Contacts of the helix formed by residues 89 - 99 (chain B) in PDB entry 2JB3
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 HIS 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A GLU* 3.8 7.1 + - - -
338A ARG* 3.0 17.3 + - - -
85B ILE* 4.0 6.4 - - + +
86B PRO* 3.3 34.5 + - + +
88B SER* 1.3 90.2 - - - +
90B ILE* 1.3 59.2 + - - +
91B THR* 3.0 13.3 + - - +
92B LEU* 3.2 16.3 + - - +
227B ASP* 3.0 22.0 + - - -
464B ALA* 5.2 3.5 - - + +
467B TRP* 3.5 36.4 - + + +
469B HIS* 3.3 37.6 + + + +
1489B FAD 4.9 1.0 + - - -
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Residues in contact with ILE 90 (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 SER 3.8 1.0 + - - -
89B HIS* 1.3 67.4 - - - +
91B THR* 1.3 66.3 + - - +
92B LEU 3.1 1.6 - - - -
93B ASP* 2.9 28.7 + - + +
94B TYR* 2.9 29.3 + - + -
469B HIS* 3.0 28.3 - - + +
472B LEU* 3.9 29.2 - - + -
473B THR* 4.0 13.0 - - + -
476B ARG* 3.4 43.3 - - - +
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Residues in contact with THR 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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85B ILE* 3.8 28.1 - - + +
89B HIS* 3.8 8.4 + - - +
90B ILE* 1.3 78.8 - - - +
92B LEU* 1.3 57.5 + - - +
94B TYR* 3.3 5.4 + - + +
95B CYS* 3.0 31.6 + - - -
242B ILE* 3.8 26.1 - - + +
243B TYR* 4.7 0.4 - - - +
468B GLN* 3.7 23.4 - - + +
469B HIS* 3.4 24.1 + - - -
472B LEU* 3.9 12.2 - - + +
1489B FAD 4.9 0.7 + - - -
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Residues in contact with LEU 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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338A ARG* 4.2 3.8 - - - +
340A TYR* 4.0 30.7 - - + +
361A ASN* 3.2 13.9 + - - +
85B ILE* 3.7 37.0 - - + -
86B PRO 3.7 19.1 - - - +
87B GLN* 3.7 20.2 - - - +
89B HIS 3.2 8.3 + - - +
90B ILE 3.1 0.8 - - - -
91B THR* 1.3 74.7 - - - +
93B ASP* 1.3 64.5 + - - +
95B CYS* 3.2 3.0 + - - -
96B ARG* 3.1 17.5 + - - +
102B ILE* 3.9 25.1 - - + -
233B PHE* 4.3 16.2 - - + -
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Residues in contact with ASP 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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338A ARG* 2.9 39.2 + - - -
90B ILE* 2.9 31.5 + - + +
92B LEU* 1.3 77.0 - - - +
94B TYR* 1.3 58.5 + - + +
96B ARG* 3.3 24.8 + - - +
97B GLU* 3.0 26.4 + - - +
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Residues in contact with TYR 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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26B CYS* 3.3 22.5 - - - -
29B PHE* 4.1 11.0 - + - -
30B GLU* 2.5 30.8 + - - -
90B ILE* 2.9 35.8 + - + -
91B THR* 3.8 9.0 - - - +
93B ASP* 1.3 76.1 - - + +
95B CYS* 1.3 58.7 + - - +
97B GLU* 4.1 9.6 - - + -
98B LEU* 2.9 39.8 + - + +
242B ILE* 5.2 3.8 - - + -
246B PHE* 3.4 38.6 - + + -
472B LEU* 4.0 17.5 - - + -
476B ARG* 3.0 33.3 + - - -
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Residues in contact with CYS 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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361A ASN* 4.1 3.6 - - - +
85B ILE* 4.9 4.7 - - - -
91B THR 3.0 20.7 + - - -
92B LEU* 3.2 10.9 + - - +
94B TYR* 1.3 74.3 - - - +
96B ARG* 1.3 58.1 + - - +
98B LEU* 5.2 0.9 - - - -
99B GLY* 2.9 8.7 + - - -
100B VAL* 2.9 51.8 + - - +
102B ILE* 3.8 24.5 - - + -
235B PRO* 4.5 2.9 - - - -
242B ILE* 3.5 33.4 - - - -
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Residues in contact with ARG 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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334A GLU* 4.6 3.8 + - - +
335A THR* 3.8 35.1 - - - +
338A ARG* 5.8 3.2 - - - +
340A TYR* 3.5 11.7 + - - -
361A ASN* 3.1 60.9 + - - +
362A SER 5.3 1.4 + - - -
92B LEU 3.1 6.4 + - - +
93B ASP* 3.5 35.3 + - - +
95B CYS* 1.3 77.9 - - - +
97B GLU* 1.3 63.1 + - - +
99B GLY* 3.3 11.3 + - - -
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Residues in contact with GLU 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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29B PHE* 4.0 23.1 - - + -
33B LYS* 3.5 17.3 + - - +
93B ASP 3.0 15.7 + - - +
94B TYR* 3.7 14.1 - - + +
96B ARG* 1.3 77.5 - - - +
98B LEU* 1.3 61.9 + - + +
99B GLY 3.8 0.3 + - - -
249B ARG* 2.9 40.4 + - - -
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Residues in contact with LEU 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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29B PHE* 4.3 11.0 - - + -
94B TYR* 2.9 22.1 + - + +
97B GLU* 1.3 81.3 - - + +
99B GLY* 1.3 60.5 + - - +
100B VAL* 3.7 16.3 - - + +
242B ILE* 3.5 33.7 - - + +
245B ALA* 3.8 17.7 - - + +
246B PHE* 3.7 35.9 - - + +
249B ARG* 3.8 38.4 + - + +
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Residues in contact with GLY 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 CYS 2.9 6.1 + - - -
96B ARG* 3.3 10.0 + - - -
97B GLU 3.5 0.8 + - - -
98B LEU* 1.3 78.4 - - - +
100B VAL* 1.3 61.0 + - - +
101B GLU* 3.6 3.7 + - - +
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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