Contacts of the helix formed by residues 590 - 599 (chain B) in PDB entry 2PZI
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 LYS 590 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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587B ASP* 3.3 21.8 + - - +
588B GLU* 4.2 9.0 - - - +
589B HIS* 1.3 76.7 - - - +
591B PHE* 1.3 60.0 + - - +
592B TYR 3.4 2.2 - - - -
593B GLN* 3.3 36.0 + - + +
594B THR* 3.0 28.8 + - - -
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Residues in contact with PHE 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B ASP* 4.1 11.4 - - + -
368B ARG* 4.1 6.1 - - - -
563B LEU* 3.7 31.2 - - + -
573B LYS* 3.4 42.0 - - + +
576B LEU* 3.7 34.1 - - + -
577B ALA* 3.9 6.1 - - + -
587B ASP* 2.7 30.0 + - - +
589B HIS* 3.6 38.8 - + + -
590B LYS* 1.3 70.5 - - - +
592B TYR* 1.3 55.9 + - - +
594B THR* 3.1 5.8 + - - -
595B VAL* 2.7 40.8 + - - +
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Residues in contact with TYR 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422B PHE* 3.5 13.9 - + - -
574B LEU* 3.8 20.6 - - + -
577B ALA* 3.5 37.3 - - + +
578B ALA* 3.5 17.5 - - - -
581B GLU* 2.7 34.6 + - + -
587B ASP* 4.4 2.9 + - + -
590B LYS* 3.4 0.6 - - - +
591B PHE* 1.3 78.0 - - - +
593B GLN* 1.3 64.6 + - - +
595B VAL* 3.3 3.9 + - - +
596B TRP* 2.9 28.4 + - - +
604B SER 4.1 10.8 - - - -
605B ALA* 3.7 18.9 - - - +
608B GLY* 3.4 26.0 - - - -
609B LEU* 3.9 19.7 - - + +
612B ALA* 5.1 6.5 - - + -
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Residues in contact with GLN 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B GLN* 5.8 1.4 + - - -
590B LYS* 3.3 41.8 + - + +
591B PHE 3.2 0.4 - - - -
592B TYR* 1.3 80.3 - - - +
594B THR* 1.3 53.7 + - - +
596B TRP* 3.9 0.5 - - - +
597B SER* 2.6 47.1 + - - +
609B LEU* 3.9 26.4 - - + +
613B ARG* 3.1 29.0 + - - +
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Residues in contact with THR 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B ASP* 5.9 2.4 - - - +
398B GLU* 3.8 35.0 - - + +
402B GLN* 5.4 4.0 + - - +
570B LEU* 4.9 0.4 - - + -
573B LYS* 4.0 15.7 - - + -
589B HIS 4.2 5.2 + - - -
590B LYS* 3.0 16.4 + - - +
591B PHE* 3.1 12.1 + - - -
593B GLN* 1.3 78.0 + - - +
595B VAL* 1.3 60.2 + - - +
597B SER* 3.9 4.1 - - - -
598B THR* 2.6 34.5 + - - +
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Residues in contact with VAL 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570B LEU* 3.9 25.7 - - + +
573B LYS* 3.7 25.8 - - + -
574B LEU* 3.9 19.3 - - + +
591B PHE 2.7 25.6 + - - +
592B TYR* 3.8 3.4 - - - +
594B THR* 1.3 72.1 - - - +
596B TRP* 1.3 58.1 + - - +
598B THR* 3.2 3.5 + - - -
599B ASN* 2.9 29.5 + - - +
602B VAL* 3.7 26.9 - - + -
605B ALA* 3.7 19.1 - - + -
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Residues in contact with TRP 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B PRO* 4.9 0.3 - - - +
592B TYR 2.9 17.7 + - - +
593B GLN 4.1 1.3 - - - +
595B VAL* 1.3 72.5 - - - +
597B SER* 1.3 68.4 + - - +
598B THR 3.1 1.7 + - - -
599B ASN 3.8 17.3 - - - -
600B ASP* 3.2 43.4 + - + +
602B VAL 3.3 30.1 - - - -
603B ILE* 4.0 4.7 - - + -
605B ALA* 3.9 11.9 - - + +
606B ALA* 3.7 30.1 - - + -
609B LEU* 4.0 10.3 - - + -
625B THR* 3.8 19.2 + - + -
628B GLU* 2.9 54.2 + - + +
629B VAL* 3.9 13.9 - - + -
630B PRO* 4.4 1.3 - - + -
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Residues in contact with SER 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B GLU 6.1 0.2 - - - -
401B ALA* 3.3 20.5 - - - +
402B GLN* 5.1 6.9 - - - +
405B GLY 5.7 0.7 - - - -
406B VAL 4.4 0.5 - - - -
407B PRO* 3.3 26.5 - - - +
593B GLN* 2.6 34.1 + - - +
594B THR* 3.9 6.2 - - - -
596B TRP* 1.3 79.0 - - - +
598B THR* 1.3 59.2 + - - +
609B LEU* 5.9 0.3 - - - +
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Residues in contact with THR 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397B ARG* 4.2 6.1 - - + +
398B GLU* 3.6 47.2 + - + +
401B ALA* 3.8 7.6 - - - +
407B PRO* 3.9 0.4 - - - -
408B ARG 2.7 48.0 + - - +
570B LEU* 4.1 19.7 - - + -
594B THR* 2.6 22.3 + - - +
595B VAL 3.2 3.9 + - - -
596B TRP 3.1 0.6 - - - -
597B SER* 1.3 80.4 - - - +
599B ASN* 1.3 58.5 + - + +
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Residues in contact with ASN 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B PRO* 4.4 0.9 - - - -
409B PRO* 3.6 30.3 - - + +
410B GLY 4.2 12.5 + - - +
570B LEU* 3.8 17.7 - - + +
595B VAL 2.9 10.5 + - - +
596B TRP* 3.8 6.9 - - - -
598B THR* 1.3 79.4 - - + +
600B ASP* 1.3 60.3 + - - +
601B GLY* 2.9 32.7 + - - -
602B VAL* 3.1 35.4 + - + +
753B GOL 6.1 0.4 - - - -
754B GOL 4.5 13.2 + - - -
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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