Contacts of the strand formed by residues 119 - 125 (chain B) in PDB entry 1JBR
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 ALA 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TYR* 3.2 35.7 - - + +
97B PRO* 3.5 0.5 - - - +
98B THR* 3.2 37.0 + - + +
116B PRO 3.9 1.0 - - - +
117B GLY 3.6 0.4 - - - -
118B PRO* 1.3 79.7 - - + +
120B ARG* 1.3 84.0 + - - +
133B ILE* 4.7 2.0 - - + -
134B VAL 3.3 11.2 - - - +
135B ALA* 4.0 4.5 - - + -
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Residues in contact with ARG 120 (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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47B TYR* 3.8 17.2 + - - -
95B GLU* 3.4 33.3 + - + +
96B PHE 3.0 25.1 - - - +
97B PRO* 4.0 2.6 - - - +
98B THR* 3.7 5.4 - - - -
116B PRO* 3.1 29.7 + - - +
117B GLY 2.8 29.1 + - - -
119B ALA* 1.3 107.4 + - - +
121B VAL* 1.3 65.7 + - - +
122B ILE* 3.7 1.4 + - + -
133B ILE* 3.4 4.0 - - - -
134B VAL* 3.0 46.5 + - + +
136B HIS* 3.8 23.7 + - - -
140B ASN 4.1 5.3 + - - -
144B LEU* 4.6 9.4 - - + -
18D G 4.8 1.2 + - - -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA* 3.7 37.7 - - + +
30B GLU 4.5 0.2 - - - +
32B ASN* 4.7 0.9 - - + -
33B SER* 4.3 7.9 - - - +
95B GLU* 3.6 3.3 - - - -
96B PHE* 2.7 52.4 + - + +
98B THR* 3.6 12.7 - - - +
120B ARG* 1.3 73.9 - - - +
122B ILE* 1.3 66.5 + - - +
123B TYR* 3.8 13.2 - - + -
130B PHE* 3.9 29.6 - - + -
132B GLY 3.7 3.1 - - - -
133B ILE* 4.4 2.2 - - - -
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Residues in contact with ILE 122 (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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51B PHE* 3.8 15.9 - - + -
70B PHE* 3.6 26.7 - - + -
93B LEU* 4.1 19.3 - - + -
94B LEU 3.5 5.4 - - - +
95B GLU* 3.7 29.4 - - + -
120B ARG* 4.4 2.0 - - + -
121B VAL* 1.3 77.6 - - - +
123B TYR* 1.3 63.6 + - - +
130B PHE* 4.0 3.5 - - - -
131B CYS* 2.8 32.5 + - + -
132B GLY 2.7 21.3 + - - +
134B VAL* 4.0 36.6 - - + -
144B LEU* 5.6 0.2 - - + -
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Residues in contact with TYR 123 (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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33B SER* 3.6 42.6 - - - +
36B ALA* 3.7 9.7 - - - +
37B PRO 4.7 1.6 + - - -
38B LEU* 5.9 0.2 - - - -
48B PRO* 3.1 30.1 - - - +
93B LEU* 3.7 3.2 - - - +
94B LEU* 2.8 59.7 + - + +
95B GLU 4.4 0.2 - - - -
96B PHE* 3.6 23.9 - - + +
121B VAL* 3.8 10.1 - - + -
122B ILE* 1.3 76.1 - - - +
124B THR* 1.3 64.5 + - - +
128B LYS* 3.8 33.0 - - + +
129B VAL 3.2 17.7 - - - +
130B PHE* 4.5 2.9 - - - -
131B CYS* 4.3 3.4 - - - -
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Residues in contact with THR 124 (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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74B ASP* 3.1 31.9 + - - +
75B CYS* 4.1 2.0 - - - -
92B TYR 3.7 5.6 - - - +
93B LEU* 4.2 7.9 - - + -
94B LEU* 4.6 3.0 - - - +
123B TYR* 1.3 78.0 - - - +
125B TYR* 1.3 61.7 + - - +
126B PRO 3.7 0.3 - - - -
127B ASN* 3.9 4.6 - - - +
128B LYS* 2.5 37.9 + - - +
129B VAL* 2.6 44.2 + - + +
131B CYS* 3.7 17.5 - - - -
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Residues in contact with TYR 125 (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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38B LEU* 3.3 35.0 - - + -
39B SER* 5.0 1.3 - - - -
85B GLY 3.8 10.8 - - - -
86B MET* 3.0 49.9 + - + +
87B GLY 4.3 9.1 + - - -
88B LYS* 5.1 6.2 + - - +
90B ASP* 3.5 22.2 - - + -
91B HIS* 3.4 22.0 - - - +
92B TYR* 2.9 55.9 + + + +
94B LEU* 3.9 11.6 - - + +
123B TYR 4.1 0.2 + - - -
124B THR* 1.3 78.3 - - - +
126B PRO* 1.3 74.9 - - + +
127B ASN* 3.6 2.0 + - - -
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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