Contacts of the strand formed by residues 132 - 140 (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 VAL 132 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28j ILE* 3.5 9.1 - - - +
76j VAL* 3.6 15.9 - - + -
77j ALA 3.6 5.6 - - - +
78j GLY 4.6 0.9 - - - -
79j ILE 3.2 29.6 - - - +
82j ASP* 3.7 6.1 - - + -
83j ALA* 3.7 19.3 - - + +
86j LEU* 4.0 17.0 - - + -
118j LYS* 4.4 5.7 + - - +
130j PHE 2.6 13.0 + - - +
131j GLY* 1.3 76.4 - - - +
133j SER* 1.3 72.5 + - - +
134j LEU* 3.6 17.3 - - + -
151j ASP 4.1 1.7 - - - -
152j PRO* 3.3 19.9 - - - +
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Residues in contact with SER 133 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28j ILE* 3.2 22.0 - - - +
76j VAL* 3.5 2.1 - - - +
77j ALA* 2.9 35.6 + - - +
132j VAL* 1.3 78.4 - - - +
134j LEU* 1.3 64.9 + - - +
150j SER 3.2 9.0 + - - -
151j ASP* 3.1 27.2 + - - -
164j ILE* 4.0 28.8 - - - +
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Residues in contact with LEU 134 (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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74j CYS* 4.1 15.5 - - - -
75j SER 3.4 5.2 - - - +
76j VAL* 4.0 14.4 - - + -
86j LEU* 4.4 8.7 - - + -
87j THR* 5.0 2.9 - - + -
90j LEU* 4.0 22.9 - - + -
114j LEU* 3.9 7.4 - - + -
118j LYS* 3.4 27.8 - - - +
132j VAL* 3.6 19.5 - - + -
133j SER* 1.3 78.1 - - - +
135j LEU* 1.3 65.7 + - - +
136j TYR* 3.6 26.4 - - + +
149j GLN* 3.2 5.9 - - - +
150j SER* 2.9 37.6 + - - +
164j ILE* 5.6 1.1 - - - -
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Residues in contact with LEU 135 (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 CYS* 3.6 38.8 - - - +
35j LEU* 3.9 17.0 - - - -
36j GLY* 4.0 4.5 - - - +
45j LEU* 3.8 16.5 - - + +
74j CYS* 3.2 5.5 - - - +
75j SER* 2.9 35.0 + - - +
134j LEU* 1.3 75.5 - - - +
136j TYR* 1.3 61.2 + - - +
137j ILE 4.2 0.2 + - - -
147j LEU* 4.6 3.6 - - + -
148j TYR 3.3 12.3 - - - +
149j GLN* 3.7 23.3 - - + -
162j THR* 3.9 21.1 - - + +
163j CYS* 4.7 0.2 - - - -
164j ILE* 4.2 17.9 - - + +
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Residues in contact with TYR 136 (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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68j LEU* 4.3 7.6 - - + -
72j MET* 5.4 10.1 - - + -
73j ALA 3.8 3.6 - - - +
74j CYS* 4.0 13.7 - - + -
90j LEU* 4.1 26.9 - - + -
107j CYS* 5.9 1.1 - - + -
110j LEU* 5.6 0.7 - - + -
111j VAL* 3.5 44.9 + - + +
114j LEU* 3.2 24.8 - - + +
115j CYS* 4.9 0.2 - - - -
118j LYS* 4.5 0.2 + - - -
134j LEU* 3.6 20.4 - - + +
135j LEU* 1.3 74.3 - - - +
137j ILE* 1.3 64.6 - - - +
146j GLN 3.7 0.9 - - - +
147j LEU* 3.2 7.6 - - - +
148j TYR* 2.9 50.7 + - + +
150j SER* 3.0 32.1 + - - -
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Residues in contact with ILE 137 (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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43j VAL* 3.6 32.8 - - + +
44j LEU 4.7 1.1 - - - +
45j LEU* 3.6 44.4 - - + +
65j ILE* 5.8 0.2 - - + -
72j MET* 3.3 5.7 - - - +
73j ALA* 2.9 45.6 + - + +
107j CYS* 5.5 1.1 - - - -
136j TYR* 1.3 78.9 - - - +
138j GLY* 1.3 59.3 + - - +
146j GLN 3.4 4.9 - - - +
147j LEU* 3.6 15.3 - - + -
214j ALA* 4.9 7.4 - - + +
215j THR 5.2 1.3 - - - -
216j LEU* 3.7 29.6 - - + +
225j ILE* 5.4 2.0 - - + -
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Residues in contact with GLY 138 (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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43j VAL* 4.6 1.2 - - - +
71j ASP 3.4 12.6 - - - -
72j MET* 4.1 7.4 - - - -
107j CYS* 3.8 9.9 - - - +
137j ILE* 1.3 78.1 - - - +
139j TRP* 1.3 61.8 + - - -
144j GLY 3.6 0.7 - - - +
145j PHE* 3.5 4.2 - - - +
146j GLN* 2.9 33.7 + - - +
216j LEU* 3.7 10.7 - - - +
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Residues in contact with TRP 139 (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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71j ASP* 3.1 30.8 + - - +
72j MET* 5.1 1.7 - - - +
105j ILE 5.3 1.0 - - - +
107j CYS* 3.8 7.2 - - - -
138j GLY* 1.3 76.0 - - - -
140j ASP* 1.3 80.6 + - - +
141j LYS* 3.8 21.3 - - + -
144j GLY* 3.2 32.4 - - - -
145j PHE* 3.6 22.3 - + + -
216j LEU* 4.1 15.5 - - + -
218j ARG* 3.2 61.2 - - + +
223j THR* 4.2 8.1 - - - +
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Residues in contact with ASP 140 (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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105j ILE 5.1 1.6 - - - +
106j PRO* 3.9 23.6 - - + +
107j CYS* 3.3 17.5 + - - -
108j GLU 4.9 0.5 + - - -
139j TRP* 1.3 91.4 - - - +
141j LYS* 1.3 58.5 + - + +
142j HIS* 2.9 15.1 + - + +
143j TYR* 2.8 34.2 + - - +
144j GLY* 3.0 26.1 + - - -
146j GLN* 2.5 25.5 + - - +
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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