Contacts of the strand formed by residues 18 - 24 (chain J) 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 ARG 18 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18G ARG* 3.2 15.2 - - - +
19G SER 3.6 13.5 - - - +
20G GLN* 3.2 34.3 + - + +
21G ASN* 4.5 2.9 - - - +
36G LEU* 3.6 12.3 - - + +
204G ASP* 4.0 8.4 + - - +
16J ASN 3.6 1.8 - - - -
17J THR* 1.3 84.6 + - - +
19J SER* 1.3 65.2 + - - +
35J ASP* 3.3 8.9 + - - +
36J LEU* 3.0 48.0 + - + +
37J ALA 4.8 5.7 + - - -
38J SER* 5.3 2.8 - - - +
204J ASP* 2.9 40.1 + - - -
206J GLU* 2.9 35.3 + - - +
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Residues in contact with SER 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G ARG* 3.8 4.9 - - - +
19G SER* 2.9 43.7 + - - +
21G ASN* 5.3 2.6 + - - -
33G GLN* 4.4 6.2 + - - -
3J THR* 6.0 2.2 - - - -
18J ARG* 1.3 78.2 - - - +
20J GLN* 1.3 64.3 + - - +
33J GLN* 3.3 21.7 + - - -
34J LEU 3.3 13.0 - - - -
35J ASP* 4.7 2.7 - - - -
36J LEU* 4.1 3.6 - - - -
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Residues in contact with GLN 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G THR* 3.5 22.3 + - - +
18G ARG* 3.5 22.8 - - + +
19J SER* 1.3 78.8 + - - +
21J ASN* 1.3 77.0 + - - +
22J VAL 3.5 0.7 + - - -
33J GLN* 3.6 4.1 - - - -
34J LEU* 2.7 43.0 + - + +
36J LEU* 3.9 16.4 - - + +
175J GLU* 3.5 45.1 + - + +
176J ARG* 5.0 8.1 - - - +
204J ASP* 5.0 0.5 - - - +
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Residues in contact with ASN 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ASN* 3.0 33.1 + - - +
17G THR 3.7 9.4 + - - +
18G ARG* 4.8 1.4 - - - +
19G SER* 5.5 3.8 + - - -
20J GLN* 1.3 84.7 + - - +
22J VAL* 1.3 61.5 - - - +
23J PHE* 3.7 25.1 - - + -
30J ILE* 3.8 29.3 - - + +
32J LYS 3.8 5.4 - - - -
33J GLN* 2.7 31.4 + - - +
175J GLU 5.3 0.7 - - - +
176J ARG* 5.9 0.9 - - - -
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Residues in contact with VAL 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J ILE* 4.6 2.2 - - + -
20J GLN 4.0 0.9 - - - +
21J ASN* 1.3 75.7 - - - +
23J PHE* 1.3 63.6 + - - +
30J ILE* 3.8 2.6 - - - -
31J GLY* 2.9 22.1 + - - -
32J LYS* 3.0 37.3 + - + +
34J LEU* 3.7 31.0 - - + +
89J GLU* 3.5 26.0 - - + +
175J GLU 3.9 14.6 - - - +
176J ARG* 4.0 15.3 - - - +
178J PRO* 3.9 10.3 - - + -
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Residues in contact with PHE 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ASN 4.2 17.3 - - - -
17G THR* 5.0 13.9 - - + -
21J ASN* 3.7 24.0 - - + -
22J VAL* 1.3 83.6 - - - +
24J ASN* 1.3 65.4 + - - +
25J PRO* 3.8 3.6 - - + -
28J GLY 3.6 24.7 - - - -
29J GLU 3.5 11.0 - - - -
30J ILE* 4.1 18.2 - - + -
31J GLY* 4.3 3.6 + - - -
88J GLU* 4.1 1.4 - - - +
89J GLU* 4.0 20.2 - - - +
176J ARG 4.8 3.9 + - - +
324J ILE 5.3 2.7 - - - +
325J THR* 5.4 11.0 - - + -
362J PHE* 3.9 28.7 - + + -
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Residues in contact with ASN 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J PHE* 1.3 74.9 - - - +
25J PRO* 1.3 63.0 - - - +
26J ALA* 3.1 24.7 + - - +
27J THR* 3.2 24.9 + - - +
28J GLY* 2.9 26.5 + - - -
29J GLU* 3.0 9.3 + - + +
31J GLY* 4.4 6.5 - - - +
87J GLY 5.4 0.9 - - - +
88J GLU* 3.7 26.2 + - + +
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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