Contacts of the strand formed by residues 85 - 91 (chain A) in PDB entry 4OBP
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 TYR 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ILE* 4.0 8.7 - - - +
70A ILE* 3.7 17.2 - - + +
73A LEU* 3.5 22.2 - - + +
74A LYS* 3.7 46.8 + - + +
77A SER* 3.0 21.2 + - - +
78A HIS* 5.1 6.5 - + + -
83A ALA 3.8 0.4 + - - -
84A THR* 1.3 82.0 - - - +
86A TYR* 1.3 76.0 + - - +
87A GLY* 3.5 14.8 - - - -
88A ALA* 3.2 24.6 + - - +
103A LEU* 3.5 33.2 - - + -
104A VAL 4.0 4.3 - - - -
105A MET* 4.3 3.8 - - - -
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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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25A PHE* 4.5 14.1 - + + -
49A GLN* 4.4 18.6 + - + -
50A LEU 4.3 7.2 + - - -
51A ALA* 4.1 11.7 - - + -
84A THR* 3.7 12.8 + - + -
85A TYR* 1.3 89.5 - - - +
87A GLY* 1.3 57.1 + - - +
104A VAL* 2.8 29.7 + - + +
105A MET* 3.6 22.9 - - - -
106A GLU* 3.4 30.6 - - + +
107A PHE 4.4 1.6 + - - -
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Residues in contact with GLY 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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85A TYR* 3.5 19.6 - - - -
86A TYR* 1.3 81.4 - - - +
88A ALA* 1.4 57.5 + - - -
89A PHE* 4.2 15.2 - - - -
103A LEU* 3.8 0.3 - - - -
104A VAL* 2.8 37.2 + - - +
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Residues in contact with ALA 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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18A LEU* 3.6 40.1 - - + +
19A ARG 4.9 0.9 + - - -
70A ILE* 4.0 26.0 - - + -
85A TYR* 3.2 14.7 + - + +
87A GLY* 1.4 73.7 - - - +
89A PHE* 1.3 74.1 + - - +
101A LEU* 4.4 1.1 - - + -
102A TRP 3.3 8.5 - - - +
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Residues in contact with PHE 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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18A LEU* 4.5 2.7 - - - -
19A ARG* 3.4 25.1 - - + +
20A ASP 4.2 2.5 - - - -
21A PRO* 3.8 32.1 - - + -
24A ILE* 4.1 24.0 - - + -
25A PHE* 3.5 37.9 - + - -
87A GLY* 4.2 12.6 - - - -
88A ALA* 1.3 82.4 - - - +
90A ILE* 1.3 63.1 + - - +
91A LYS 4.2 0.4 - - - -
101A LEU* 3.4 4.8 - - - +
102A TRP* 2.7 42.7 + - + +
104A VAL* 3.7 22.7 - - + -
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Residues in contact with ILE 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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15A LEU* 3.4 52.0 - - + +
18A LEU* 3.9 16.2 - - + +
19A ARG 3.1 8.9 + - - +
20A ASP* 3.4 20.4 + - - +
21A PRO* 4.0 3.1 - - - -
58A VAL* 4.4 7.9 - - + -
89A PHE* 1.3 78.3 - - - +
91A LYS* 1.3 60.5 + - - +
92A LYS* 3.6 18.7 + - + +
99A ASP* 3.7 34.5 - - + +
100A GLN 3.2 8.7 - - - +
101A LEU* 3.8 15.0 - - + -
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Residues in contact with LYS 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 ASP* 3.8 19.1 + - - +
21A PRO* 3.9 21.6 - - + +
22A ALA* 4.6 11.5 - - - +
89A PHE 4.2 0.2 - - - -
90A ILE* 1.3 69.9 - - - +
92A LYS* 1.4 68.4 + - - +
93A SER* 3.6 5.4 + - - +
100A GLN* 2.8 45.5 + - + +
102A TRP* 3.9 34.3 - - + +
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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