Contacts of the strand formed by residues 18 - 24 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16G ASN* 3.6 1.5 - - - -
17G THR* 1.3 87.4 + - - +
19G SER* 1.3 63.3 + - - +
35G ASP* 3.1 11.1 + - - +
36G LEU* 3.1 53.9 + - + +
37G ALA 4.2 10.5 + - - -
38G SER* 4.9 2.0 - - - +
204G ASP* 3.3 22.6 + - - -
206G GLU* 3.2 32.0 + - - +
18J ARG* 3.2 12.7 - - - +
19J SER 3.8 13.7 - - - +
20J GLN* 3.5 23.8 - - - +
21J ASN* 4.8 2.2 - - - +
36J LEU* 3.7 15.9 - - + -
175J GLU* 5.8 0.2 - - - -
204J ASP* 3.1 26.7 + - - +
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Residues in contact with SER 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G THR* 5.5 4.0 - - - -
18G ARG* 1.3 77.5 - - - +
20G GLN* 1.3 61.8 + - - +
33G GLN* 3.1 25.5 + - - +
34G LEU 3.3 16.6 - - - -
35G ASP* 4.4 3.4 - - - -
36G LEU* 4.2 4.5 - - - -
18J ARG* 3.6 4.2 - - - +
19J SER* 2.9 41.8 + - - +
20J GLN* 5.0 0.2 - - - +
21J ASN* 5.5 2.9 + - - -
33J GLN* 5.2 1.9 + - - -
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Residues in contact with GLN 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G SER* 1.3 77.1 - - - +
21G ASN* 1.3 79.5 + - - +
22G VAL 3.4 0.3 + - - -
33G GLN* 3.5 3.8 - - - -
34G LEU* 2.7 45.2 + - + +
36G LEU* 3.7 16.4 - - + +
175G GLU* 3.9 36.9 + - - +
176G ARG* 5.5 5.1 - - - +
204G ASP* 5.2 1.2 - - - +
17J THR* 3.5 17.2 + - - +
18J ARG* 3.2 30.0 + - - +
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Residues in contact with ASN 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G GLN* 1.3 87.1 + - - +
22G VAL* 1.3 61.6 + - - +
23G PHE* 3.8 27.3 - - + -
30G ILE* 3.2 29.3 - - + +
32G LYS 3.8 4.9 - - - -
33G GLN* 2.7 31.2 + - - +
175G GLU 5.1 1.7 - - - +
176G ARG* 6.0 0.5 - - - -
16J ASN 2.9 28.9 + - - -
17J THR* 3.8 14.1 + - - +
18J ARG* 4.5 2.0 + - - +
19J SER* 5.3 2.9 + - - -
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Residues in contact with VAL 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G ILE* 4.5 2.5 - - + -
20G GLN* 5.9 0.2 - - + -
21G ASN* 1.3 74.3 - - - +
23G PHE* 1.3 61.2 + - - +
30G ILE* 3.8 2.1 - - - -
31G GLY* 2.9 23.1 + - - -
32G LYS* 2.9 36.6 + - + +
34G LEU* 3.5 32.8 - - + +
89G GLU* 3.7 26.2 - - + +
175G GLU 3.8 16.6 - - - +
176G ARG* 4.4 11.7 - - - +
178G PRO* 4.3 8.7 - - + -
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Residues in contact with PHE 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G ASN* 3.8 31.6 - - + -
22G VAL* 1.3 78.1 - - - +
24G ASN* 1.3 59.2 + - - +
25G PRO* 3.6 9.2 - - + +
28G GLY 3.7 23.1 - - - -
29G GLU 3.4 11.9 - - - +
30G ILE* 3.7 23.1 - - + -
31G GLY* 4.2 1.6 - - - +
89G GLU* 3.8 19.4 - - - +
176G ARG 5.0 3.6 + - - +
324G ILE 5.3 3.6 - - - +
325G THR* 5.5 9.0 - - + -
362G PHE* 4.1 31.9 - + + -
16J ASN 4.9 4.3 - - - -
17J THR* 5.0 17.0 - - + -
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Residues in contact with ASN 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G PHE* 1.3 71.2 - - - +
25G PRO* 1.3 66.4 - - - +
26G ALA* 3.1 21.6 + - - +
27G THR* 3.3 28.2 + - - +
28G GLY* 2.9 27.0 + - - -
29G GLU* 2.9 12.7 + - + +
31G GLY* 4.3 6.7 - - - +
87G GLY 5.1 1.4 - - - +
88G GLU* 3.5 26.2 + - + +
91G GLY* 5.8 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