Contacts of the helix formed by residues 90 - 100 (chain D) in PDB entry 5JTO
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 GLU 90 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D GLU* 4.9 3.8 - - - +
5D ASN* 3.0 53.2 + - - +
7D THR* 3.0 35.2 + - - -
88D GLY 3.9 5.6 - - - +
89D ILE* 1.3 76.4 - - - +
91D GLY* 1.3 67.2 + - - +
92D THR 3.6 0.2 + - - -
93D GLN* 3.3 23.1 + - - +
94D MET* 3.6 9.4 - - - +
275G LYS* 5.9 1.2 + - - -
276G PRO* 3.9 11.2 - - + -
277G LEU* 5.3 2.5 - - + -
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Residues in contact with GLY 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLU* 3.5 38.9 + - - -
90D GLU* 1.3 77.0 - - - +
92D THR* 1.3 61.4 + - - -
95D ALA* 3.5 15.6 + - - +
276G PRO* 3.4 21.6 - - - +
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Residues in contact with THR 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLU 5.0 2.1 + - - +
91D GLY* 1.3 70.9 - - - -
93D GLN* 1.4 60.3 + - - +
94D MET 3.4 0.2 - - - -
95D ALA* 3.6 11.0 - - + +
96D HIS* 3.1 29.6 + - - +
141D LEU* 4.5 10.0 - - + +
144D GLN* 6.0 4.9 - - - +
147D GLU* 5.8 8.1 - - + -
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Residues in contact with GLN 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ASN 4.9 2.4 - - - +
6D ASN* 3.7 20.6 + - - +
9D MET* 5.7 3.8 - - - +
89D ILE* 3.5 37.3 - - + +
90D GLU* 3.3 13.6 + - - +
92D THR* 1.4 79.4 + - - +
94D MET* 1.4 64.1 + - - +
96D HIS* 3.5 6.6 + - - +
97D CYS* 3.1 22.9 + - + +
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Residues in contact with MET 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D TYR* 5.9 0.2 - - + -
86D ILE* 3.7 34.5 - - + -
89D ILE* 3.4 31.0 - - + +
90D GLU* 3.5 25.4 + - - +
91D GLY 3.9 4.5 - - - +
92D THR 3.4 0.2 - - - -
93D GLN* 1.4 75.5 - - - +
95D ALA* 1.3 55.7 - - - +
97D CYS* 3.1 2.4 + - - +
98D LEU* 2.8 53.4 + - + +
276G PRO* 3.1 25.4 - - + +
277G LEU* 3.7 11.2 - - + -
278G LEU* 3.5 24.5 - - + +
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Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D GLY 3.5 11.6 + - - +
92D THR* 3.6 14.8 - - + +
93D GLN 3.4 0.2 - - - -
94D MET* 1.3 80.4 - - - +
96D HIS* 1.3 54.9 + - - +
98D LEU* 4.4 2.9 - - - -
99D GLY* 3.1 23.4 + - - -
141D LEU* 4.6 13.3 - - + +
144D GLN* 5.3 4.7 - - - +
276G PRO* 5.0 5.1 - - + +
280G LEU* 3.4 39.1 - - + +
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Residues in contact with HIS 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D THR 3.1 18.1 + - - +
93D GLN* 3.7 7.0 + - - +
94D MET 3.2 0.2 - - - -
95D ALA* 1.3 74.3 - - - +
97D CYS* 1.3 63.2 + - - +
99D GLY* 3.3 1.3 + - - -
100D ALA* 2.9 38.8 + - + +
101D TYR* 6.4 1.1 - - + -
134D ASP* 2.9 31.0 + - + -
137D PHE* 5.9 5.3 - - + +
138D MET* 4.2 25.5 - - + +
141D LEU* 4.1 18.3 - - + +
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Residues in contact with CYS 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 4.7 5.4 - - - -
89D ILE* 3.8 28.9 - - + -
93D GLN 3.1 13.4 + - - +
94D MET 3.1 5.4 + - - +
96D HIS* 1.3 83.3 - - - +
98D LEU* 1.3 57.8 + - - +
101D TYR* 3.0 35.1 + - + -
102D CYS* 3.0 44.4 + - - -
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Residues in contact with LEU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D VAL* 5.1 12.4 - - + +
94D MET* 2.8 43.7 + - + +
95D ALA* 3.8 4.9 - - - +
97D CYS* 1.3 78.4 - - - +
99D GLY* 1.3 56.3 + - - +
102D CYS* 3.9 11.7 - - - +
103D PRO* 3.1 22.0 - - - +
276G PRO 3.8 3.1 - - - +
278G LEU* 3.6 20.9 - - + +
279G GLY 3.4 27.8 - - - +
280G LEU* 3.7 18.6 - - + +
281G PHE* 3.4 28.0 - - + +
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Residues in contact with GLY 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D ALA 3.1 17.2 + - - -
96D HIS 3.8 1.1 - - - -
98D LEU* 1.3 76.6 - - - +
100D ALA* 1.3 58.4 + - - +
103D PRO* 3.6 11.4 - - - +
133D PHE* 3.9 3.1 - - - +
137D PHE* 3.2 45.1 - - - -
280G LEU* 4.3 0.7 - - - -
281G PHE* 3.7 14.4 - - - -
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Residues in contact with ALA 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D HIS* 2.9 21.8 + - + +
98D LEU 3.3 0.4 - - - -
99D GLY* 1.3 79.0 - - - +
101D TYR* 1.3 61.9 + - + +
102D CYS 3.6 1.3 - - - -
103D PRO* 3.4 4.7 - - - +
104D ASN* 3.2 27.1 + - - +
133D PHE* 4.1 11.1 - - - -
134D ASP* 3.4 46.9 - - - +
137D PHE* 5.6 1.6 - - + -
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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