Contacts of the strand formed by residues 142 - 148 (chain B) in PDB entry 2ZOT
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 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B GLU* 4.7 8.9 + - - -
81B THR* 3.8 34.4 + - + +
82B LEU 3.1 7.6 - - - +
83B SER* 4.2 6.4 - - - -
90B PHE* 3.7 3.3 - - - -
140B ARG* 3.6 9.9 - - - +
141B THR* 1.3 89.3 + - - +
143B ILE* 1.3 76.1 + - - +
144B GLN* 5.9 9.8 - - + +
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Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B VAL 3.8 0.6 - - - +
81B THR* 3.5 3.1 - - - +
82B LEU* 2.9 59.7 + - + +
90B PHE* 4.4 1.3 - - + -
93B PHE* 3.4 49.4 - - + -
95B LEU* 3.8 16.2 - - + -
122B THR* 4.4 12.1 - - + -
140B ARG* 3.5 27.8 - - + +
142B ARG* 1.3 87.0 - - - +
144B GLN* 1.3 63.1 + - - +
145B VAL* 5.1 4.0 - - + -
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Residues in contact with GLN 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ARG* 3.0 39.4 + - + +
80B VAL 3.2 10.3 - - - +
81B THR* 4.0 11.7 + - + +
117B ILE* 3.7 33.1 + - + +
118B ASP* 4.8 3.3 + - - +
122B THR* 5.2 4.2 + - - +
142B ARG* 5.9 10.8 - - + +
143B ILE* 1.3 77.0 - - - +
145B VAL* 1.3 69.1 + - - +
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ARG* 3.5 4.0 - - - +
80B VAL* 2.7 44.3 + - + +
95B LEU* 3.8 19.1 - - + -
114B PHE* 3.6 33.4 - - + -
115B GLN 3.6 15.5 - - - +
116B ILE* 5.0 4.7 - - - -
117B ILE* 3.8 10.7 - - - +
122B THR* 5.0 6.1 - - + +
132B VAL* 3.9 29.2 - - + -
143B ILE* 5.1 4.3 - - + -
144B GLN* 1.3 79.4 - - - +
146B PHE* 1.3 59.4 + - - +
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Residues in contact with PHE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A THR* 5.1 3.4 - - - -
54A ARG 3.7 20.4 - - - -
55A ARG* 3.1 48.2 - - + -
170A TYR* 3.9 14.8 - + - -
77B SER* 3.5 14.6 - - - +
78B TYR 3.1 10.8 - - - -
79B ARG* 3.7 35.9 - - + -
114B PHE* 3.4 12.1 - - - -
115B GLN* 3.0 46.5 + - + +
116B ILE 5.4 0.7 - - - -
117B ILE* 3.6 34.3 - - + -
145B VAL* 1.3 76.2 - - - +
147B TRP* 1.3 59.8 + - - +
148B ILE* 4.2 2.5 - - + +
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Residues in contact with TRP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B TYR* 4.3 3.8 - + + -
76B THR 3.2 2.6 - - - +
78B TYR* 2.6 51.3 + + + +
80B VAL* 4.0 11.9 - - + -
97B ALA* 3.4 15.2 - - + +
111B ALA 3.9 4.7 - - - -
112B GLY* 3.3 22.3 - - - -
113B THR 3.4 20.9 - - - -
114B PHE* 3.9 26.9 - + + -
146B PHE* 1.3 75.7 - - - +
148B ILE* 1.3 59.5 + - - +
149B ALA* 4.0 6.7 - - + -
150B PRO* 3.6 28.5 - - + -
157B VAL* 3.5 30.7 - - + -
159B LEU* 3.8 20.9 - - + -
181B LEU* 3.7 21.1 - - + -
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU* 3.7 40.2 - - + +
57A GLY* 4.5 5.6 - - - -
75B GLY* 3.5 28.9 - - - +
76B THR 3.2 6.3 - - - +
77B SER* 4.7 4.0 - - - +
112B GLY* 3.6 2.3 - - - -
113B THR* 2.7 60.7 + - + +
115B GLN* 4.1 17.0 - - + +
146B PHE* 5.6 1.1 - - + -
147B TRP* 1.3 72.0 - - - +
149B ALA* 1.3 69.6 + - - +
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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