Contacts of the helix formed by residues 85 - 99 (chain D) in PDB entry 2I5B
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 THR 85 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D THR* 5.6 1.1 - - - +
83D LEU 3.1 1.4 + - - -
84D PRO* 1.3 81.3 + - - +
86D VAL* 1.3 64.2 + - + +
87D ASP* 3.3 20.4 - - + +
88D ILE* 3.0 52.2 + - + +
89D ILE* 3.0 14.7 + - - +
120D TYR* 3.8 4.5 - - - -
123D HIS* 4.4 4.9 - - - -
119E LEU 4.4 2.1 + - - -
121E PRO* 3.3 29.2 - - + +
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Residues in contact with VAL 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D THR* 1.3 71.9 - - + +
87D ASP* 1.3 70.4 + - - +
89D ILE* 3.0 11.0 + - - +
90D GLU* 2.9 43.1 + - - +
120D TYR* 3.0 18.4 + - + +
122D GLU* 4.3 14.1 - - + +
123D HIS* 4.8 1.5 - - - +
126D ALA* 3.8 24.5 - - + -
130D GLN* 5.4 0.2 - - - +
122E GLU* 2.6 34.5 - - - +
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Residues in contact with ASP 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D THR* 4.6 19.4 - - + +
85D THR* 3.3 13.3 - - + +
86D VAL* 1.3 90.9 - - - +
88D ILE* 1.3 59.6 + - - +
90D GLU* 3.4 16.8 + - - +
91D LEU* 3.0 26.7 + - - +
121E PRO* 4.9 12.1 - - - +
122E GLU* 4.9 1.6 - - - +
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Residues in contact with ILE 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ILE* 5.3 1.3 - - + -
39D THR* 3.9 25.6 - - + +
56D PRO* 5.7 3.4 - - + -
57D ILE 4.4 7.0 - - - +
59D THR* 5.0 10.5 - - + +
62D ILE* 3.7 30.1 - - + -
83D LEU* 3.8 22.2 - - + -
84D PRO* 3.7 25.4 - - + -
85D THR* 3.0 29.2 + - + +
87D ASP* 1.3 73.9 - - - +
89D ILE* 1.3 66.7 + - - +
91D LEU* 3.4 6.1 + - + +
92D ALA* 3.0 22.2 + - - +
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Residues in contact with ILE 89 (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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83D LEU* 3.9 24.0 - - + +
85D THR 3.0 14.2 + - - +
86D VAL* 3.0 7.4 + - - +
88D ILE* 1.3 75.0 - - - +
90D GLU* 1.3 59.4 + - + +
92D ALA* 3.2 3.1 + - - +
93D ALA* 2.8 27.2 + - - +
123D HIS* 3.3 47.6 - - + +
126D ALA* 3.8 31.2 - - + +
127D LEU* 3.5 23.8 - - + -
130D GLN* 4.8 4.7 - - + -
131D LEU* 4.3 14.8 - - + +
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Residues in contact with GLU 90 (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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86D VAL* 2.9 31.6 + - + +
87D ASP* 3.8 18.9 - - - +
89D ILE* 1.3 75.0 - - + +
91D LEU* 1.3 60.2 + - - +
93D ALA* 4.2 1.1 - - - +
94D LYS* 2.8 31.9 + - - +
126D ALA* 5.5 0.2 - - + -
130D GLN* 3.2 40.8 + - - +
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Residues in contact with LEU 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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59D THR* 3.9 19.1 - - + +
62D ILE* 3.7 38.4 - - + -
63D ARG* 3.9 42.8 - - + +
66D LEU* 4.0 9.9 - - + -
87D ASP 3.0 17.0 + - - +
88D ILE* 3.7 7.0 - - + +
90D GLU* 1.3 75.1 - - - +
92D ALA* 1.3 60.4 + - - +
94D LYS* 3.2 15.6 + - + +
95D THR* 2.8 43.2 + - - +
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Residues in contact with ALA 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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9D ILE* 4.2 26.9 - - + +
66D LEU* 5.4 1.3 - - - -
80D THR* 4.2 8.1 - - + -
83D LEU* 4.0 23.8 - - + -
88D ILE 3.0 14.7 + - - +
89D ILE 3.5 7.2 - - - +
91D LEU* 1.3 77.9 - - - +
93D ALA* 1.3 57.7 + - - +
95D THR* 3.3 4.0 + - - -
96D ILE* 3.0 33.6 + - - +
131D LEU* 4.3 3.1 - - + -
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Residues in contact with ALA 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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89D ILE 2.8 18.8 + - - +
90D GLU 4.2 2.2 - - - +
92D ALA* 1.3 73.1 - - - +
94D LYS* 1.3 64.4 + - - +
96D ILE* 3.2 3.4 + - - +
97D LYS* 3.1 34.2 + - - -
130D GLN* 3.5 39.9 - - + +
131D LEU* 3.7 13.0 - - + +
134D LEU* 3.7 10.3 - - + +
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Residues in contact with LYS 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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63D ARG* 5.3 9.4 - - - +
90D GLU 2.8 24.6 + - - +
91D LEU* 3.5 18.2 - - + +
93D ALA* 1.3 74.5 - - - +
95D THR* 1.3 65.7 + - - +
97D LYS* 3.9 10.9 - - - +
98D GLU* 3.0 64.1 + - + +
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Residues in contact with THR 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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9D ILE* 5.3 1.3 - - + -
66D LEU* 3.9 28.5 - - + +
70D THR* 4.1 32.8 - - + +
91D LEU* 2.8 29.2 + - - +
92D ALA* 3.6 6.5 - - - -
94D LYS* 1.3 75.7 - - - +
96D ILE* 1.3 58.8 + - - +
98D GLU* 5.0 1.3 - - - -
99D LYS* 2.8 43.4 + - + +
101D LEU* 4.5 6.1 - - + -
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Residues in contact with ILE 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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9D ILE* 5.4 2.9 - - + -
78D MET* 3.5 23.6 - - + -
80D THR* 4.5 7.6 - - + -
92D ALA 3.0 20.2 + - - +
93D ALA* 3.2 6.3 + - - +
95D THR* 1.3 74.7 - - - +
97D LYS* 1.3 58.7 + - - +
100D GLN* 3.1 21.8 + - - -
101D LEU* 3.1 25.1 + - + +
104D VAL* 3.8 42.8 - - + -
106D ILE* 4.6 0.4 - - + -
131D LEU* 4.1 23.1 - - + -
134D LEU* 4.1 22.7 - - + -
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Residues in contact with LYS 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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93D ALA* 3.1 32.4 + - - +
94D LYS* 3.9 9.7 - - - +
96D ILE* 1.3 74.2 - - - +
98D GLU* 1.3 62.9 + - + +
100D GLN* 2.8 30.4 + - - +
130D GLN* 5.2 8.4 - - - +
134D LEU* 3.8 31.9 - - + -
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Residues in contact with GLU 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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94D LYS* 3.0 55.6 + - + +
95D THR* 4.3 1.3 - - - +
97D LYS* 1.3 81.7 - - + +
99D LYS* 1.3 68.9 + - + +
100D GLN* 3.5 3.8 + - - +
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Residues in contact with LYS 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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70D THR* 3.7 31.5 + - - +
71D ASP* 2.7 37.0 + - - +
95D THR* 2.8 29.1 + - + +
98D GLU* 1.3 79.1 - - + +
100D GLN* 1.3 68.7 + - - +
101D LEU* 3.3 23.4 + - + +
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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