Contacts of the strand formed by residues 19 - 24 (chain E) in PDB entry 4ZZ7
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 SER 19 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213C HIS* 5.9 3.0 - - - -
3E THR* 5.5 3.8 - - - -
18E ARG* 1.3 83.0 - - - +
20E GLN* 1.3 63.9 + - - +
33E GLN* 2.7 29.4 + - - +
34E LEU 3.3 17.0 - - - -
35E ASP* 4.5 3.8 - - - -
36E LEU* 4.3 4.0 - - - +
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Residues in contact with GLN 20 (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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19E SER* 1.3 80.6 + - - +
21E ASN* 1.3 77.5 + - - +
33E GLN* 3.5 8.6 - - - -
34E LEU* 2.7 38.6 + - + +
36E LEU* 3.8 27.4 - - + +
175E GLU* 3.6 32.0 + - - +
176E ARG* 5.7 3.4 - - - +
204E ASP* 5.1 5.7 - - - +
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Residues in contact with ASN 21 (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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20E GLN* 1.3 88.6 + - - +
22E VAL* 1.3 60.5 + - - +
23E PHE* 3.9 30.1 - - + -
30E ILE* 3.3 36.6 - - + +
32E LYS 3.8 4.0 - - - -
33E GLN* 2.4 33.4 + - - +
175E GLU 5.1 1.9 - - - +
176E ARG* 5.9 0.7 - - - -
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Residues in contact with VAL 22 (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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4E ILE* 4.3 5.6 - - + -
21E ASN* 1.3 76.1 - - - +
23E PHE* 1.3 66.2 + - - +
30E ILE* 3.7 3.3 - - - -
31E GLY* 3.0 22.8 + - - -
32E LYS* 2.9 36.4 + - + +
34E LEU* 3.8 27.1 - - + +
89E GLU* 3.9 24.2 - - + +
175E GLU 4.0 11.9 - - - +
176E ARG* 4.2 15.7 - - - +
178E PRO* 4.1 11.0 - - + -
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Residues in contact with PHE 23 (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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21E ASN* 3.9 27.1 - - + -
22E VAL* 1.3 81.4 - - - +
24E ASN* 1.3 65.6 + - - +
25E PRO* 3.5 10.2 - - + +
28E GLY 3.5 25.1 - - - -
29E GLU 3.4 10.1 - - - -
30E ILE* 3.7 23.8 - - + -
31E GLY* 4.5 2.0 - - - -
88E GLU 3.8 0.5 - - - +
89E GLU* 3.7 18.9 - - - +
176E ARG 4.9 4.3 + - - +
324E ILE 5.2 3.4 - - - +
325E THR* 5.5 10.3 - - + -
362E PHE* 4.1 26.0 - + + -
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Residues in contact with ASN 24 (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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23E PHE* 1.3 71.5 - - - +
25E PRO* 1.3 56.0 - - - +
26E ALA* 3.1 23.9 + - - +
27E THR* 3.4 24.4 + - - +
28E GLY* 2.7 35.2 + - - -
29E GLU* 2.9 11.5 + - + +
31E GLY* 4.4 5.7 - - - +
87E GLY 5.1 1.6 - - - +
88E GLU* 3.4 30.0 + - + +
91E GLY* 5.9 0.2 - - - -
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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