Contacts of the strand formed by residues 83 - 89 (chain A) in PDB entry 2CR6
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 GLY 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A LEU* 4.1 0.2 - - - -
50A ASP* 3.0 19.3 - - - -
81A ASP 2.8 8.0 + - - -
82A SER* 1.3 74.8 - - - +
84A THR* 1.3 69.6 + - - -
97A ALA* 4.0 1.7 - - - -
98A LEU* 2.8 26.8 + - - +
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Residues in contact with THR 84 (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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49A LEU* 3.2 8.8 - - - +
50A ASP* 3.0 17.0 + - - -
83A GLY* 1.3 83.1 + - - -
85A ILE* 1.3 64.3 + - - +
86A TYR* 3.1 42.2 + - + +
95A SER* 4.2 9.0 - - - -
96A ALA 3.0 33.4 + - - +
97A ALA* 4.4 2.9 - - - +
98A LEU 4.0 0.7 - - - +
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Residues in contact with ILE 85 (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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20A LEU* 4.0 10.3 - - + +
33A PHE* 3.3 45.1 - - + -
47A TRP* 3.5 37.7 - - + -
48A PHE 3.4 11.2 - - - +
49A LEU* 3.8 10.7 - - + +
54A LEU* 4.5 1.3 - - + -
72A LEU* 4.3 3.6 - - + -
74A LEU* 4.2 12.8 - - + -
84A THR* 1.3 68.9 - - - +
86A TYR* 1.3 60.6 + - - +
87A PHE 3.7 4.2 + - - +
94A ALA 3.5 1.4 - - - +
95A SER* 3.3 9.0 - - - -
96A ALA 3.1 24.6 + - - +
98A LEU* 3.5 25.3 - - + +
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Residues in contact with TYR 86 (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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48A PHE* 2.7 47.4 + - + +
50A ASP* 3.8 30.7 - - - -
84A THR* 3.1 38.5 + - + +
85A ILE* 1.3 69.9 - - - +
87A PHE* 1.3 66.0 + - - +
88A GLU* 4.4 3.0 - - - +
93A ARG* 4.2 22.2 - - - -
94A ALA 3.5 13.5 - - - -
95A SER* 4.2 15.9 - - - -
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Residues in contact with PHE 87 (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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16A ILE* 4.7 3.6 - - + -
20A LEU* 4.4 9.0 - - + -
35A CYS* 4.3 6.3 - - - -
37A ILE* 3.7 37.5 - - + -
45A VAL* 3.9 11.9 - - + -
46A HIS 3.2 27.4 - - - -
47A TRP* 3.4 42.4 - + + +
70A HIS* 4.0 9.6 - + - -
85A ILE* 3.7 4.0 + - - +
86A TYR* 1.3 72.8 - - - +
88A GLU* 1.3 68.3 + - - +
89A ALA* 3.2 28.0 - - + -
93A ARG* 3.0 33.1 - - - +
94A ALA* 3.2 29.5 + - + -
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Residues in contact with GLU 88 (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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42A TYR* 4.6 0.3 + - - -
45A VAL* 4.5 1.6 - - - -
46A HIS* 3.3 47.6 + - + +
48A PHE* 3.1 38.0 - - + -
86A TYR* 3.7 1.9 + - - +
87A PHE* 1.3 90.5 - - - +
89A ALA* 1.3 65.2 + - - +
92A GLN 3.9 4.9 - - - +
93A ARG* 4.2 30.6 + - + +
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Residues in contact with ALA 89 (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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14A VAL* 3.0 34.1 - - + +
37A ILE* 3.9 2.9 - - + -
42A TYR* 3.2 28.5 - - + -
46A HIS* 6.2 0.2 - - - -
87A PHE* 3.2 22.6 - - + -
88A GLU* 1.3 76.8 - - - +
90A GLY* 1.3 63.0 + - - +
91A ASP 3.2 1.6 + - - -
92A GLN* 3.3 16.6 + - + +
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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