Contacts of the helix formed by residues 88 - 99 (chain C) in PDB entry 4U2M
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 ASN 88 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ASN* 6.3 0.4 - - - +
68C ALA* 4.5 19.9 + - + +
72C GLN* 3.7 17.0 - - - +
83C SER 3.1 22.6 + - - -
84C LEU* 3.5 7.4 - - - +
85C SER* 2.9 34.3 + - - +
87C GLU* 1.3 78.0 - - + +
89C VAL* 1.3 72.9 + - - +
90C ASP 3.2 2.6 + - - -
91C ASP* 3.3 9.8 + - - +
92C VAL* 2.9 29.1 + - + +
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Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 4.8 4.0 - - + -
85C SER 3.1 15.2 + - - +
86C PRO* 3.8 15.9 - - + +
87C GLU 3.7 0.8 - - - -
88C ASN* 1.3 85.4 + - - +
90C ASP* 1.3 68.5 + - - +
92C VAL* 3.8 3.7 - - - +
93C LEU* 2.9 26.9 + - - +
108C CYS* 3.8 39.3 - - + +
111C LEU* 4.2 17.3 - - + -
112C LYS* 4.2 19.1 - - + -
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Residues in contact with ASP 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLN* 5.7 0.7 - - - +
86C PRO 5.4 2.2 + - - +
88C ASN 3.3 0.6 - - - -
89C VAL* 1.3 78.4 - - - +
91C ASP* 1.3 64.5 + - - +
93C LEU* 3.2 8.5 + - - +
94C ALA* 2.9 31.2 + - - +
112C LYS* 2.8 40.7 + - - -
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Residues in contact with ASP 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASP* 5.2 12.7 - - - +
66C ASN* 3.8 24.8 - - + +
68C ALA* 4.3 8.2 - - + +
69C GLY* 4.0 16.4 - - - +
87C GLU 4.1 14.9 - - - +
88C ASN* 3.5 8.5 - - - +
90C ASP* 1.3 77.6 - - - +
92C VAL* 1.3 64.5 + - - +
94C ALA* 3.5 5.2 + - - +
95C VAL* 3.1 27.9 + - - +
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C ALA 4.4 0.4 - - - +
69C GLY* 4.2 15.0 - - - +
72C GLN* 3.8 26.0 - - + -
73C VAL* 4.4 8.2 - - + +
82C LEU* 4.4 6.5 - - + -
84C LEU* 3.9 21.5 - - + -
88C ASN* 2.9 30.4 + - - +
89C VAL 3.8 3.8 - - - +
91C ASP* 1.3 72.4 - - - +
93C LEU* 1.3 58.4 + - - +
95C VAL* 3.3 2.8 + - - +
96C ALA* 2.9 27.2 + - - +
104C ILE* 3.6 26.9 - - + -
108C CYS* 3.7 8.3 - - - -
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Residues in contact with LEU 93 (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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89C VAL 2.9 18.8 + - - +
90C ASP* 3.2 7.6 + - - +
92C VAL* 1.3 77.6 - - - +
94C ALA* 1.3 53.2 + - - +
96C ALA* 3.8 1.7 - - - -
97C THR* 2.6 48.2 + - - +
105C ILE* 4.0 39.0 - - + +
108C CYS* 3.8 14.8 - - + -
109C HIS* 3.8 26.0 - - + +
112C LYS* 4.5 17.5 - - - -
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Residues in contact with ALA 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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90C ASP 2.9 17.8 + - - +
91C ASP* 3.8 6.3 - - - +
93C LEU* 1.3 74.5 - - - +
95C VAL* 1.3 65.9 + - + +
97C THR* 3.4 6.8 + - - -
98C PHE* 3.1 23.7 + - - +
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Residues in contact with VAL 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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64C ILE 5.3 0.4 - - - +
65C SER* 3.2 36.6 - - - -
66C ASN 4.7 0.9 - - - +
69C GLY* 4.1 1.6 - - - -
70C LEU* 4.1 24.0 - - + +
73C VAL* 3.8 19.1 - - + -
91C ASP 3.1 16.9 + - - +
92C VAL 3.8 3.1 - - - +
94C ALA* 1.3 78.2 - - + +
96C ALA* 1.3 58.1 + - - +
98C PHE* 3.3 8.6 + - + +
99C LEU* 3.0 48.5 + - + +
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Residues in contact with ALA 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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73C VAL* 5.0 3.6 - - + -
92C VAL 2.9 17.9 + - - +
93C LEU* 3.8 4.9 - - - +
95C VAL* 1.3 78.2 - - - +
97C THR* 1.3 58.1 + - - +
99C LEU* 3.4 2.6 + - - +
100C GLN* 3.0 7.3 + - - -
101C MET* 2.8 36.2 + - + +
104C ILE* 3.5 35.4 - - + -
105C ILE* 3.8 14.2 - - + +
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Residues in contact with THR 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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93C LEU* 2.6 37.1 + - - +
94C ALA* 3.6 6.9 - - - -
96C ALA* 1.3 74.6 - - - +
98C PHE* 1.3 65.7 + - - +
100C GLN* 3.0 18.9 + - - +
105C ILE* 3.9 15.4 - - + +
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Residues in contact with PHE 98 (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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48C TYR* 3.4 60.8 - + - +
63C ASP* 3.5 27.1 - - + -
64C ILE 5.9 4.7 - - - -
94C ALA 3.1 10.7 + - - +
95C VAL* 3.5 11.9 - - + +
97C THR* 1.3 81.3 - - - +
99C LEU* 1.3 72.8 + - + +
100C GLN* 3.5 5.2 + - - +
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Residues in contact with LEU 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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46C SER* 2.9 25.1 + - - +
47C GLU 4.3 1.0 + - - -
48C TYR* 3.5 35.3 + - + +
49C PHE* 3.6 36.3 - - + -
70C LEU* 4.8 4.3 - - + -
73C VAL* 4.2 7.9 - - + -
95C VAL* 3.0 38.7 + - + +
96C ALA 4.1 1.1 - - - +
97C THR 3.1 0.2 - - - -
98C PHE* 1.3 88.7 - - + +
100C GLN* 1.3 70.3 + - - +
101C MET* 3.3 26.3 + - + +
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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