Contacts of the strand formed by residues 59 - 64 (chain E) in PDB entry 1Z6Z
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 ARG 59 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E GLY 5.9 0.2 - - - -
32E SER 3.1 17.9 + - - +
33E VAL* 3.3 14.3 - - + +
34E LEU 2.8 27.4 + - - +
58E LEU* 1.3 72.2 - - - +
60E VAL* 1.3 62.7 + - - +
61E VAL* 5.2 5.8 - - + -
84E PRO* 4.3 25.6 - - + -
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Residues in contact with VAL 60 (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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34E LEU* 3.4 9.6 - - + +
36E LEU* 3.8 26.7 - - + -
48E GLU* 3.8 45.1 - - + +
51E LEU* 4.0 23.6 - - + -
58E LEU* 3.8 22.0 + - + +
59E ARG* 1.3 75.7 - - - +
61E VAL* 1.3 71.1 + - - +
62E ARG* 4.2 2.4 + - + -
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Residues in contact with VAL 61 (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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33E VAL* 4.3 14.1 - - + -
34E LEU 2.9 11.4 + - - +
35E VAL* 3.3 10.2 - - + +
36E LEU* 2.8 28.6 + - - +
59E ARG* 4.8 7.2 - - + +
60E VAL* 1.3 78.7 - - - +
62E ARG* 1.3 64.6 + - - +
63E VAL* 4.0 19.5 - - + -
79E ALA* 5.3 3.1 - - + -
83E LEU* 4.0 26.0 - - + -
84E PRO* 4.9 7.2 - - + -
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Residues in contact with ARG 62 (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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36E LEU* 3.7 8.7 - - + +
41E ASP* 2.9 29.7 + - - -
44E LEU* 3.5 44.2 - - + +
45E ARG* 3.5 20.2 - - - +
48E GLU* 2.7 33.3 + - + +
60E VAL* 4.1 5.6 + - + -
61E VAL* 1.3 76.1 - - - +
63E VAL* 1.3 63.7 + - - +
64E PRO* 3.6 9.8 - - - +
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Residues in contact with VAL 63 (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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35E VAL* 4.0 22.4 - - + -
36E LEU 2.9 12.3 + - - +
37E SER* 2.8 33.3 + - - +
38E ALA 3.6 0.3 - - - +
44E LEU* 4.1 2.0 - - - +
61E VAL* 4.0 8.5 - - + -
62E ARG* 1.3 78.8 - - - +
64E PRO* 1.3 64.2 - - + +
65E ALA* 3.4 6.8 + - + -
75E GLN* 4.0 11.0 - - + +
76E LEU* 3.7 39.3 - - + +
79E ALA* 3.8 22.0 - - + -
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Residues in contact with PRO 64 (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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38E ALA 3.1 11.0 - - - +
39E ARG 4.1 7.9 - - - +
41E ASP* 3.5 41.5 - - + +
44E LEU* 4.0 5.8 - - + -
62E ARG* 3.6 11.2 - - + +
63E VAL* 1.3 82.2 - - + +
65E ALA* 1.3 64.2 + - - +
75E GLN* 4.6 11.1 - - - +
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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