +
491K ILE* 4.8 4.3 - - + -
492K ILE* 1.3 75.4 - - - +
494K VAL* 1.3 66.1 + - - +
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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