Contacts of the helix formed by residues 83 - 95 (chain C) in PDB entry 1MVW
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 83 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C ASP 5.2 4.3 - - - +
81C GLN* 3.1 14.4 + - - +
82C GLY* 1.3 71.6 - - - +
84C PHE* 1.3 62.9 + - - +
85C GLU* 3.2 15.9 + - - +
86C ASP* 3.1 38.1 + - + +
87C PHE* 3.4 17.5 + - + -
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Residues in contact with PHE 84 (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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82C GLY 3.8 3.2 + - - -
83C THR* 1.3 71.9 + - - +
85C GLU* 1.3 95.3 + - - +
86C ASP 3.3 0.2 - - - -
87C PHE* 3.3 10.4 + - - +
88C VAL* 3.2 34.8 + - + +
143C VAL* 5.4 0.2 - - + -
147C MET* 3.6 34.3 - - + -
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Residues in contact with GLU 85 (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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83C THR* 3.2 11.6 + - - +
84C PHE* 1.3 112.8 - - - +
86C ASP* 1.3 62.5 + - - +
88C VAL* 3.3 2.9 + - - +
89C GLU* 2.9 52.6 + - - +
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Residues in contact with ASP 86 (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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790A THR* 5.0 3.2 + - - -
83C THR* 3.1 36.5 + - + +
85C GLU* 1.3 80.8 - - - +
87C PHE* 1.3 64.1 + - + +
89C GLU* 3.6 11.7 - - - +
90C GLY* 2.9 26.3 + - - -
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Residues in contact with PHE 87 (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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789A ALA* 3.7 25.8 - - + -
790A THR* 3.9 25.7 + - + +
793A ARG* 3.6 50.9 - - + -
81C GLN 4.4 4.7 - - - -
82C GLY* 4.0 8.7 - - - -
83C THR* 3.4 33.2 - - + -
84C PHE* 3.3 14.1 + - - +
85C GLU 3.3 0.6 - - - -
86C ASP* 1.3 84.9 - - + +
88C VAL* 1.3 61.7 + - - +
90C GLY* 3.4 7.3 + - - -
91C LEU* 3.4 21.9 + - - +
143C VAL* 4.2 15.3 - - + -
147C MET* 4.0 11.4 - - - -
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Residues in contact with VAL 88 (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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84C PHE* 3.2 25.3 + - + +
85C GLU* 4.0 3.1 - - - +
87C PHE* 1.3 77.0 - - - +
89C GLU* 1.3 60.0 + - + +
91C LEU* 3.4 6.3 + - - +
92C ARG* 2.9 31.9 + - + +
139C TYR* 4.1 18.5 - - + +
140C GLU* 5.3 12.1 - - + +
143C VAL* 4.0 27.1 - - + -
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Residues in contact with GLU 89 (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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85C GLU* 2.9 46.2 + - - +
86C ASP* 3.6 13.7 + - - +
88C VAL* 1.3 76.3 - - + +
90C GLY* 1.3 64.8 + - - +
92C ARG* 3.6 8.1 - - + +
93C VAL* 3.0 33.6 + - + +
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Residues in contact with GLY 90 (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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786A ILE* 5.8 11.0 - - - -
790A THR* 5.9 2.9 - - - -
86C ASP 2.9 18.3 + - - -
87C PHE 3.4 2.2 + - - -
88C VAL 3.3 0.4 - - - -
89C GLU* 1.3 77.3 - - - +
91C LEU* 1.3 62.8 + - - +
93C VAL* 3.2 14.0 + - - +
94C PHE* 3.3 11.3 + - - +
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Residues in contact with LEU 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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790A THR* 6.3 5.4 - - + -
87C PHE 3.4 9.5 + - - +
88C VAL 3.4 3.9 + - - +
89C GLU 3.4 0.2 - - - -
90C GLY* 1.3 76.9 - - - +
92C ARG* 1.3 57.1 + - - +
94C PHE* 3.1 33.6 + - + +
95C ASP* 2.9 24.9 - - - +
102C VAL* 4.5 6.1 - - + -
107C LEU* 4.7 11.4 - - + -
139C TYR* 3.1 42.3 + - + -
142C PHE* 4.5 12.1 - - + -
143C VAL* 3.8 20.6 - - + -
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Residues in contact with ARG 92 (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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88C VAL* 2.9 24.3 + - + +
89C GLU* 3.2 11.4 + - + +
91C LEU* 1.3 76.2 - - - +
93C VAL* 1.3 60.6 + - + +
95C ASP 3.2 21.9 - - - +
97C GLU 4.8 8.7 - - - -
98C GLY* 3.9 9.9 + - - -
99C ASN* 3.7 20.8 - - - +
100C GLY* 3.7 22.0 - - - +
139C TYR* 3.0 24.5 + - - -
140C GLU* 3.8 24.0 + - - +
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Residues in contact with VAL 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 GLU* 3.0 17.6 + - + +
90C GLY* 3.2 10.1 + - - +
92C ARG* 1.3 79.0 - - + +
94C PHE* 1.3 62.3 + - - +
95C ASP* 3.4 2.3 + - - -
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Residues in contact with PHE 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 GLY 3.3 10.7 + - - +
91C LEU* 3.1 26.2 + - + +
93C VAL* 1.3 80.0 - - - +
95C ASP* 1.3 59.7 + - - +
102C VAL* 3.6 40.2 - - + -
106C GLU* 3.8 30.1 - - + +
107C LEU* 4.3 4.9 - - + -
110C VAL* 3.7 34.1 - - + -
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Residues in contact with ASP 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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91C LEU 2.9 8.5 + - - +
92C ARG* 3.2 15.1 - - - +
93C VAL 3.4 1.9 - - - -
94C PHE* 1.3 82.2 - - - +
96C LYS* 1.3 79.3 + - - +
97C GLU 4.1 3.5 - - - +
99C ASN 3.7 6.1 - - - +
101C THR 3.1 30.2 + - - +
102C VAL* 3.4 15.2 - - - +
103C MET 5.6 0.2 - - - +
106C GLU* 5.1 5.2 - - - +
139C TYR* 2.8 42.4 + - - -
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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