Contacts of the helix formed by residues 90 - 104 (chain B) in PDB entry 5U03
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 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B ASP 3.8 0.4 + - - +
41B PRO* 2.7 22.7 + - + +
42B TYR 2.6 25.1 + - - -
43B ILE* 3.3 14.7 - - + +
89B THR* 1.3 69.7 - - - +
91B GLY* 1.3 56.4 + - - +
93B ILE* 3.2 9.6 + - + +
94B TYR* 2.7 55.4 + - - -
155B GLU 4.3 6.1 - - - +
158B PRO* 6.4 1.1 - - + -
159B PHE* 3.8 33.0 - - + -
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Residues in contact with GLY 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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42B TYR 3.4 2.2 + - - -
43B ILE 2.9 26.3 + - - -
44B ASN 4.1 2.9 - - - -
45B ILE* 4.7 6.1 - - - -
89B THR* 3.2 3.2 + - - -
90B THR* 1.3 79.0 + - - +
92B LYS* 1.3 66.5 + - - +
94B TYR* 3.3 11.0 + - - +
95B GLN* 3.2 20.3 + - - +
98D ILE* 4.1 9.9 - - - +
101D GLU* 5.1 0.4 - - - -
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Residues in contact with LYS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 3.6 28.1 - - + +
84B LYS* 5.4 4.2 - - - +
85B ASP* 5.7 5.4 + - - +
87B ASN 4.4 5.8 - - - +
88B LEU* 3.7 37.5 - - + -
89B THR* 3.1 24.6 + - + +
91B GLY* 1.3 77.3 - - - +
93B ILE* 1.4 64.3 + - + +
95B GLN* 3.2 4.6 + - - +
96B TYR* 3.0 21.6 + - + +
124B TRP* 3.7 26.4 - - + -
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 5.3 10.5 - - + -
89B THR 3.0 19.6 + - - +
90B THR* 3.6 10.8 - - + +
92B LYS* 1.4 71.9 - - + +
94B TYR* 1.3 73.8 + - + +
96B TYR* 3.1 7.3 + - - +
97B VAL* 2.8 39.1 + - + +
117B ILE* 4.5 20.0 - - + -
120B ALA* 5.1 3.6 - - + -
121B ILE* 4.4 12.1 - - + -
124B TRP* 4.0 26.9 - - + +
159B PHE* 3.9 32.8 - - + -
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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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43B ILE* 4.1 35.2 - - + +
90B THR* 2.7 39.4 + - - +
91B GLY* 3.5 11.2 - - - +
92B LYS 3.2 0.2 - - - -
93B ILE* 1.3 80.4 - - + +
95B GLN* 1.3 59.0 + - - +
97B VAL* 3.7 3.3 - - - +
98B ILE* 2.7 40.5 + - + +
117B ILE* 6.1 6.7 - - + -
94D TYR* 3.4 59.1 + + - -
98D ILE* 3.5 20.0 - - + -
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Residues in contact with GLN 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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45B ILE* 6.5 0.7 - - + -
91B GLY 3.2 9.2 + - - +
92B LYS* 3.9 6.3 - - - +
94B TYR* 1.3 79.0 - - - +
96B TYR* 1.3 63.8 + - - +
98B ILE* 3.3 6.5 + - - +
99B ASN* 2.8 60.1 + - - +
95D GLN* 2.6 46.3 + - - +
98D ILE* 3.7 19.6 - - + +
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Residues in contact with TYR 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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92B LYS* 3.0 15.5 + - + +
93B ILE* 3.4 9.6 - - - +
95B GLN* 1.3 79.0 - - - +
97B VAL* 1.3 74.5 + - + +
99B ASN* 3.2 11.0 + - + +
100B LYS* 3.2 50.2 + - + +
106B TYR* 5.6 0.9 - - - -
120B ALA* 5.2 4.3 - - + -
123B GLU* 5.1 2.9 - - - -
124B TRP* 3.8 36.1 - + + -
127B ARG* 2.9 35.0 + - - -
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Residues in contact with VAL 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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93B ILE* 2.8 37.5 + - + +
94B TYR* 3.8 2.5 - - - +
96B TYR* 1.3 82.7 - - + +
98B ILE* 1.3 54.8 + - + +
100B LYS* 2.8 9.3 + - - +
101B GLU* 2.7 54.3 + - + +
106B TYR* 4.4 16.2 - - + +
111B VAL* 4.2 7.2 - - + -
116B HIS* 5.9 1.1 - - + +
117B ILE* 3.9 25.4 - - + -
120B ALA* 4.6 10.3 - - + -
43D ILE* 5.1 1.1 - - + -
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Residues in contact with ILE 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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94B TYR* 2.7 33.8 + - + +
95B GLN* 3.7 6.7 - - - +
97B VAL* 1.3 75.3 - - + +
99B ASN* 1.3 65.0 + - - +
101B GLU* 3.0 23.8 + - - +
102B ARG* 2.9 23.1 + - + +
43D ILE* 5.1 0.7 - - + +
45D ILE* 5.9 7.9 - - + -
91D GLY* 4.1 10.3 - - - +
94D TYR* 3.5 37.0 - - + -
95D GLN* 3.7 33.4 - - + +
98D ILE* 4.3 3.8 - - + -
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Residues in contact with ASN 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 GLN* 2.8 53.9 + - - +
96B TYR* 3.4 11.5 - - + +
98B ILE* 1.3 75.8 - - - +
100B LYS* 1.3 58.1 + - + +
102B ARG* 3.0 10.0 + - - +
103B LYS* 2.9 44.3 + - - +
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Residues in contact with LYS 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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96B TYR* 3.2 50.4 + - + +
97B VAL* 2.8 8.3 + - - +
99B ASN* 1.3 78.1 - - + +
101B GLU* 1.3 62.4 + - - +
103B LYS* 3.2 12.3 + - + +
104B GLY 3.1 3.6 + - - -
105B ASP* 2.8 63.6 + - - +
106B TYR* 3.2 35.7 - - + +
123B GLU* 5.9 2.7 - - - -
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Residues in contact with GLU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 2.7 27.1 + - + +
98B ILE* 3.0 24.7 + - + +
100B LYS* 1.3 77.0 - - - +
102B ARG* 1.3 58.6 + - - +
104B GLY* 2.9 19.6 + - - -
106B TYR* 4.1 15.4 - - + +
108B GLY* 5.1 3.8 - - - -
111B VAL* 3.1 27.1 - - + +
43D ILE* 3.1 20.9 - - - +
44D ASN* 3.1 51.3 + - - +
45D ILE* 4.2 2.6 + - + +
49D THR* 5.8 2.6 - - - +
91D GLY* 5.1 0.3 - - - -
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Residues in contact with ARG 102 (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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98B ILE* 2.9 14.0 + - + +
99B ASN* 3.4 11.0 - - - +
101B GLU* 1.3 77.9 + - - +
103B LYS* 1.3 63.0 + - + +
104B GLY* 3.2 1.7 + - - -
44D ASN* 6.1 0.2 - - - -
45D ILE* 4.3 13.8 + - - +
46D ASP* 2.5 31.9 + - - +
49D THR* 3.5 29.9 - - - +
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Residues in contact with LYS 103 (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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99B ASN* 2.9 29.0 + - - +
100B LYS* 3.4 14.2 - - + +
101B GLU 3.1 0.2 - - - -
102B ARG* 1.3 77.6 - - + +
104B GLY* 1.4 58.5 + - - +
105B ASP* 3.3 29.5 + - - +
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Residues in contact with GLY 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLU 2.9 15.2 + - - -
102B ARG 3.0 2.9 - - - -
103B LYS* 1.4 79.8 - - - +
105B ASP* 1.3 57.6 + - - +
106B TYR 3.0 7.2 - - - -
107B LEU* 2.9 22.9 + - - +
108B GLY* 4.2 12.6 - - - -
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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