Contacts of the strand formed by residues 48 - 55 (chain B) in PDB entry 1R88
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 ARG 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B SER* 3.0 30.2 + - - +
46B MET* 3.8 13.0 + - + +
47B GLY* 1.3 79.8 - - - +
49B ASP* 1.3 74.3 + - - +
50B ILE* 3.8 25.7 - - + +
51B PRO* 5.9 1.4 - - - +
99B GLY* 3.8 23.2 + - - -
113B SER* 3.0 40.2 + - - +
116B TRP* 4.0 11.5 - - - +
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Residues in contact with ASP 49 (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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40B MET* 3.8 44.4 - - + +
41B VAL 3.6 4.5 - - - +
42B PRO* 3.4 27.1 - - - +
48B ARG* 1.3 87.6 + - - +
50B ILE* 1.3 61.1 + - - +
51B PRO* 3.8 7.0 - - - +
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Residues in contact with ILE 50 (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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39B LEU 4.4 0.2 - - - -
40B MET* 3.6 2.0 - - - -
41B VAL 2.9 29.8 + - - +
43B SER* 3.8 17.3 - - - -
46B MET* 3.8 16.6 - - + -
48B ARG* 3.8 40.8 - - + +
49B ASP* 1.3 72.8 - - - +
51B PRO* 1.3 74.3 - - + +
52B VAL* 3.4 7.4 + - + +
97B PRO* 4.3 1.8 - - + -
98B ALA 3.6 20.2 - - - +
116B TRP* 3.9 7.6 - - + -
119B PHE* 3.6 40.8 - - + -
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Residues in contact with PRO 51 (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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39B LEU 3.4 8.7 - - - +
40B MET* 3.8 19.7 - - + -
48B ARG* 5.9 1.6 - - - +
49B ASP 3.8 7.6 - - - +
50B ILE* 1.3 89.1 - - + +
52B VAL* 1.3 61.8 + - - +
53B ALA 4.2 0.4 - - - -
72B PRO 4.2 13.0 - - - +
73B ASP* 3.5 30.5 - - - +
96B ALA 4.8 0.2 - - - -
97B PRO* 3.5 0.5 - - - +
98B ALA* 2.8 37.9 + - + +
99B GLY* 5.6 0.9 - - - -
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLU 3.4 0.7 - - - +
38B ASN* 4.9 1.3 - - - -
39B LEU* 2.9 45.0 + - + +
41B VAL* 3.8 23.6 - - + -
50B ILE* 3.6 20.9 - - + +
51B PRO* 1.3 79.0 - - - +
53B ALA* 1.3 70.0 + - - +
54B PHE* 3.5 1.5 + - + -
95B VAL* 3.7 30.3 - - + -
96B ALA 3.7 8.5 - - - +
97B PRO* 4.2 8.7 - - + -
119B PHE* 4.3 6.7 - - + -
124B LEU* 4.3 6.5 - - + -
128B LEU* 5.8 0.7 - - + -
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Residues in contact with ALA 53 (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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36B TYR* 3.4 26.7 - - + +
37B GLU 3.5 6.7 - - - -
38B ASN* 5.0 2.2 - - - +
51B PRO 4.2 0.6 - - - -
52B VAL* 1.3 70.6 - - - +
54B PHE* 1.3 58.5 + - - +
74B VAL* 5.7 3.4 - - + -
75B SER* 5.8 1.1 - - - +
78B VAL* 3.9 15.3 - - + -
84B MET* 3.9 13.6 - - + +
94B VAL 3.5 1.4 - - - +
95B VAL* 3.4 4.9 - - - -
96B ALA* 2.9 40.5 + - + +
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Residues in contact with PHE 54 (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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36B TYR* 3.9 4.4 - - - -
37B GLU* 3.0 56.4 + - + +
39B LEU* 3.4 32.8 - - + -
52B VAL* 4.8 2.9 - - + -
53B ALA* 1.3 75.6 - - - +
55B LEU* 1.3 57.7 + - - +
56B ALA* 3.8 31.3 + - + -
93B SER* 3.8 25.1 - - - -
94B VAL 3.3 10.8 - - - -
95B VAL* 3.9 11.0 - - + -
128B LEU* 4.4 6.1 - - + -
132B ARG* 3.9 29.8 - - + -
134B LEU* 4.1 18.4 - - + -
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Residues in contact with LEU 55 (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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34B ALA* 5.6 6.7 - - + -
35B PRO 3.5 25.6 - - - +
36B TYR* 4.3 5.2 - - + -
53B ALA 4.3 0.2 - - - -
54B PHE* 1.3 74.2 - - - +
56B ALA* 1.3 76.1 + - - +
57B GLY* 4.5 0.2 - - - -
84B MET* 3.8 33.7 - - + +
88B ALA* 3.8 33.7 - - + -
89B GLY 5.4 0.4 - - - +
92B ILE 4.5 1.2 - - - +
93B SER* 3.3 3.1 - - - -
94B VAL* 3.0 38.5 + - + -
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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