Contacts of the strand formed by residues 144 - 150 (chain j) in PDB entry 5GJQ
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 GLY 144 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139j TRP* 3.2 22.0 - - - -
140j ASP 3.0 34.9 + - - -
141j LYS 4.7 0.4 - - - -
142j HIS 3.6 1.2 - - - -
143j TYR* 1.3 74.7 - - - +
145j PHE* 1.3 65.4 + - - -
146j GLN* 3.2 7.1 + - - -
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Residues in contact with PHE 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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38j LEU* 3.7 28.5 - - + +
39j ALA 4.9 2.2 - - - +
40j ASN 4.1 14.6 - - - -
41j ASP* 3.9 6.7 - - - -
42j GLY* 3.6 28.5 - - - +
43j VAL* 3.7 20.0 - - + -
138j GLY 3.5 2.7 - - - -
139j TRP* 3.9 18.4 - + + -
143j TYR 3.4 5.9 + - - +
144j GLY* 1.3 72.8 - - - -
146j GLN* 1.3 66.6 + - - +
216j LEU* 3.4 33.9 - - + -
217j THR* 4.0 3.6 - - - -
218j ARG* 3.9 28.5 - - + -
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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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38j LEU* 4.2 7.2 - - - -
43j VAL* 4.3 2.6 - - - +
107j CYS* 3.7 9.9 - - + +
108j GLU* 4.8 1.2 - - - +
136j TYR 3.7 0.6 - - - +
137j ILE* 3.4 6.9 - - - +
138j GLY 2.9 30.8 + - - +
140j ASP* 2.5 37.9 + - - +
143j TYR* 3.5 30.5 - - + +
144j GLY 3.2 12.4 + - - +
145j PHE* 1.3 82.1 - - - +
147j LEU* 1.3 61.3 - - - +
148j TYR* 2.4 45.6 + - + +
57k ARG* 3.8 4.5 + - - +
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Residues in contact with LEU 147 (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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36j GLY* 3.3 37.7 - - - +
37j ILE 4.2 2.2 - - - +
38j LEU* 4.4 8.9 - - + +
43j VAL* 4.3 9.0 - - + -
45j LEU* 4.7 0.2 - - + -
135j LEU* 4.6 9.4 - - + -
136j TYR 3.2 17.5 - - - +
137j ILE* 3.6 18.6 - - + -
146j GLN* 1.3 76.6 - - - +
148j TYR* 1.3 72.1 + - - +
158j GLY* 3.5 4.3 - - - -
159j TRP 3.0 35.3 + - - +
160j LYS 4.2 3.1 - - - +
161j ALA* 3.9 20.2 - - - +
162j THR* 4.1 15.7 - - + -
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Residues in contact with TYR 148 (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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107j CYS* 4.0 20.2 - - + -
108j GLU* 3.5 33.2 + - + +
111j VAL* 4.2 14.4 - - + -
135j LEU* 3.3 9.2 - - - +
136j TYR* 2.9 47.5 + - + +
146j GLN* 2.4 46.6 + - + -
147j LEU* 1.3 78.0 - - - +
149j GLN* 1.3 62.5 + - - +
156j TYR* 4.1 13.5 - + + -
157j GLY 3.3 11.0 - - - -
158j GLY* 3.7 20.2 - - - -
159j TRP* 4.5 3.1 - - - +
57k ARG* 3.5 13.5 + - - -
58k THR* 4.1 11.2 - - + -
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Residues in contact with GLN 149 (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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134j LEU 3.2 11.7 - - - +
135j LEU* 3.7 9.4 - - + -
136j TYR* 4.5 2.9 - - - -
148j TYR* 1.3 77.9 - - - +
150j SER* 1.3 69.0 + - - +
151j ASP* 3.9 16.7 + - - +
155j ASN 4.1 0.2 - - - +
156j TYR* 3.0 6.7 - - - +
157j GLY 2.8 29.5 + - - +
159j TRP* 3.1 33.4 + - + +
162j THR* 3.2 16.6 + - - -
163j CYS 4.3 2.4 + - - -
164j ILE* 3.3 34.8 - - + +
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Residues in contact with SER 150 (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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115j CYS* 3.5 24.7 - - - -
118j LYS* 2.6 26.9 + - - -
133j SER* 3.2 8.5 + - - -
134j LEU* 2.9 36.8 + - - +
136j TYR* 3.0 24.3 + - - -
149j GLN* 1.3 76.9 - - - +
151j ASP* 1.3 64.6 + - - +
155j ASN 3.4 4.7 - - - -
156j TYR* 4.0 1.3 - - - -
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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