Contacts of the strand formed by residues 85 - 91 (chain A) in PDB entry 2BME
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 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A LYS 3.3 5.2 + - - +
13A PHE* 3.2 14.8 - - - -
14A LEU 2.9 20.3 + - - -
83A ALA* 3.5 5.7 - - - +
84A ALA* 1.3 82.1 - - - +
86A ALA* 1.3 63.8 + - - +
116A ILE* 4.0 3.8 - - - -
117A VAL 3.2 11.0 - - - -
167A CYS* 3.7 15.5 - - - -
171A ILE* 4.0 0.7 - - - -
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Residues in contact with ALA 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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13A PHE* 5.1 0.2 - - - +
14A LEU* 3.2 22.0 - - + +
16A ILE* 4.4 18.6 - - + -
80A TYR* 5.8 0.7 - - + -
85A GLY* 1.3 75.8 - - - +
87A LEU* 1.3 68.0 + - - +
88A LEU 3.9 0.2 - - - -
116A ILE* 4.2 15.0 - - + +
117A VAL 2.8 7.1 + - - +
118A ILE* 3.2 15.3 - - + -
119A ILE* 2.9 24.3 + - - +
167A CYS* 3.9 2.8 - - - -
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 4.4 5.4 - - + -
14A LEU 2.9 11.0 + - - +
15A VAL* 3.4 13.7 - - + +
16A ILE* 2.9 29.1 + - - +
26A LEU* 5.8 4.9 - - + -
86A ALA* 1.3 77.5 - - - +
88A LEU* 1.3 59.8 + - - +
89A VAL* 3.9 3.8 + - + -
119A ILE* 3.5 7.9 - - + -
121A CYS* 4.0 19.1 - - - -
163A ALA* 3.9 23.3 - - + +
164A PHE* 3.6 52.7 - - + -
167A CYS* 4.3 23.3 - - + -
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Residues in contact with LEU 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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16A ILE* 3.5 25.4 - - + +
17A GLY* 4.1 1.8 - - - -
86A ALA 3.9 1.2 + - - -
87A LEU* 1.3 70.2 - - - +
89A VAL* 1.3 62.2 + - - +
101A LEU* 3.6 28.0 - - + +
104A TRP* 3.6 36.1 - - + -
105A LEU* 3.8 35.4 - - + -
118A ILE* 3.8 17.5 - - + -
119A ILE 2.9 7.9 + - - +
120A LEU* 3.5 15.0 - - + +
121A CYS 2.9 25.8 + - - -
141A PHE* 6.1 0.2 - - + -
147A LEU* 5.1 1.6 - - + -
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Residues in contact with VAL 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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15A VAL* 3.9 20.4 - - + -
16A ILE 2.9 17.3 + - - +
17A GLY* 3.5 18.7 - - - -
18A ASN 4.0 1.0 + - - -
21A THR* 3.7 27.5 + - - +
23A LYS* 4.1 4.7 - - + -
26A LEU* 3.9 23.6 - - + -
87A LEU* 4.0 7.2 - - + +
88A LEU* 1.3 78.6 - - - +
90A TYR* 1.3 73.9 + - - +
97A THR 5.1 0.9 - - - +
101A LEU* 4.4 6.3 - - - +
104A TRP* 5.7 0.2 - - - -
121A CYS* 3.4 13.5 - - + +
123A ASN* 3.8 18.8 - - + -
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Residues in contact with TYR 90 (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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21A THR* 3.7 11.4 - - - -
89A VAL* 1.3 74.3 - - - +
91A ASP* 1.3 67.6 + - - +
92A ILE* 4.0 16.4 - - + +
97A THR* 3.5 24.7 - - - +
98A TYR* 3.8 20.2 - + + -
101A LEU* 3.7 22.9 - - + -
120A LEU* 4.1 14.8 - - + -
121A CYS 3.0 12.7 + - - +
122A GLY* 3.4 24.8 - - - -
123A ASN* 2.8 35.0 + - - +
133A VAL* 3.8 20.8 + - + +
138A ALA* 3.1 24.8 - - + +
149A PHE* 3.3 18.8 - + - -
151A GLU* 4.6 1.6 + - - -
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Residues in contact with ASP 91 (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 GLY 4.1 1.6 - - - +
21A THR* 3.7 18.8 - - + +
90A TYR* 1.3 78.2 - - - +
92A ILE* 1.3 66.2 + - - +
93A THR* 2.6 39.7 + - - +
94A SER* 2.9 35.0 + - - +
97A THR* 2.9 15.4 + - + +
123A ASN 3.8 4.5 - - - -
124A LYS* 3.0 40.0 + - - +
133A VAL* 4.6 0.5 - - - +
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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