Contacts of the strand formed by residues 142 - 146 (chain J) in PDB entry 5T0G
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 PRO 142 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36J ARG* 4.4 31.2 - - + +
37J GLY 3.2 29.6 - - - +
38J ARG* 4.8 5.6 - - - -
41J VAL* 4.4 9.0 - - + -
135J GLY 4.4 1.1 - - - +
136J PHE* 4.3 4.9 - - + -
137J ASP* 3.7 9.1 - - - +
140J GLY 4.2 3.1 - - - +
141J THR* 1.3 90.6 - - - +
143J ARG* 1.3 63.0 + - - +
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Residues in contact with ARG 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J ARG* 5.7 1.3 - - - +
41J VAL* 5.2 0.5 - - - +
68J ASN* 3.0 29.1 + - - +
69J VAL* 3.7 14.5 - - - +
101J PRO* 5.7 1.2 - - - +
102J VAL 3.1 23.0 + - - -
103J THR* 3.6 10.7 - - - +
104J VAL* 3.4 40.0 - - + +
134J VAL* 3.7 1.6 - - - +
135J GLY* 2.9 38.2 + - - +
136J PHE 2.9 38.2 + - - +
137J ASP* 2.8 43.9 + - - +
138J PHE* 4.0 6.5 - - - +
142J PRO* 1.3 77.0 - - - +
144J LEU* 1.3 64.8 + - - +
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Residues in contact with LEU 144 (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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34J GLY 6.2 0.7 - - - -
35J VAL* 4.7 4.9 - - - +
36J ARG* 3.6 38.7 - - + +
104J VAL* 4.4 4.1 - - - +
132J LEU* 5.1 8.5 - - + -
133J ILE 3.1 15.5 - - - +
134J VAL* 4.2 14.4 - - + -
143J ARG* 1.3 74.8 - - - +
145J TYR* 1.3 87.3 + - - +
155J ALA* 3.3 16.2 - - + +
156J TRP* 3.1 50.7 - - + +
157J LYS 4.5 3.8 - - - +
158J ALA* 5.0 2.9 - - - +
159J ASN* 5.9 3.6 - - + +
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Residues in contact with TYR 145 (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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104J VAL* 3.5 40.3 - - + +
105J GLU* 3.9 29.4 - - + +
108J THR* 4.0 20.0 - - + +
132J LEU* 3.3 6.1 - - - +
133J ILE* 2.8 34.7 + - - +
144J LEU* 1.3 87.2 - - - +
146J GLN* 1.3 60.0 + - - +
153J TYR* 4.1 21.8 - + + -
154J HIS* 3.4 27.6 - - - -
155J ALA* 3.4 22.7 - - + +
62K SER 5.6 0.2 + - - -
63K SER* 4.7 11.6 - - - -
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Residues in contact with GLN 146 (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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108J THR* 5.2 1.3 - - - -
131J ALA 3.5 5.8 - - - +
132J LEU* 3.4 25.7 - - + +
133J ILE* 5.4 0.4 - - - -
144J LEU* 5.8 0.7 - - + -
145J TYR* 1.3 76.1 - - - +
147J THR* 1.3 76.6 + - - +
148J ASP* 5.1 6.3 + - - +
152J THR* 4.6 5.4 + - - +
153J TYR* 3.3 23.7 - - - +
154J HIS* 2.8 52.3 + - + +
156J TRP* 3.8 32.3 - - + -
161J ILE* 5.5 1.4 - - - +
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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