Contacts of the helix formed by residues 90 - 101 (chain B) in PDB entry 4BT9
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 SER 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A VAL* 3.6 33.7 + - - -
86A LEU* 4.1 10.2 - - - +
28B TYR* 3.7 14.1 - - - -
88B ASP* 2.6 25.6 + - - -
89B MET* 1.3 78.1 - - - +
91B ASP* 1.3 65.3 + - - +
92B GLY 3.3 2.7 - - - -
93B PHE* 3.1 5.5 + - - +
94B ILE* 2.9 31.6 + - - +
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Residues in contact with ASP 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ASP* 4.1 17.3 + - + +
89B MET 3.5 2.2 - - - -
90B SER* 1.3 79.7 + - - +
92B GLY* 1.3 65.3 + - - +
94B ILE* 4.2 4.2 - - - +
95B SER* 2.9 41.3 + - - -
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Residues in contact with GLY 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B SER* 4.7 1.8 - - - -
89B MET 4.8 2.2 + - - -
90B SER 3.3 0.6 - - - -
91B ASP* 1.3 80.7 + - - +
93B PHE* 1.3 62.2 + - - +
95B SER* 3.9 4.0 - - - -
96B ASN* 3.0 24.9 + - - +
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Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TRP* 3.9 23.1 - + - -
81A LEU* 4.9 3.1 - - + -
82A GLU* 5.0 2.9 - - - -
85A VAL* 4.1 27.6 - - + -
21B LEU* 3.8 22.0 - - + -
24B SER* 3.5 26.0 + - - +
25B LEU* 3.6 26.7 - - + -
28B TYR* 4.0 22.0 - - + -
89B MET 5.4 0.8 + - - -
90B SER 3.1 8.8 + - - +
92B GLY* 1.3 76.2 - - - +
94B ILE* 1.3 73.1 + - + +
96B ASN* 3.3 2.3 + - - +
97B LEU* 2.8 55.9 + - + +
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Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 3.7 37.0 - - + +
85A VAL* 4.3 6.1 - - + -
86A LEU* 3.9 32.8 - - + -
90B SER* 2.9 27.3 + - - +
91B ASP* 4.2 4.0 - - - +
93B PHE* 1.3 94.6 - - + +
95B SER* 1.3 55.7 + - - +
97B LEU* 3.8 3.2 - - + +
98B THR* 2.7 47.3 + - - +
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASP* 2.9 35.1 + - - -
92B GLY* 3.9 4.5 - - - -
94B ILE* 1.3 75.9 - - - +
96B ASN* 1.3 64.3 + - - +
98B THR* 3.6 5.7 - - - -
99B ILE* 3.1 35.1 + - - +
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Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ASP* 4.4 7.3 + - - +
21B LEU* 3.4 23.6 - - - +
24B SER* 3.5 24.7 - - - +
92B GLY 3.0 17.8 + - - +
93B PHE 3.6 4.5 - - - +
95B SER* 1.3 76.1 - - - +
97B LEU* 1.3 55.8 + - - +
99B ILE* 3.2 8.6 + - - +
100B GLN* 2.9 56.0 + - - +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A TRP* 4.2 15.7 - - + +
82A GLU* 3.6 41.7 - - + +
21B LEU* 3.8 34.7 - - + +
93B PHE* 2.8 41.0 + - + +
94B ILE* 3.9 4.9 - - + +
96B ASN* 1.3 72.6 - - - +
98B THR* 1.3 64.3 + - - +
100B GLN* 3.3 1.0 + - - -
101B ARG* 3.2 42.3 + - - +
104B PHE* 4.0 13.9 - - + -
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A GLU* 4.7 6.1 + - - -
94B ILE* 2.7 32.2 + - - +
95B SER* 3.6 7.4 - - - -
97B LEU* 1.3 80.6 - - - +
99B ILE* 1.3 66.3 + - + +
101B ARG* 3.4 20.9 + - - +
102B GLN 4.4 1.4 + - - -
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Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B SER* 3.1 29.1 + - - +
96B ASN* 3.7 6.7 - - - +
98B THR* 1.3 79.3 - - + +
100B GLN* 1.3 78.5 + - - +
101B ARG 3.2 0.9 + - - -
102B GLN* 3.3 22.8 + - - +
103B TYR* 4.3 8.6 - - + -
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Residues in contact with GLN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B THR* 4.2 23.5 + - + +
20B ASP* 6.4 3.1 - - + -
21B LEU* 3.7 28.9 - - + -
96B ASN* 2.9 37.3 + - - +
97B LEU 3.3 4.0 + - - +
99B ILE* 1.3 90.0 - - - +
101B ARG* 1.3 56.5 + - - +
102B GLN 3.1 1.3 - - - -
103B TYR* 2.8 42.7 + - - +
104B PHE* 3.4 10.0 - - - -
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU 4.9 1.6 + - - -
75A ASN 5.9 0.4 + - - -
78A TRP* 3.6 8.5 + - - +
79A SER* 3.3 37.1 + - - +
82A GLU* 2.7 34.9 + - - -
97B LEU* 3.2 36.7 + - - +
98B THR* 3.7 13.8 + - - +
99B ILE 3.2 1.4 - - - -
100B GLN* 1.3 72.9 - - - +
102B GLN* 1.3 66.5 + - - +
103B TYR 2.9 2.6 + - - -
104B PHE* 3.1 50.2 + - + +
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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