Contacts of the helix formed by residues 588 - 594 (chain F) in PDB entry 1ZM9
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 PRO 588 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419F VAL* 3.6 30.1 - - + -
570F ALA* 3.4 28.3 - - + +
571F ILE* 3.9 7.9 - - + -
572F PRO* 5.5 0.2 - - + -
586F SER 3.2 9.2 - - - +
587F ILE* 1.3 86.9 - - + +
589F ASP* 1.3 56.3 + - - +
590F LYS 3.2 1.6 - - - +
591F GLU* 2.8 34.6 + - + +
592F GLN* 3.1 9.4 + - - +
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Residues in contact with ASP 589 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587F ILE 3.5 5.8 + - - +
588F PRO* 1.3 69.2 - - - +
590F LYS* 1.3 65.5 + - + +
592F GLN* 3.1 11.5 + - - +
593F ALA* 3.1 20.8 + - - +
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Residues in contact with LYS 590 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419F VAL* 3.6 24.9 - - + -
420F GLU* 4.7 15.7 + - - +
423F LEU* 3.7 40.7 - - + +
588F PRO 3.2 0.6 - - - -
589F ASP* 1.3 80.2 - - + +
591F GLU* 1.3 60.9 + - - +
593F ALA* 3.2 20.4 - - - +
594F ILE 3.6 3.6 + - - -
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Residues in contact with GLU 591 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419F VAL* 4.7 1.9 - - + +
422F LEU* 3.4 17.6 - - + +
423F LEU* 5.0 0.4 - - - -
439F TYR* 3.2 25.7 + - - +
500F ARG* 3.3 14.5 + - - +
569F SER* 3.0 19.4 + - - -
570F ALA* 2.6 45.3 + - + +
571F ILE* 4.3 6.1 - - - -
587F ILE* 4.9 3.6 - - + -
588F PRO* 2.8 26.0 + - + +
590F LYS* 1.3 71.1 - - - +
592F GLN* 1.3 61.8 + - - +
593F ALA 3.0 2.0 - - - -
594F ILE* 3.0 20.9 - - - +
595F SER* 2.5 25.3 + - - +
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Residues in contact with GLN 592 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475F PRO* 6.1 3.0 - - - +
587F ILE* 4.3 24.5 - - + +
588F PRO 3.1 7.6 + - - +
589F ASP* 3.1 14.9 + - - +
591F GLU* 1.3 78.1 - - - +
593F ALA* 1.3 58.5 + - - +
595F SER* 3.0 34.8 + - - -
596F ALA* 4.3 1.0 + - - +
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Residues in contact with ALA 593 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589F ASP 3.1 11.1 + - - +
590F LYS* 3.2 16.6 - - - +
592F GLN* 1.3 79.6 - - - +
594F ILE* 1.3 62.2 + - + +
595F SER 3.6 0.7 + - - -
596F ALA* 4.7 5.9 + - - +
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Residues in contact with ILE 594 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422F LEU* 3.6 31.2 - - + -
423F LEU* 3.8 27.8 - - + -
426F HIS* 3.4 55.0 + - + +
436F PHE* 4.3 5.0 - - - +
500F ARG* 3.1 21.8 + - - +
590F LYS 3.9 2.2 - - - +
591F GLU* 3.0 15.9 - - - +
593F ALA* 1.3 81.9 - - + +
595F SER* 1.3 58.8 + - - +
596F ALA 3.6 3.6 + - - +
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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