Contacts of the helix formed by residues 594 - 603 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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592E PRO 5.6 1.3 - - - +
593E ILE* 1.3 75.4 - - - +
595E GLU* 1.3 66.9 + - - +
596E GLU* 4.2 9.6 - - + +
597E VAL* 2.8 32.8 + - + +
598E SER* 3.1 9.8 + - - -
623E TYR 4.9 6.2 - - - +
624E GLY 5.8 0.2 - - - +
625E TRP* 5.0 6.1 + - - +
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Residues in contact with GLU 595 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593E ILE 3.5 3.6 + - - -
594E ASP* 1.3 70.6 - - - +
596E GLU* 1.3 58.1 + - + +
598E SER* 3.3 5.1 + - - -
599E LEU* 2.8 61.3 + - + +
682E ARG* 2.6 43.4 + - - -
683E SER* 4.4 3.7 + - - +
725E GLN* 4.6 6.6 + - - +
800E HIS* 5.2 7.8 - - - +
801E TRP* 4.9 11.1 + - - +
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Residues in contact with GLU 596 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594E ASP* 2.9 7.7 + - + -
595E GLU* 1.3 79.3 - - + +
597E VAL* 1.3 53.9 + - + +
599E LEU* 3.2 11.1 + - + +
600E ALA* 2.7 34.6 + - - +
622E ASP 5.4 0.9 - - - +
623E TYR* 4.3 25.4 - - + -
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Residues in contact with VAL 597 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593E ILE* 3.6 13.9 - - + -
594E ASP* 2.8 37.4 + - + +
596E GLU* 1.3 70.5 - - + +
598E SER* 1.3 57.2 + - - +
600E ALA* 3.0 7.4 + - - +
601E ILE* 2.7 46.9 + - + +
606E ILE* 4.4 19.5 - - + -
619E MET* 5.0 9.2 - - + -
623E TYR* 4.6 21.1 - - + +
625E TRP* 4.4 22.2 - - + +
645E LEU* 5.6 1.6 - - + -
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Residues in contact with SER 598 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593E ILE* 3.8 4.6 - - - +
594E ASP 3.1 9.9 + - - -
595E GLU* 3.5 9.6 - - - -
597E VAL* 1.3 76.8 - - - +
599E LEU* 1.3 52.9 + - - +
601E ILE* 3.1 7.5 + - - +
602E GLU* 2.7 40.9 + - - +
643E PRO* 4.1 15.8 - - - +
682E ARG* 3.9 14.4 - - - -
683E SER* 2.8 40.1 + - - -
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Residues in contact with LEU 599 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595E GLU* 2.8 50.0 + - + +
596E GLU* 3.4 9.6 - - + +
598E SER* 1.3 75.6 - - - +
600E ALA* 1.3 52.0 + - - +
602E GLU* 3.0 21.8 + - - +
603E ASN* 2.6 54.1 + - - +
682E ARG* 3.3 9.0 - - - +
800E HIS* 6.4 0.9 - - + -
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Residues in contact with ALA 600 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596E GLU 2.7 15.8 + - - +
597E VAL* 3.1 15.5 - - - +
599E LEU* 1.3 78.0 - - - +
601E ILE* 1.3 58.7 + - - +
603E ASN* 3.4 3.6 + - - +
605E ILE* 3.0 39.2 + - + +
606E ILE* 3.3 22.1 + - + -
623E TYR* 3.6 23.3 - - + +
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Residues in contact with ILE 601 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593E ILE* 5.2 3.8 - - + -
597E VAL* 2.7 32.3 + - + +
598E SER* 3.1 7.8 + - - +
600E ALA* 1.3 72.3 - - - +
602E GLU* 1.3 64.4 + - - +
603E ASN 3.3 0.5 + - - -
604E GLY* 3.4 9.4 + - - -
606E ILE* 3.7 31.0 - - + +
608E PRO* 5.6 2.6 - - + +
636E PHE* 3.9 24.7 - - + -
641E ASN 3.7 15.7 - - - +
642E GLY 3.7 18.8 - - - +
643E PRO* 4.0 25.1 - - + -
645E LEU* 4.4 16.4 - - + -
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Residues in contact with GLU 602 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598E SER 2.7 17.8 + - - +
599E LEU* 3.2 19.1 - - - +
601E ILE* 1.3 74.5 - - - +
603E ASN* 1.3 65.2 + - - +
604E GLY 3.6 2.4 + - - -
643E PRO* 4.0 18.2 - - + +
682E ARG* 2.6 50.8 + - - -
801E TRP* 4.3 7.7 + - - -
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Residues in contact with ASN 603 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417E ASN* 4.0 24.2 + - + +
424E ASP* 5.8 1.4 - - - +
425E ASP 5.9 1.0 + - - -
599E LEU* 2.6 39.8 + - - +
600E ALA 3.5 1.3 - - - +
601E ILE 3.2 0.2 - - - -
602E GLU* 1.3 80.7 - - - +
604E GLY* 1.3 54.2 + - - +
605E ILE* 2.9 27.3 + - + +
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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