Contacts of the helix formed by residues 95 - 100 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239B GLN* 2.7 34.4 + - - -
525C GLU* 3.4 23.4 + - + +
526C GLU* 3.8 7.4 - - + -
42D SER 5.9 0.6 + - - -
44D ASP* 3.7 11.6 + - - +
45D TYR* 4.2 2.0 - - - -
93D SER* 3.2 19.2 + - - -
94D PRO* 1.3 93.7 + - + +
96D MSE 1.3 61.1 + - - +
97D LYS* 4.1 20.4 - - + -
98D ASP* 3.0 25.5 + - - +
99D LEU* 2.9 26.5 + - - +
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Residues in contact with MSE 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ASP* 2.9 24.3 + - - +
45D TYR* 3.7 21.2 - - + -
65D VAL* 3.7 30.5 - - + +
67D PRO* 3.9 32.1 - - + -
95D HIS* 1.3 71.6 - - - +
97D LYS* 1.3 62.7 + - - +
99D LEU* 4.0 3.8 - - + -
100D LEU* 3.1 47.3 + - + +
107D PHE* 5.7 0.7 - - + -
108D VAL* 3.9 28.8 - - + +
112D TYR 3.6 22.7 - - - +
114D ARG* 4.5 3.6 - - + -
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Residues in contact with LYS 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524C PRO* 4.1 17.1 - - - +
526C GLU* 3.1 20.8 + - - +
527C MSE 5.3 1.6 - - - +
581C GLY* 6.1 3.6 - - - -
44D ASP* 5.2 1.9 + - - +
90D ARG* 3.2 17.8 + - - -
95D HIS* 4.1 19.4 - - + +
96D MSE 1.3 77.6 - - - +
98D ASP* 1.3 91.3 + - - +
100D LEU* 3.4 7.6 - - - +
101D SER 4.6 2.1 - - - +
105D ASP* 5.7 8.6 - - + +
108D VAL* 3.8 26.1 - - + +
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Residues in contact with ASP 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526C GLU* 3.3 27.3 - - + +
527C MSE 4.0 0.9 - - - -
528C ALA* 3.1 33.8 + - + +
90D ARG* 2.9 21.7 + - - +
91D LEU* 3.6 14.2 - - + +
93D SER* 3.7 17.0 - - - +
95D HIS* 3.0 12.0 + - - +
97D LYS* 1.3 110.6 + - - +
99D LEU* 1.3 63.0 + - - +
100D LEU 3.4 0.7 - - - -
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Residues in contact with LEU 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D TYR* 3.5 46.0 - - + +
47D LYS* 3.9 16.8 - - - +
65D VAL* 4.2 13.9 - - + -
88D THR 3.3 21.7 - - - +
89D GLU* 3.4 13.7 - - + +
90D ARG 2.8 28.2 + - - -
91D LEU 3.4 19.5 - - - +
92D ALA* 4.8 0.4 - - - -
93D SER* 4.1 10.7 - - - +
95D HIS 2.9 16.0 + - - +
96D MSE 3.8 5.2 - - - +
98D ASP* 1.3 78.0 - - - +
100D LEU* 1.3 61.7 + - + +
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D VAL* 4.2 9.6 - - + -
87D ARG 4.9 2.0 - - - +
88D THR* 3.9 36.8 - - + +
90D ARG* 3.1 24.3 + - - -
96D MSE 3.1 45.8 + - + +
97D LYS 3.4 3.4 - - - +
99D LEU* 1.3 86.8 - - + +
101D SER* 1.3 68.4 + - - +
104D ASP* 3.9 19.7 - - + +
107D PHE* 6.2 0.7 - - + -
108D VAL* 3.9 13.0 - - + -
114D ARG* 3.8 24.7 - - + -
116D PHE* 5.8 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