Contacts of the helix formed by residues 90 - 104 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A ASP 4.4 0.2 - - - +
41A PRO* 2.7 22.6 + - + +
42A TYR 2.6 24.9 + - - -
43A ILE* 3.3 14.9 - - + +
89A THR* 1.3 69.4 - - - +
91A GLY* 1.3 56.3 + - - +
93A ILE* 3.6 8.9 - - + +
94A TYR* 2.7 55.3 + - - -
155A GLU 4.3 6.1 - - - +
158A PRO* 6.4 0.9 - - + -
159A PHE* 3.8 33.0 - - + -
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Residues in contact with GLY 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A TYR 3.4 2.0 + - - -
43A ILE 2.9 26.9 + - - -
44A ASN 4.1 3.4 - - - -
45A ILE* 4.7 5.4 - - - -
89A THR* 3.2 3.2 + - - -
90A THR* 1.3 78.5 + - - +
92A LYS* 1.3 65.9 + - - +
94A TYR* 3.3 10.8 + - - +
95A GLN* 3.2 21.0 + - - +
98C ILE* 4.1 9.9 - - - +
101C GLU* 5.1 0.4 - - - -
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 3.6 27.7 - - + +
84A LYS* 5.4 4.0 - - - +
85A ASP* 5.7 5.8 + - - +
87A ASN 4.4 5.8 - - - +
88A LEU* 3.7 38.1 - - + -
89A THR* 3.1 24.9 + - - +
91A GLY* 1.3 77.8 - - - +
93A ILE* 1.4 63.7 + - + +
95A GLN* 3.2 4.1 + - - +
96A TYR* 3.0 22.1 + - + +
124A TRP* 3.7 26.6 - - + -
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 5.3 9.9 - - + -
89A THR 3.0 18.9 + - - +
90A THR* 3.2 11.2 + - + +
92A LYS* 1.4 74.1 - - + +
94A TYR* 1.3 73.2 + - + +
96A TYR* 3.1 6.8 + - - +
97A VAL* 2.8 39.0 + - + +
117A ILE* 4.5 20.2 - - + -
120A ALA* 5.1 3.8 - - + -
121A ILE* 4.4 12.1 - - + -
124A TRP* 4.0 27.1 - - + +
159A PHE* 3.9 32.5 - - + -
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Residues in contact with TYR 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE* 4.1 35.0 - - + +
90A THR* 2.7 40.0 + - - +
91A GLY* 3.5 10.8 - - - +
92A LYS 3.2 0.2 - - - -
93A ILE* 1.3 78.3 - - + +
95A GLN* 1.3 58.7 + - - +
97A VAL* 3.7 2.8 - - - +
98A ILE* 2.7 40.2 + - + +
117A ILE* 6.1 7.6 - - + -
94C TYR* 3.4 57.8 + + - -
98C ILE* 3.5 20.4 - - + -
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Residues in contact with GLN 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE* 6.5 0.4 - - + -
91A GLY 3.2 9.4 + - - +
92A LYS* 3.9 6.7 - - - +
94A TYR* 1.3 79.2 - - - +
96A TYR* 1.3 63.6 + - - +
98A ILE* 3.7 6.4 - - - +
99A ASN* 2.8 61.1 + - - +
95C GLN* 2.6 45.4 + - - +
98C ILE* 3.7 21.1 - - + +
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Residues in contact with TYR 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LYS* 3.0 14.6 + - + +
93A ILE* 3.4 10.1 - - - +
95A GLN* 1.3 79.3 - - - +
97A VAL* 1.3 76.7 + - + +
99A ASN* 3.2 11.8 + - - +
100A LYS* 3.2 51.1 + - + +
106A TYR* 5.6 0.4 - - - -
120A ALA* 5.2 4.3 - - + -
123A GLU* 5.1 2.9 - - - -
124A TRP* 3.8 37.9 - + + -
127A ARG* 2.9 34.9 + - - -
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ILE* 2.8 37.2 + - + +
94A TYR* 3.8 3.1 - - - +
96A TYR* 1.3 81.8 - - + +
98A ILE* 1.3 55.3 + - + +
100A LYS* 2.8 8.9 + - - +
101A GLU* 2.7 55.6 + - + +
106A TYR* 4.4 16.2 - - + +
111A VAL* 4.2 7.2 - - + -
116A HIS* 5.9 1.1 - - + +
117A ILE* 3.9 24.9 - - + -
120A ALA* 4.6 11.7 - - + -
43C ILE* 5.1 0.9 - - + -
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Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR* 2.7 33.2 + - + +
95A GLN* 3.7 6.7 - - - +
97A VAL* 1.3 76.0 - - + +
99A ASN* 1.3 65.1 + - - +
101A GLU* 3.0 24.3 + - + +
102A ARG* 2.9 22.3 + - + +
43C ILE* 5.9 0.7 - - + -
45C ILE* 5.9 6.7 - - + -
91C GLY* 4.1 9.6 - - - +
94C TYR* 3.5 37.9 - - + -
95C GLN* 3.7 33.2 - - + +
98C ILE* 4.3 4.0 - - + -
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Residues in contact with ASN 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLN* 2.8 53.6 + - - +
96A TYR* 3.4 12.4 - - - +
98A ILE* 1.3 76.7 - - - +
100A LYS* 1.3 58.3 + - + +
102A ARG* 3.0 9.3 + - - +
103A LYS* 2.9 43.9 + - - +
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A TYR* 3.2 48.8 + - + +
97A VAL* 2.8 8.7 + - - +
99A ASN* 1.3 76.5 - - + +
101A GLU* 1.3 62.8 + - - +
103A LYS* 3.2 12.9 + - + +
104A GLY 3.1 3.5 + - - -
105A ASP* 2.8 63.5 + - - +
106A TYR* 3.2 35.2 - - + +
123A GLU* 5.9 2.5 - - - -
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Residues in contact with GLU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A VAL* 2.7 25.9 + - + +
98A ILE* 3.0 24.0 + - + +
100A LYS* 1.3 77.4 - - - +
102A ARG* 1.3 59.0 + - - +
104A GLY* 2.9 19.2 + - - -
106A TYR* 4.1 16.4 - - + +
108A GLY* 5.1 4.0 + - - -
111A VAL* 3.1 25.0 - - + +
43C ILE* 3.1 19.6 - - - +
44C ASN* 3.0 55.0 + - - +
45C ILE* 4.2 2.4 + - + +
49C THR* 5.8 2.9 - - - +
91C GLY* 5.1 0.7 - - - -
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Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ILE* 2.9 12.8 + - + +
99A ASN* 3.0 11.2 + - - +
101A GLU* 1.3 78.6 + - - +
103A LYS* 1.3 61.2 + - + +
104A GLY* 3.2 1.7 + - - -
44C ASN* 6.1 0.2 - - - -
45C ILE* 4.2 14.2 + - - +
46C ASP* 2.5 32.2 + - - +
49C THR* 3.5 29.7 - - - +
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Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASN* 2.9 28.0 + - - +
100A LYS* 3.4 14.6 - - + +
101A GLU 3.1 0.2 - - - -
102A ARG* 1.3 77.0 - - + +
104A GLY* 1.4 60.5 + - - +
105A ASP* 3.3 30.3 + - - +
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Residues in contact with GLY 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A GLU 2.9 17.7 + - - -
102A ARG 3.0 2.5 + - - -
103A LYS* 1.4 80.1 - - - +
105A ASP* 1.3 57.3 + - - +
106A TYR 3.0 6.3 - - - -
107A LEU* 2.9 22.2 + - - +
108A GLY* 4.2 12.8 - - - -
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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