Contacts of the helix formed by residues 90 - 104 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C ASP 3.8 0.4 + - - +
41C PRO* 2.7 22.2 + - + +
42C TYR 2.6 25.5 + - - -
43C ILE* 3.3 14.2 - - + +
89C THR* 1.3 70.1 - - - +
91C GLY* 1.3 56.2 + - - +
93C ILE* 3.6 9.9 - - + +
94C TYR* 2.7 54.9 + - - +
155C GLU 4.3 5.8 - - - +
158C PRO* 6.4 1.1 - - + -
159C PHE* 3.8 32.8 - - + -
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Residues in contact with GLY 91 (chain C).
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* 4.1 9.3 - - - +
101A GLU* 5.1 0.7 - - - -
42C TYR 3.4 1.8 + - - -
43C ILE 2.9 26.5 + - - -
44C ASN 4.1 3.1 - - - -
45C ILE* 4.7 5.6 - - - -
89C THR* 3.2 3.6 + - - -
90C THR* 1.3 79.2 + - - +
92C LYS* 1.3 66.6 + - - +
94C TYR* 3.3 10.2 + - - +
95C GLN* 3.2 21.7 + - - +
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Residues in contact with LYS 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 3.6 28.2 - - + +
84C LYS* 5.4 4.0 - - - +
85C ASP* 5.7 5.4 + - - +
87C ASN 4.4 5.2 - - - +
88C LEU* 3.7 37.0 - - + -
89C THR* 3.1 24.5 + - - +
91C GLY* 1.3 77.4 - - - +
93C ILE* 1.4 63.6 + - + +
95C GLN* 3.2 3.9 + - - +
96C TYR* 3.0 22.0 + - + +
124C TRP* 3.7 26.5 - - + -
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU* 5.3 10.3 - - + -
89C THR 3.0 20.2 + - - +
90C THR* 3.6 11.7 - - + +
92C LYS* 1.4 72.6 - - + +
94C TYR* 1.3 73.2 + - + +
96C TYR* 3.1 7.8 + - - +
97C VAL* 2.8 38.3 + - + +
117C ILE* 4.5 20.2 - - + -
120C ALA* 5.1 3.8 - - + -
121C ILE* 4.4 11.4 - - + -
124C TRP* 4.0 27.1 - - + +
159C PHE* 3.9 32.5 - - + -
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Residues in contact with TYR 94 (chain C).
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* 3.4 58.8 + + + -
98A ILE* 3.5 19.7 - - + -
43C ILE* 4.1 35.3 - - + +
90C THR* 2.7 39.5 + - - +
91C GLY* 3.5 10.5 - - - +
92C LYS 3.2 0.2 - - - -
93C ILE* 1.3 78.7 - - + +
95C GLN* 1.3 57.7 + - - +
97C VAL* 3.7 3.3 - - - +
98C ILE* 2.7 40.6 + - + +
117C ILE* 6.1 6.5 - - + -
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Residues in contact with GLN 95 (chain C).
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* 2.6 46.8 + - - +
98A ILE* 3.7 20.3 - - + +
45C ILE* 6.5 0.4 - - + -
91C GLY 3.2 9.4 + - - +
92C LYS* 3.9 7.0 - - - +
94C TYR* 1.3 78.8 - - - +
96C TYR* 1.3 63.8 + - - +
98C ILE* 3.7 6.2 - - - +
99C ASN* 2.8 61.6 + - - +
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Residues in contact with TYR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LYS* 3.0 14.8 + - + +
93C ILE* 3.4 10.3 - - - +
95C GLN* 1.3 80.2 - - - +
97C VAL* 1.3 74.8 + - + +
99C ASN* 3.2 11.0 + - + +
100C LYS* 3.2 52.1 + - + +
106C TYR* 5.6 0.7 - - - -
120C ALA* 5.2 4.3 - - + -
123C GLU* 5.1 3.4 - - - -
124C TRP* 3.8 35.7 - + + -
127C ARG* 2.9 34.2 + - - -
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Residues in contact with VAL 97 (chain C).
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* 5.1 1.1 - - + -
93C ILE* 2.8 37.7 + - + +
94C TYR* 3.8 2.5 - - - +
96C TYR* 1.3 82.0 - - + +
98C ILE* 1.3 55.5 + - + +
100C LYS* 2.8 10.4 + - - +
101C GLU* 2.7 54.9 + - + +
106C TYR* 4.4 16.2 - - + +
111C VAL* 4.2 6.5 - - + -
116C HIS* 6.1 0.7 - - + -
117C ILE* 3.9 25.4 - - + -
120C ALA* 4.6 10.8 - - + -
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Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 5.1 0.4 - - + +
45A ILE* 5.9 7.6 - - + -
91A GLY* 4.1 9.4 - - - +
94A TYR* 3.5 38.8 - - + -
95A GLN* 3.7 33.4 - - + +
98A ILE* 4.3 3.6 - - + -
94C TYR* 2.7 33.4 + - + +
95C GLN* 3.7 6.3 - - - +
97C VAL* 1.3 75.5 - - + +
99C ASN* 1.3 64.9 + - - +
101C GLU* 3.0 24.5 + - + +
102C ARG* 2.9 22.7 + - + +
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Residues in contact with ASN 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLN* 2.8 54.1 + - - +
96C TYR* 3.4 11.5 - - + +
97C VAL 3.1 0.2 - - - -
98C ILE* 1.3 77.0 - - - +
100C LYS* 1.3 56.9 + - + +
102C ARG* 3.0 10.0 + - - +
103C LYS* 2.9 44.0 + - - +
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Residues in contact with LYS 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C TYR* 3.2 47.9 + - + +
97C VAL* 2.8 8.3 + - - +
99C ASN* 1.3 78.5 - - + +
101C GLU* 1.3 61.4 + - - +
103C LYS* 3.2 11.9 + - + +
104C GLY 3.1 3.5 + - - -
105C ASP* 2.8 62.6 + - - +
106C TYR* 3.2 36.3 - - + +
123C GLU* 5.9 2.7 - - - -
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Residues in contact with GLU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.1 20.6 - - - +
44A ASN* 3.0 55.3 + - - +
45A ILE* 4.2 2.6 + - + +
49A THR* 5.8 2.6 - - - +
91A GLY* 5.1 0.5 - - - -
97C VAL* 2.7 26.1 + - + +
98C ILE* 3.2 23.8 - - + +
100C LYS* 1.3 77.8 - - - +
102C ARG* 1.3 59.6 + - - +
104C GLY* 2.9 19.8 + - - -
105C ASP 5.0 0.2 - - - +
106C TYR* 4.1 15.4 + - + +
108C GLY* 5.1 3.6 - - - -
111C VAL* 3.1 25.1 - - + +
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Residues in contact with ARG 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ASN* 6.1 0.4 - - - -
45A ILE* 4.2 14.0 + - - +
46A ASP* 2.5 32.7 + - - +
49A THR* 3.4 30.3 - - - +
98C ILE* 2.9 13.4 + - + +
99C ASN* 3.4 10.8 - - - +
101C GLU* 1.3 77.4 + - - +
103C LYS* 1.3 62.1 + - + +
104C GLY* 3.0 1.6 + - - -
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Residues in contact with LYS 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C ASN* 2.9 28.6 + - - +
100C LYS* 3.4 14.2 - - - +
102C ARG* 1.3 78.6 - - + +
104C GLY* 1.3 59.1 + - - +
105C ASP* 3.3 30.1 + - - +
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Residues in contact with GLY 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C GLU 2.9 15.5 + - - -
102C ARG 3.0 2.5 - - - -
103C LYS* 1.3 79.9 - - - +
105C ASP* 1.3 57.5 + - - +
106C TYR 3.0 7.4 - - - -
107C LEU* 2.9 22.4 + - - +
108C 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