Contacts of the strand formed by residues 95 - 99 (chain A) in PDB entry 1BAR
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 ASN 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLU* 3.6 18.4 - - - +
88A ARG 3.4 13.9 - - - +
89A LEU* 4.3 12.1 - - - +
93A GLY 3.7 10.5 + - - -
94A TYR* 1.3 78.8 + - - +
96A THR* 1.3 67.1 + - - +
97A TYR* 3.7 24.5 - - + +
131A LEU* 3.3 9.2 - - - -
132A PHE* 2.8 35.9 + - - +
134A PRO* 3.5 24.9 - - - +
136B PRO* 5.1 5.9 - - - +
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Residues in contact with THR 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU 3.5 0.2 - - - +
87A GLU* 3.4 4.2 - - - +
88A ARG* 2.8 64.6 + - + +
90A GLU* 3.3 15.7 + - - +
95A ASN* 1.3 78.4 + - - +
97A TYR* 1.3 61.9 + - - +
98A ILE* 4.3 1.3 - - + -
108A PHE* 3.3 19.8 - - + -
125A PHE* 5.0 0.9 - - - -
130A ILE* 3.2 33.5 + - - +
131A LEU* 4.0 6.1 - - - +
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Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.4 14.1 - - + +
46A LEU* 4.2 13.5 - - + +
54A VAL* 4.0 14.8 - - + -
56A ILE* 4.1 17.5 - - + -
85A PHE* 4.0 10.3 - - + -
86A LEU 3.0 5.8 - - - +
87A GLU* 3.0 52.8 + - + -
95A ASN* 3.7 25.4 - - + +
96A THR* 1.3 71.6 - - - +
98A ILE* 1.3 63.6 + - - +
99A SER 3.7 0.5 + - - -
108A PHE* 3.4 5.7 - - - +
109A VAL* 3.1 47.5 + - + +
130A ILE 4.7 2.2 + - - -
132A PHE* 4.4 27.1 - + + -
134A PRO* 4.0 13.2 - - - +
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Residues in contact with ILE 98 (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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85A PHE* 3.3 2.5 - - - -
86A LEU* 2.6 49.2 + - + +
88A ARG* 3.3 38.8 - - + +
96A THR 4.0 0.6 - - - -
97A TYR* 1.3 71.7 - - - +
99A SER* 1.3 79.7 + - - +
103A ALA* 3.5 27.4 - - + +
106A HIS* 4.6 1.8 - - + -
107A TRP 3.6 11.2 - - - +
108A PHE* 3.3 38.8 - - + -
89B LEU* 4.0 10.1 - - + -
93B GLY* 4.0 13.7 - - - -
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Residues in contact with SER 99 (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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67A MET* 3.7 26.5 - - - +
84A LEU 4.3 0.2 - - - -
85A PHE* 3.2 24.3 - - - -
97A TYR 3.7 0.6 + - - -
98A ILE* 1.3 72.1 - - - +
100A LYS* 1.3 65.4 + - - +
101A LYS* 3.7 1.6 + - - +
102A HIS* 3.0 31.8 + - - -
103A ALA* 2.9 17.3 + - - -
107A TRP* 2.8 20.7 + - - -
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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