Contacts of the strand formed by residues 153 - 158 (chain D) in PDB entry 2ZJQ
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 ASP 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D VAL* 3.1 4.0 + - - -
37D ASN* 3.0 43.1 + - + +
130D LEU 2.6 27.8 + - - +
131D GLY* 3.4 6.2 - - - -
132D ILE 4.0 0.7 - - - +
152D MET* 1.3 74.7 - - - +
154D ILE* 1.3 76.8 + - - +
155D THR* 4.3 2.4 + - - -
2282X G 5.6 1.3 + - - -
2283X G 2.8 46.0 + - - +
2284X U 3.9 23.5 + - + +
2292X C 5.4 4.3 - - - +
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Residues in contact with ILE 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ILE* 3.4 27.1 - - + -
35D VAL 2.8 19.3 - - - +
36D VAL* 3.2 12.1 - - + -
99D PHE* 4.7 9.4 - - + -
103D LEU* 5.8 7.6 - - + -
130D LEU* 2.7 57.7 + - + +
132D ILE* 3.9 18.8 - - + -
152D MET* 3.2 33.7 - - + -
153D ASP* 1.3 86.9 - - - +
155D THR* 1.3 66.2 + - - +
156D ILE* 5.4 1.3 - - + -
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Residues in contact with THR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LYS 3.4 2.4 - - - +
34D ILE* 3.1 14.6 - - - +
35D VAL* 3.0 41.2 + - + +
128D TYR 4.6 0.4 - - - -
129D ASN* 4.8 9.2 - - - +
130D LEU 5.0 0.2 - - - +
153D ASP* 4.9 3.1 + - - -
154D ILE* 1.3 78.2 - - - +
156D ILE* 1.3 64.7 + - - +
157D VAL* 4.3 6.7 - - + -
2282X G 5.4 2.0 + - - +
2292X C 3.2 23.0 + - - +
2293X G 3.4 42.8 + - - +
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Residues in contact with ILE 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ILE* 5.7 1.6 - - + -
34D ILE* 3.5 19.5 - - + -
127D ASN* 3.3 9.2 - - - +
128D TYR* 2.8 73.1 + - + +
130D LEU* 4.8 18.8 - - + -
154D ILE* 4.1 1.9 + - + -
155D THR* 1.3 74.0 - - - +
157D VAL* 1.3 60.5 + - - +
158D THR* 3.1 29.2 - - + -
170D LEU* 3.7 14.4 - - + -
175D LEU* 5.2 6.7 - - + -
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Residues in contact with VAL 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ILE* 3.3 7.3 - - - +
32D GLU* 2.5 63.1 + - + +
33D LYS* 3.0 50.8 + - + +
34D ILE* 4.4 0.2 - - - +
35D VAL* 4.4 2.7 - - + -
127D ASN* 3.7 7.2 - - - +
155D THR* 4.3 11.7 - - + -
156D ILE* 1.3 74.7 - - - +
158D THR* 1.3 60.2 + - - +
2293X G 4.2 15.5 - - - +
2294X U 4.6 11.9 - - - +
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Residues in contact with THR 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ARG 3.0 15.0 - - - +
31D ILE* 4.5 9.6 - - + -
32D GLU* 4.6 2.0 - - - -
125D ARG 4.4 0.3 - - - +
126D GLY 2.5 27.9 + - - +
127D ASN* 2.6 35.2 + - - +
156D ILE* 3.1 30.5 - - + -
157D VAL* 1.3 78.5 - - - +
159D THR* 1.3 58.5 + - - +
160D ALA* 3.0 16.4 + - - +
166D ALA* 5.5 1.1 - - + -
169D LEU* 4.9 4.3 - - + -
170D LEU* 4.4 11.4 - - + -
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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