Contacts of the helix formed by residues 95 - 100 (chain C) in PDB entry 1MPX
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 HIS 95 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLN* 2.6 35.2 + - - -
42C SER 6.1 0.4 - - - -
44C ASP* 3.7 11.8 + - - +
45C TYR* 4.2 1.8 - - - -
93C SER* 3.1 21.3 + - - -
94C PRO* 1.3 93.4 + - + +
96C MSE 1.3 60.7 + - - +
97C LYS* 3.2 14.3 + - + +
98C ASP* 3.1 23.7 + - - +
99C LEU* 2.9 26.0 + - - +
525D GLU* 3.4 24.2 + - + +
526D GLU* 3.9 7.4 - - + -
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Residues in contact with MSE 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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44C ASP* 2.9 24.7 + - - +
45C TYR* 3.7 21.3 - - + -
65C VAL* 3.7 29.6 - - + +
67C PRO* 4.0 30.7 - - + -
95C HIS* 1.3 71.0 - - - +
97C LYS* 1.3 63.0 + - - +
99C LEU* 4.0 3.6 - - + -
100C LEU* 3.1 47.2 + - + +
107C PHE 5.4 0.4 - - - +
108C VAL* 3.9 28.3 - - + +
112C TYR 3.6 23.3 - - - +
114C ARG* 4.6 3.8 - - + +
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Residues in contact with LYS 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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44C ASP* 5.3 0.6 + - - -
90C ARG* 3.1 18.2 + - - -
95C HIS* 4.2 13.4 + - + +
96C MSE 1.3 78.4 - - - +
98C ASP* 1.3 89.9 + - - +
100C LEU* 3.3 7.1 - - - +
101C SER 4.6 2.3 - - - +
105C ASP* 5.6 9.3 - - + +
108C VAL* 3.8 25.6 - - + +
524D PRO* 4.0 21.9 - - - +
526D GLU* 2.9 24.6 + - - +
527D MSE 4.9 6.1 - - - +
581D GLY* 6.4 0.7 - - - -
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Residues in contact with ASP 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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90C ARG* 2.9 21.9 + - - +
91C LEU* 3.6 14.2 - - + +
93C SER* 3.7 17.3 - - - +
95C HIS* 3.1 15.9 + - - +
97C LYS* 1.3 110.8 + - - +
99C LEU* 1.3 64.1 + - - +
100C LEU 3.3 0.4 - - - -
526D GLU* 3.4 24.4 - - + +
527D MSE 4.0 0.7 - - - -
528D ALA* 3.1 34.7 + - + +
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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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45C TYR* 3.5 47.8 - - + +
47C LYS* 4.0 13.0 - - - +
65C VAL* 4.1 16.8 - - + -
88C THR 3.3 21.5 - - - +
89C GLU* 3.4 13.0 + - + +
90C ARG 2.8 27.9 + - - -
91C LEU 3.4 20.0 - - - +
92C ALA* 4.7 0.7 - - - -
93C SER* 4.0 10.3 - - - +
95C HIS 2.9 16.4 + - - +
96C MSE 3.3 6.3 + - - +
98C ASP* 1.3 78.4 - - - +
100C LEU* 1.3 61.3 + - + +
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Residues in contact with LEU 100 (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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65C VAL* 4.2 14.1 - - + -
87C ARG 4.9 2.2 - - - +
88C THR* 3.9 36.8 - - + +
90C ARG* 3.1 24.5 + - - -
96C MSE 3.1 45.4 + - + +
97C LYS 3.3 4.1 - - - +
99C LEU* 1.3 83.2 - - + +
101C SER* 1.3 67.9 + - - +
104C ASP* 3.9 19.7 - - + +
107C PHE* 6.4 0.4 - - + -
108C VAL* 3.9 14.8 - - + -
114C ARG* 3.8 23.6 - - + -
116C PHE* 5.7 0.2 - - + -
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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