Contacts of the helix formed by residues 1763 - 1768 (chain E) in PDB entry 2ZLE
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 SER1763 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026C ALA* 4.4 0.9 - - - +
1759E THR* 3.7 19.7 + - - -
1760E GLU* 3.0 18.8 + - - +
1762E ASN* 1.3 86.8 - - - +
1764E GLU* 1.3 67.2 + - - +
1765E LEU* 4.1 6.2 + - - -
1766E ALA* 3.0 23.9 + - - +
1767E LYS* 3.4 7.1 + - - +
1778E PHE* 3.8 6.4 - - - -
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Residues in contact with GLU1764 (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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1234D VAL 4.4 0.5 - - - +
1235D THR* 2.1 60.8 + - - +
1236D ASP* 4.0 12.9 + - - +
1237D GLN* 2.8 17.9 - - - +
1762E ASN 3.6 1.3 + - - -
1763E SER* 1.3 73.1 - - - +
1765E LEU* 1.3 56.1 + - + +
1767E LYS* 3.4 7.8 + - - +
1768E ALA* 2.6 39.8 + - + +
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Residues in contact with LEU1765 (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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1022C GLU* 3.9 20.6 - - + +
1023C LEU* 3.2 0.2 - - - +
1025C LYS* 6.0 0.7 - - + -
1026C ALA* 3.6 7.9 - - + -
1763E SER* 3.1 5.2 - - - +
1764E GLU* 1.3 79.8 - - + +
1766E ALA* 1.3 58.7 + - - +
1767E LYS 3.2 1.8 - - - -
1768E ALA* 3.9 5.2 - - + -
1769E MET* 3.0 54.2 - - + +
1778E PHE* 3.6 1.6 - - - -
1780E SER* 3.9 21.8 - - - +
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Residues in contact with ALA1766 (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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1023C LEU* 2.5 34.9 - - + +
1761E LEU* 3.6 28.7 - - - +
1762E ASN 4.6 0.2 - - - -
1763E SER* 3.0 22.4 + - - +
1765E LEU* 1.3 74.0 - - - +
1767E LYS* 1.3 57.8 + - - +
1770E LYS* 3.3 1.0 + - - -
1771E VAL* 3.1 25.7 + - + +
1774E GLN* 4.8 1.8 + - - +
1778E PHE* 3.6 12.8 - - + -
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Residues in contact with LYS1767 (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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1761E LEU 5.1 3.1 - - - +
1762E ASN* 3.6 27.8 + - - +
1763E SER 3.4 8.2 + - - +
1764E GLU* 3.8 8.3 - - - +
1765E LEU 3.2 0.2 - - - -
1766E ALA* 1.3 78.9 - - + +
1768E ALA* 1.3 57.6 + - - +
1769E MET 2.9 4.7 - - - -
1770E LYS* 2.8 36.5 + - - +
1774E GLN* 5.7 3.1 - - - +
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Residues in contact with ALA1768 (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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1022C GLU* 2.0 39.6 - - - +
1236D ASP* 4.8 16.1 + - + +
1764E GLU* 2.6 24.4 + - + +
1765E LEU* 4.2 4.7 - - + -
1767E LYS* 1.3 72.0 - - - +
1769E MET* 1.3 51.2 + - - +
1770E LYS* 4.6 2.8 - - - +
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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