Contacts of the strand formed by residues 454 - 459 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388H LEU* 3.5 23.3 - - + -
406H TRP* 4.3 11.0 - - + -
407H GLU 3.5 3.6 - - - +
408H SER* 3.8 13.7 - - - -
416H GLU* 3.8 8.7 - - + -
441H LEU* 3.7 15.9 - - + -
443H VAL* 3.9 14.6 - - + -
447H ARG* 3.4 50.3 - - + -
448H TRP* 4.0 17.0 - + - -
452H ASN* 3.6 33.4 - - + -
453H VAL* 1.3 74.3 - - - +
455H SER* 1.3 58.9 + - - +
471H SER* 3.2 3.6 - - - -
472H LEU* 2.6 47.6 + - + +
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Residues in contact with SER 455 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406H TRP* 3.5 8.6 - - - -
407H GLU* 3.0 55.3 + - - +
408H SER* 5.2 0.5 - - - -
453H VAL* 5.1 2.9 + - - +
454H PHE* 1.3 75.5 - - - +
456H CYS* 1.3 61.7 + - - +
457H SER* 3.8 1.7 + - - -
469H GLN* 4.3 18.1 + - - -
470H LYS 3.1 13.5 - - - -
471H SER* 3.4 14.4 - - - -
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Residues in contact with CYS 456 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369H VAL* 4.4 4.4 - - + +
371H THR* 4.1 8.7 - - + -
390H CYS* 2.0 53.2 - - + -
402H VAL* 4.0 20.6 - - - -
405H GLU 3.5 4.3 - - - -
406H TRP* 4.1 12.0 - - + -
455H SER* 1.3 71.8 - - - +
457H SER* 1.3 60.7 + - - +
458H VAL* 3.9 8.4 + - - -
468H THR 3.9 0.5 - - - +
469H GLN* 3.3 5.6 - - - -
470H LYS* 2.8 32.8 + - - +
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Residues in contact with SER 457 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401H ALA 3.7 0.5 - - - +
402H VAL* 3.3 4.0 - - - +
405H GLU* 2.7 54.1 + - - +
407H GLU* 3.7 16.1 + - - +
455H SER 4.2 4.5 + - - -
456H CYS* 1.3 72.2 - - - +
458H VAL* 1.3 62.0 + - - +
459H MET* 4.2 3.7 - - - +
467H TYR* 3.3 34.9 + - - -
468H THR 3.4 5.2 - - - -
469H GLN* 3.8 8.1 + - - +
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Residues in contact with VAL 458 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367H PRO* 4.9 2.5 - - + -
369H VAL* 3.9 26.2 - - + -
392H VAL* 3.9 28.9 - - + -
400H ILE* 3.2 32.3 - - + -
401H ALA 3.3 2.0 - - - -
402H VAL* 4.2 4.5 - - + -
456H CYS* 4.1 7.9 - - - -
457H SER* 1.3 79.2 - - - +
459H MET* 1.3 61.0 + - - +
460H HIS* 4.8 2.2 - - + -
463H LEU* 3.1 16.0 - - + +
467H TYR* 3.5 2.4 - - - -
468H THR* 2.9 44.4 + - + -
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Residues in contact with MET 459 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261H LYS* 3.9 16.2 - - + -
264H LEU* 3.0 17.7 - - + +
265H MET* 3.1 36.8 - - + +
400H ILE* 3.5 1.1 - - - +
401H ALA* 2.8 59.3 + - + +
402H VAL 4.7 0.2 - - - -
405H GLU* 4.1 33.9 - - + +
457H SER* 4.2 6.7 - - - +
458H VAL* 1.3 71.6 - - - +
460H HIS* 1.3 61.0 + - - +
466H HIS 3.4 7.2 - - - +
467H TYR* 3.4 33.7 - - + -
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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