Contacts of the helix formed by residues 87 - 95 (chain C) in PDB entry 3MP4
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 ASP 87 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ILE* 5.5 1.9 - - - +
51C VAL 4.4 0.2 - - - +
52C SER 4.4 0.2 - - - -
53C THR* 3.1 26.4 + - - +
56C LYS* 2.8 44.1 + - - +
74C THR* 5.2 0.9 + - - -
83C PRO 4.7 1.7 + - - -
84C GLN 4.7 0.9 - - - -
85C MET* 3.8 7.4 - - - +
86C GLY* 1.3 71.3 - - - +
88C HIS* 1.3 60.5 + - - +
89C THR 3.2 3.1 - - - -
90C GLU* 3.0 26.1 - - - +
91C VAL* 2.8 35.2 + - + +
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Residues in contact with HIS 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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74C THR* 3.1 40.0 - - + +
75C SER 3.6 15.3 - - - +
76C PHE* 3.3 23.4 - + + -
77C VAL 3.5 26.9 + - - -
79C PRO* 4.1 10.3 - - + +
85C MET 2.8 24.9 + - - +
86C GLY 3.6 13.9 + - - -
87C ASP* 1.3 77.2 + - - +
89C THR* 1.3 92.9 + - - +
91C VAL* 4.2 2.2 - - - -
92C LEU* 3.1 17.5 + - - +
115C ALA* 5.9 1.6 - - + -
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Residues in contact with THR 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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76C PHE* 3.5 18.5 - - + -
87C ASP 3.1 1.0 + - - -
88C HIS* 1.3 99.7 + - - +
90C GLU* 1.3 73.7 + - - +
91C VAL 3.0 1.4 + - - -
92C LEU* 3.0 13.2 + - - +
93C LYS* 3.2 41.7 + - + +
115C ALA* 5.1 4.8 - - + +
119C ALA* 4.6 4.6 - - + +
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Residues in contact with GLU 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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53C THR* 4.3 16.8 - - + +
57C ILE* 4.7 3.6 - - - +
86C GLY 4.4 3.0 - - - +
87C ASP* 3.0 34.1 - - + +
89C THR* 1.3 83.8 + - - +
91C VAL* 1.3 56.2 + - - +
93C LYS* 3.4 19.5 - - - +
94C GLY* 2.8 26.9 + - - -
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Residues in contact with VAL 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C THR* 3.5 22.7 - - + -
56C LYS* 4.1 20.6 - - + -
57C ILE* 4.4 11.7 - - + +
60C ILE* 4.3 13.2 - - + -
73C THR* 4.3 20.6 - - + +
74C THR* 4.8 3.1 - - - +
87C ASP* 2.8 44.5 + - - +
88C HIS* 3.6 7.2 - - - +
89C THR 3.0 1.0 + - - -
90C GLU* 1.3 75.5 - - - +
92C LEU* 1.3 67.2 + - - +
94C GLY* 3.1 9.0 + - - -
95C ILE* 3.2 16.6 + - - +
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Residues in contact with LEU 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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73C THR* 4.0 20.2 - - + +
76C PHE* 3.5 21.8 - - + -
88C HIS 3.1 9.4 + - - +
89C THR 3.0 9.2 + - - +
91C VAL* 1.3 79.4 - - - +
93C LYS* 1.3 57.8 + - - +
95C ILE* 3.1 17.5 - - + +
97C LYS* 3.1 26.3 + - - -
103C TYR* 4.3 10.5 - - + +
105C VAL* 3.9 20.2 - - + -
116C ALA 3.9 0.2 - - - +
119C ALA* 3.4 30.3 - - + +
120C GLY 5.4 0.2 - - - -
121C ALA* 3.8 29.4 - - + +
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Residues in contact with LYS 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 THR* 3.2 28.2 + - + +
90C GLU* 3.4 29.7 - - - +
92C LEU* 1.3 74.8 - - - +
94C GLY* 1.3 60.6 + - - +
95C ILE 3.5 2.1 + - - +
97C LYS* 3.7 10.9 + - - +
119C ALA* 3.6 34.5 - - + +
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Residues in contact with GLY 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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57C ILE* 3.6 23.2 - - - +
61C ASP* 5.2 0.5 - - - +
90C GLU 2.8 21.0 + - - -
91C VAL 3.1 2.6 + - - -
93C LYS* 1.3 76.6 - - - +
95C ILE* 1.3 63.6 + - - +
96C GLN* 5.6 0.5 - - - +
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Residues in contact with ILE 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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57C ILE* 3.9 19.3 - - + +
60C ILE* 3.6 35.9 - - + -
61C ASP* 3.9 7.0 - - - +
73C THR* 3.6 28.7 - - + +
91C VAL* 3.2 11.4 + - + +
92C LEU* 3.1 20.2 - - + +
93C LYS 3.8 1.7 - - - +
94C GLY* 1.3 80.0 - - - +
96C GLN* 1.3 68.5 + - - +
97C LYS* 2.9 25.5 + - - +
103C TYR* 3.7 26.9 - - + -
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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