Contacts of the strand formed by residues 83 - 87 (chain B) in PDB entry 2XMR
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 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B THR 3.6 0.9 - - - +
40B VAL* 3.2 5.9 - - - +
41B TYR* 2.9 47.7 + - + +
42B GLY* 3.5 15.4 - - - +
51B ILE* 3.2 21.3 - - + +
69B PHE* 4.2 12.6 - - + -
75B GLN* 4.0 14.5 - - - +
78B ILE* 3.2 33.6 + - + +
79B GLN* 4.5 7.3 + - - +
81B PHE* 2.9 25.7 + - - -
82B VAL* 1.3 74.4 - - - +
84B VAL* 1.3 63.6 + - - +
85B HIS* 3.6 7.6 - - + +
1305B ACT 2.8 54.0 + - + +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 3.9 31.4 - - + -
39B THR 3.4 3.6 - - - +
40B VAL* 4.5 4.9 - - + -
50B ALA* 4.1 10.3 - - + -
51B ILE 2.8 10.1 + - - +
52B LEU* 3.3 19.5 - - + +
53B THR 3.1 22.9 + - - -
83B ARG* 1.3 76.6 - - - +
85B HIS* 1.3 62.5 + - - +
86B VAL* 3.7 2.3 + - + -
117B VAL* 4.1 11.9 - - + -
118B LEU* 5.7 0.9 - - + -
121B LEU* 3.7 12.8 - - + -
123B PHE* 3.7 33.2 - - + -
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Residues in contact with HIS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 3.3 2.4 - - - -
39B THR* 2.7 38.4 + - - +
41B TYR* 3.5 31.6 - + - -
51B ILE 5.2 0.7 - - - -
53B THR* 2.7 38.4 + - + +
61B TYR* 3.4 40.7 - + + +
69B PHE* 3.7 26.0 - + - -
83B ARG* 3.6 10.4 - - + +
84B VAL* 1.3 72.9 + - - +
86B VAL* 1.3 62.3 + - - +
87B ASP* 3.9 2.6 + - - +
1305B ACT 2.9 26.8 + - + +
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 4.0 15.7 - - + -
37B THR 3.9 4.9 - - - +
38B PHE* 4.0 12.8 - - + -
52B LEU* 4.0 29.8 - - + -
53B THR* 3.1 25.0 + - - +
54B TYR* 3.7 29.1 - - + -
55B HIS* 3.2 21.3 + - - -
61B TYR* 4.3 5.2 - - - +
84B VAL* 4.4 2.9 - - + +
85B HIS* 1.3 73.7 - - - +
87B ASP* 1.3 76.4 + - - +
114B ILE* 5.8 3.4 - - + -
117B VAL* 5.0 8.1 - - + -
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 3.5 10.7 - - - +
37B THR* 3.0 31.5 + - - +
38B PHE* 5.1 0.2 - - - -
39B THR* 4.8 7.1 + - - -
55B HIS* 3.6 2.9 - - - -
60B ASN* 3.3 9.6 - - - +
61B TYR* 2.9 38.9 + - - +
85B HIS 3.9 3.9 + - - +
86B VAL* 1.3 75.1 - - - +
88B ALA* 1.3 66.2 + - - +
91B MET 4.5 0.7 - - - -
92B GLU* 3.7 40.8 - - + +
93B GLU 5.0 0.7 + - - -
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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