Contacts of the helix formed by residues 522 - 532 (chain H) in PDB entry 1PQB
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 THR 522 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520H ASP 4.4 1.1 + - - -
521H MET* 1.3 80.7 - - - +
523H LEU* 1.3 64.8 + - - +
524H LYS* 4.0 2.4 + - - +
525H GLU* 3.3 25.9 + - - +
526H ALA* 3.1 23.4 + - - +
578H LEU 4.0 4.7 - - - -
579H ASP* 3.2 29.3 + - - +
580H LYS* 4.6 0.9 - - - +
581H ILE 3.1 11.4 - - - +
582H LYS* 4.0 21.8 - - - +
583H LEU* 4.3 2.2 - - - -
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Residues in contact with LEU 523 (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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491H ILE* 4.1 8.1 - - + -
522H THR* 1.3 73.9 - - - +
524H LYS* 1.3 63.6 + - - +
526H ALA* 3.4 1.2 + - - +
527H LEU* 3.1 47.7 + - + +
552H PHE* 3.5 34.5 - - + -
554H PHE* 4.9 7.0 - - + -
562H ILE* 5.7 0.9 - - + -
574H ILE* 4.0 12.3 - - + -
578H LEU* 3.7 24.7 + - + +
581H ILE* 2.9 23.7 + - + +
583H LEU* 3.9 14.7 - - + +
589H ILE* 4.0 25.8 - - + -
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Residues in contact with LYS 524 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522H THR* 3.3 0.6 - - - +
523H LEU* 1.3 78.8 - - - +
525H GLU* 1.3 66.5 + - - +
527H LEU* 3.3 5.9 + - - +
528H LYS* 3.1 35.3 + - + +
535H GLU* 2.8 40.5 + - - +
538H GLY 3.8 9.3 + - - -
540H LEU* 3.7 43.5 - - + +
578H LEU* 3.3 28.9 + - + +
579H ASP* 4.1 23.1 - - + +
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Residues in contact with GLU 525 (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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521H MET* 4.0 15.3 - - + -
522H THR* 3.3 22.2 + - - +
524H LYS* 1.3 80.4 - - - +
526H ALA* 1.3 61.0 + - - +
528H LYS* 3.1 29.7 + - - +
529H ILE* 2.9 50.2 + - + +
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Residues in contact with ALA 526 (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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491H ILE* 3.9 14.4 - - + -
505H ILE* 4.1 12.3 - - + -
521H MET* 3.8 10.5 - - - -
522H THR 3.1 9.6 + - - +
523H LEU 3.6 4.5 - - - +
525H GLU* 1.3 75.9 - - - +
527H LEU* 1.3 58.7 + - - +
529H ILE* 4.1 5.2 - - - -
530H ALA* 2.8 37.5 + - - +
583H LEU* 3.5 32.1 - - + -
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Residues in contact with LEU 527 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491H ILE* 3.8 16.8 - - + -
523H LEU* 3.1 42.8 + - + +
524H LYS* 3.5 9.2 - - - +
526H ALA* 1.3 78.7 - - - +
528H LYS* 1.3 57.4 + - - +
531H PHE* 3.2 25.9 + - + -
532H GLY 3.3 6.8 + - - -
533H PHE* 3.3 33.8 + - + -
540H LEU* 3.8 22.9 - - + -
547H ILE* 3.9 18.6 - - + -
552H PHE* 4.2 14.1 - - + -
578H LEU* 4.9 1.3 - - + -
591H ILE* 4.1 15.0 - - + -
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Residues in contact with LYS 528 (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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524H LYS* 3.1 25.0 + - + +
525H GLU* 3.4 34.2 + - - +
526H ALA 3.1 0.4 - - - -
527H LEU* 1.3 75.9 - - - +
529H ILE* 1.3 60.4 + - + +
532H GLY* 3.0 26.2 + - - -
533H PHE 3.6 23.4 - - - +
534H ASN* 4.8 3.1 - - - +
535H GLU* 2.7 36.2 + - - +
540H LEU* 4.0 13.2 - - + -
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Residues in contact with ILE 529 (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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217H THR* 6.5 0.2 - - + -
250H GLU* 3.5 21.8 - - - +
253H HIS* 3.8 41.8 - - + +
255H LEU* 4.2 2.5 - - + -
256H VAL* 3.7 24.4 - - + +
505H ILE* 4.4 4.5 - - + -
521H MET* 3.8 29.4 - - + -
525H GLU* 2.9 42.6 + - + +
526H ALA* 3.8 5.4 - - - +
528H LYS* 1.3 73.1 - - + +
530H ALA* 1.3 63.1 + - + +
532H GLY 4.7 0.7 + - - -
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Residues in contact with ALA 530 (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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250H GLU* 3.9 18.8 - - - +
256H VAL* 4.4 10.3 - - + -
503H ARG* 3.8 30.5 + - + +
505H ILE* 3.6 30.1 - - + -
526H ALA 2.8 23.2 + - - +
529H ILE* 1.3 75.3 - - - +
531H PHE* 1.3 64.8 + - + +
532H GLY 3.7 0.2 - - - -
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Residues in contact with PHE 531 (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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491H ILE* 3.3 50.9 - - + -
493H PHE* 3.6 32.1 - + + -
501H VAL* 3.6 29.6 - - + -
503H ARG* 3.5 28.9 - - + -
527H LEU* 3.2 24.1 + - + +
530H ALA* 1.3 82.6 - - + +
532H GLY* 1.3 63.4 + - - +
533H PHE* 3.8 17.0 - + + -
542H TYR* 3.6 16.8 - - - -
591H ILE* 6.3 0.2 - - + -
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Residues in contact with GLY 532 (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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528H LYS 3.0 16.9 + - - -
529H ILE 4.7 0.6 + - - -
530H ALA 3.7 1.0 - - - -
531H PHE* 1.3 78.8 - - - +
533H PHE* 1.3 66.6 + - - +
534H ASN* 3.9 5.0 + - - +
542H TYR* 4.6 7.2 - - - -
543H GLN 5.4 1.7 + - - -
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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