Contacts of the helix formed by residues 594 - 603 (chain C) 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 ASP 594 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592C PRO 5.8 0.2 - - - -
593C ILE* 1.3 76.0 - - - +
595C GLU* 1.3 58.6 + - - +
596C GLU* 4.1 8.7 - - + +
597C VAL* 2.7 42.0 + - + +
598C SER* 2.9 10.4 + - - -
623C TYR 5.0 5.4 - - - +
625C TRP* 4.9 6.6 + - - +
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Residues in contact with GLU 595 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593C ILE 3.5 3.0 + - - -
594C ASP* 1.3 70.4 - - - +
596C GLU* 1.3 59.8 + - + +
598C SER* 3.2 4.5 + - - -
599C LEU* 2.8 66.8 + - + +
682C ARG* 2.5 40.3 + - - -
683C SER* 4.0 5.0 + - - -
725C GLN* 4.3 7.5 + - - +
800C HIS* 5.4 5.7 - - - +
801C TRP 5.1 10.5 + - - +
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Residues in contact with GLU 596 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594C ASP* 2.8 8.6 + - + +
595C GLU* 1.3 81.8 - - + +
597C VAL* 1.3 57.6 + - + +
599C LEU* 3.2 19.1 + - - +
600C ALA* 2.7 29.6 + - - +
623C TYR* 4.4 21.5 - - + -
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Residues in contact with VAL 597 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593C ILE* 3.6 15.3 - - + -
594C ASP* 2.7 40.1 + - + +
596C GLU* 1.3 74.1 - - + +
598C SER* 1.3 51.6 + - - +
600C ALA* 3.0 8.2 + - - +
601C ILE* 2.7 46.1 + - + +
606C ILE* 4.5 18.6 - - + -
619C MET* 5.0 7.2 - - + -
623C TYR* 4.7 18.1 - - + +
625C TRP* 4.3 25.4 - - + +
645C LEU* 5.6 1.8 - - + -
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Residues in contact with SER 598 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593C ILE* 3.9 4.9 - - - +
594C ASP 2.9 10.8 + - - -
595C GLU* 3.5 10.1 - - - -
597C VAL* 1.3 77.4 - - - +
599C LEU* 1.3 51.8 + - - +
601C ILE* 3.0 8.5 + - - +
602C GLU* 2.7 39.7 + - - +
643C PRO* 4.1 15.9 - - - +
682C ARG* 4.0 14.1 - - - -
683C SER* 2.7 42.3 + - - -
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Residues in contact with LEU 599 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595C GLU* 2.8 50.9 + - + +
596C GLU* 3.5 23.3 - - - +
598C SER* 1.3 71.8 - - - +
600C ALA* 1.3 51.9 + - - +
602C GLU* 3.0 22.4 + - - +
603C ASN* 2.6 54.3 + - - +
682C ARG* 3.3 6.3 - - - +
800C HIS* 6.1 4.3 - - + -
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Residues in contact with ALA 600 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596C GLU 2.7 14.5 + - - +
597C VAL* 3.1 11.2 - - - +
599C LEU* 1.3 79.2 - - - +
601C ILE* 1.3 62.4 + - - +
603C ASN* 3.3 3.4 + - - -
605C ILE* 3.0 38.1 + - + -
606C ILE* 3.3 21.7 + - + -
623C TYR* 3.7 25.4 - - + +
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Residues in contact with ILE 601 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593C ILE* 5.3 4.0 - - + -
597C VAL* 2.7 29.8 + - + +
598C SER* 3.3 7.4 - - - +
600C ALA* 1.3 74.3 - - - +
602C GLU* 1.3 62.6 + - - +
603C ASN 3.2 0.7 + - - -
604C GLY* 3.3 10.0 + - - -
606C ILE* 3.6 33.6 - - + +
608C PRO* 5.6 2.5 - - + +
636C PHE* 3.8 29.6 - - + -
641C ASN 3.8 23.2 - - - +
642C GLY 3.9 5.2 - - - +
643C PRO* 4.0 24.5 - - + -
645C LEU* 4.4 16.8 - - + -
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Residues in contact with GLU 602 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598C SER 2.7 17.6 + - - +
599C LEU* 3.2 21.1 - - - +
601C ILE* 1.3 73.3 - - - +
603C ASN* 1.3 64.1 + - - +
604C GLY 3.3 3.2 + - - -
641C ASN 6.0 0.4 - - - -
643C PRO* 4.2 17.6 - - + +
682C ARG* 2.7 48.3 + - - -
801C TRP* 4.1 8.8 + - - -
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Residues in contact with ASN 603 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424C ASP* 6.1 0.7 - - - -
599C LEU* 2.6 41.9 + - - +
600C ALA* 3.5 1.8 - - - +
601C ILE 3.1 0.6 - - - -
602C GLU* 1.3 79.8 - - - +
604C GLY* 1.3 54.0 + - - -
605C ILE* 2.9 28.2 + - + +
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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