Contacts of the strand formed by residues 120 - 128 (chain A) in PDB entry 2JBO
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 ILE 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A VAL* 4.1 9.0 - - - +
108A HIS* 3.4 45.5 - - + +
109A TRP* 3.6 39.8 - - + +
112A SER* 3.0 21.1 + - - +
119A ARG* 1.3 80.6 + - - +
121A VAL* 1.3 64.0 + - - +
122A ASP* 4.0 6.3 - - - +
123A VAL* 3.8 28.0 - - + -
136A ILE* 3.9 23.6 - - + -
137A VAL 3.9 3.8 - - - +
138A MET* 4.2 2.9 - - + +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 4.2 8.3 - - - +
90A PHE* 3.8 31.4 - - + -
109A TRP* 5.4 4.4 - - - -
119A ARG* 3.6 18.6 + - + +
120A ILE* 1.3 75.1 - - - +
122A ASP* 1.3 76.1 + - - +
137A VAL* 2.8 21.5 + - + +
139A GLU* 4.5 3.8 - - + +
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 6.1 0.9 - - - -
53A GLN 5.4 2.0 - - - +
55A LYS* 3.4 35.2 + - + +
63A TYR* 3.0 26.6 + - - -
109A TRP* 5.7 3.4 - - - -
120A ILE* 4.2 2.8 - - - +
121A VAL* 1.3 85.6 - - - +
123A VAL* 1.3 65.8 + - - +
124A TYR* 3.8 13.2 + - - -
137A VAL* 2.8 43.0 + - - +
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 4.0 21.1 - - + +
53A GLN 3.5 6.2 + - - +
54A ILE* 3.5 23.6 - - + -
55A LYS* 2.8 33.3 + - - +
105A VAL* 4.2 22.2 - - + -
120A ILE* 3.8 20.2 - - + -
122A ASP* 1.3 85.3 + - - +
124A TYR* 1.3 64.3 + - - +
134A LEU* 4.9 10.3 - - + -
135A LEU 3.4 10.5 - - - +
136A ILE* 4.3 10.8 - - + -
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Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE* 4.1 2.7 - - - -
55A LYS* 3.1 35.5 - - + +
57A ASN* 3.3 28.3 - - - -
59A ILE* 3.4 40.2 - - + -
62A ASP* 2.6 32.7 + - - +
63A TYR* 3.4 13.2 - + - -
122A ASP* 3.8 27.0 + - - -
123A VAL* 1.3 80.4 - - - +
125A GLU* 1.3 59.1 + - - +
126A ASN* 3.9 12.6 - - - +
133A CYS 3.6 0.2 - - - +
134A LEU* 3.4 3.6 - - - -
135A LEU* 2.8 45.9 + - + +
137A VAL* 4.3 3.1 - - + -
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ILE* 3.4 18.2 - - + +
55A LYS 2.9 9.1 + - - -
56A LYS* 3.6 38.5 + - + +
97A ASP* 3.8 13.5 - - - +
102A ARG* 3.3 18.6 + - - +
124A TYR* 1.3 73.0 - - - +
126A ASN* 1.3 70.1 + - - +
132A LYS* 3.3 32.1 + - + +
133A CYS 3.1 12.1 - - - +
134A LEU* 4.1 7.2 - - + -
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Residues in contact with ASN 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LYS 3.5 8.6 + - - -
57A ASN 3.1 21.8 + - - -
58A ALA* 3.7 5.8 - - - +
59A ILE* 3.1 26.2 + - - +
124A TYR* 3.9 7.6 + - - +
125A GLU* 1.3 88.8 + - - +
127A LEU* 1.3 67.5 + - - +
128A TYR* 6.0 0.9 - - + -
132A LYS* 3.6 3.3 - - - -
133A CYS* 2.8 35.6 + - + +
135A LEU* 3.5 26.9 - - + +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ASN* 1.3 79.6 - - - +
128A TYR* 1.3 63.1 + - - +
129A ALA 4.2 0.7 - - - -
130A GLY* 3.7 37.7 - - - +
131A ARG 3.6 9.0 - - - -
132A LYS* 4.0 9.2 - - + +
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Residues in contact with TYR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A MET* 3.4 40.2 - - + -
126A ASN* 6.0 0.4 - - + -
127A LEU* 1.3 76.9 - - - +
129A ALA* 1.3 80.5 + - + +
131A ARG* 2.8 38.4 + - - +
133A CYS* 4.0 13.9 - - + -
135A LEU* 5.8 0.9 - - + -
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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