Contacts of the helix formed by residues 593 - 598 (chain E) in PDB entry 1ZXE
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 LEU 593 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592E SER* 1.3 85.2 + - - +
594E ARG* 1.3 66.8 + - - +
595E TYR 3.5 1.1 + - - -
596E ALA* 3.6 8.1 + - + +
597E SER* 3.1 23.3 + - - -
664E GLU* 3.6 45.8 - - + +
768E ARG 3.9 20.2 - - - +
769E ARG* 5.8 1.8 - - - -
649F SER* 3.5 24.0 - - - +
650F LEU* 4.2 1.3 - - + -
651F ASN* 4.6 1.3 - - - -
825F TYR* 3.9 11.2 - - - +
829F GLN* 3.7 37.0 - - + +
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Residues in contact with ARG 594 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593E LEU* 1.3 73.8 - - - +
595E TYR* 1.3 54.9 + - - +
597E SER* 3.1 6.0 + - - -
598E ASP* 2.7 49.0 + - + +
599E PHE* 4.9 3.0 - - + -
660E ALA* 3.8 14.1 - - - +
661E ALA 5.0 0.2 + - - -
662E TRP* 3.6 43.0 - - + +
787E GLN* 4.2 8.5 + - - -
648F ALA* 3.0 32.3 + - - +
649F SER 2.9 21.0 + - - +
650F LEU 4.9 0.9 - - - +
651F ASN* 4.4 4.8 - - - +
657F ARG* 3.5 26.9 - - - +
658F TYR 3.3 7.5 + - - -
659F TYR* 2.7 43.1 + - - +
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Residues in contact with TYR 595 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594E ARG* 1.3 72.7 - - - +
596E ALA* 1.3 62.3 + - + +
599E PHE* 2.9 68.5 + + + +
601E GLU* 2.8 38.8 + - + +
614E VAL* 3.1 21.7 - - - +
616E ALA* 4.2 2.5 - - + +
627E ILE* 3.8 21.1 - - + -
629E LYS* 3.7 16.8 - - - -
662E TRP* 4.1 6.9 - + + +
664E GLU* 2.9 25.7 + - - +
785E PHE* 3.5 27.6 - + + -
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Residues in contact with ALA 596 (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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592E SER 4.6 11.9 - - - +
593E LEU* 3.6 10.1 + - + +
594E ARG 3.4 0.2 - - - -
595E TYR* 1.3 82.7 - - + +
597E SER* 1.3 58.8 + - - +
599E PHE 4.2 8.3 - - - +
664E GLU* 4.7 1.2 + - - +
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Residues in contact with SER 597 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592E SER 4.7 10.3 - - - -
593E LEU 3.1 19.4 + - - -
594E ARG 3.3 2.1 + - - -
596E ALA* 1.3 78.9 - - - +
598E ASP* 1.3 64.3 + - - +
599E PHE 3.7 0.4 - - - -
619E ALA* 4.5 8.1 - - - +
651F ASN* 2.7 35.1 + - - -
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Residues in contact with ASP 598 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594E ARG* 2.7 24.6 + - + +
597E SER* 1.3 76.7 - - - +
599E PHE* 1.3 72.6 + - + +
618E ASN* 3.5 10.8 + - - +
619E ALA* 2.8 33.5 + - - +
620E LEU* 3.8 25.2 - - - +
651F ASN* 3.4 16.4 + - - -
657F ARG* 2.9 35.9 + - - -
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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