Contacts of the strand formed by residues 454 - 459 (chain K) in PDB entry 1HZH
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 PHE 454 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388K LEU* 3.5 28.0 - - + -
406K TRP* 4.2 11.9 - - + -
407K GLU 3.6 4.7 - - - +
408K SER* 4.1 13.2 - - - -
416K GLU* 4.1 4.9 - - + -
441K LEU* 3.7 15.5 - - + -
443K VAL* 4.0 17.5 - - + -
447K ARG* 3.6 45.3 - - + -
448K TRP* 4.1 12.8 - + - -
452K ASN* 3.2 38.1 - - + -
453K VAL* 1.3 73.9 - - - +
455K SER* 1.3 64.5 + - - +
471K SER* 3.3 4.0 - - - -
472K LEU* 2.8 40.7 + - + +
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Residues in contact with SER 455 (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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406K TRP* 3.2 13.4 - - - -
407K GLU* 2.9 51.6 + - - +
408K SER* 6.0 0.2 - - - -
453K VAL* 4.8 2.8 - - - +
454K PHE* 1.3 76.0 + - - +
456K CYS* 1.3 62.9 + - - +
457K SER* 3.8 1.0 + - - -
469K GLN* 4.7 16.2 + - - +
470K LYS 3.4 8.5 - - - -
471K SER* 3.3 19.9 + - - -
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Residues in contact with CYS 456 (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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369K VAL* 4.2 4.8 - - + +
371K THR* 4.1 8.5 - - + -
390K CYS* 2.0 53.6 - - + -
402K VAL* 3.8 19.5 - - - -
405K GLU 3.5 4.5 - - - -
406K TRP* 4.2 9.1 - - + -
455K SER* 1.3 74.1 - - - +
457K SER* 1.3 61.8 + - - +
458K VAL* 4.2 7.0 - - - -
468K THR 3.9 0.3 - - - +
469K GLN* 3.3 5.2 - - - -
470K LYS* 3.0 32.2 + - - +
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Residues in contact with SER 457 (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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401K ALA 4.4 0.2 - - - -
402K VAL* 3.2 6.8 - - - +
405K GLU* 2.6 50.3 + - - +
407K GLU* 3.4 21.5 + - - +
455K SER 3.8 0.5 + - - -
456K CYS* 1.3 72.5 - - - +
458K VAL* 1.3 63.9 + - - +
459K MET* 5.7 2.9 - - - -
467K TYR* 3.3 31.7 + - - -
468K THR 3.7 3.8 - - - -
469K GLN* 3.7 9.1 + - - +
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Residues in contact with VAL 458 (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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367K PRO* 4.6 2.9 - - + -
369K VAL* 3.8 26.7 - - + -
392K VAL* 4.0 25.6 - - + -
400K ILE* 3.5 33.9 - - + -
401K ALA 3.4 2.9 - - - +
402K VAL* 4.5 4.3 - - + -
456K CYS* 4.2 6.1 - - - +
457K SER* 1.3 80.9 - - - +
459K MET* 1.3 65.3 + - - +
463K LEU* 3.4 11.0 - - + +
467K TYR* 3.4 6.4 - - - -
468K THR* 3.0 42.7 + - + +
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Residues in contact with MET 459 (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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261K LYS* 3.6 39.7 - - + -
264K LEU* 3.5 26.1 - - + +
265K MET* 4.0 25.6 - - - +
400K ILE* 3.5 3.3 - - - +
401K ALA* 3.0 44.7 + - + +
405K GLU* 3.8 14.4 - - + +
457K SER* 6.1 2.7 - - - -
458K VAL* 1.3 70.7 - - - +
460K HIS* 1.3 61.2 + - - +
466K HIS 3.2 8.3 - - - +
467K TYR* 3.4 36.8 - - + -
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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