Contacts of the helix formed by residues 95 - 100 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A SER 5.7 1.1 + - - -
44A ASP* 3.7 11.2 + - - +
45A TYR* 4.3 2.0 - - - -
93A SER* 3.1 19.6 + - - -
94A PRO* 1.3 93.7 + - + +
96A MSE 1.3 61.0 + - - +
97A LYS* 4.1 15.4 + - + +
98A ASP* 3.1 24.9 + - - +
99A LEU* 2.9 26.5 + - - +
525B GLU* 3.4 24.0 + - + +
526B GLU* 3.8 9.0 - - + -
239C GLN* 2.6 34.1 + - - -
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Residues in contact with MSE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ASP* 2.9 24.9 + - - +
45A TYR* 3.8 15.6 - - + -
65A VAL* 3.6 41.1 - - + +
67A PRO* 3.9 30.1 - - + -
95A HIS* 1.3 71.0 - - - +
97A LYS* 1.3 62.1 + - - +
99A LEU* 4.1 4.3 - - + -
100A LEU* 3.1 47.0 + - + +
107A PHE 5.8 0.4 - - - -
108A VAL* 3.8 26.9 - - + +
112A TYR 3.6 19.3 - - - +
114A ARG* 4.5 4.0 - - + +
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Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ASP* 5.2 0.4 + - - -
90A ARG* 3.1 17.7 + - - -
95A HIS* 4.1 17.0 + - + +
96A MSE 1.3 78.8 - - - +
98A ASP* 1.3 90.5 + - - +
100A LEU* 3.4 6.6 - - - +
101A SER 4.6 2.6 - - - +
105A ASP* 5.7 7.7 - - + +
108A VAL* 3.8 27.3 - - + +
524B PRO* 4.1 20.4 - - - +
525B GLU* 6.2 0.2 - - - +
526B GLU* 3.1 22.4 + - - +
527B MSE 4.8 7.0 - - - +
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Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 2.9 22.5 + - - -
91A LEU* 3.6 13.4 - - + +
93A SER* 3.7 13.0 - - - +
95A HIS* 3.1 17.9 + - - +
97A LYS* 1.3 113.0 + - - +
99A LEU* 1.3 63.5 + - - +
100A LEU 3.3 0.7 - - - -
526B GLU* 3.4 22.9 - - + +
527B MSE 4.0 0.3 - - - -
528B ALA* 3.0 34.8 + - + +
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TYR* 3.6 46.0 - - + +
47A LYS* 3.8 14.8 - - - +
65A VAL* 4.1 17.9 - - + -
88A THR 3.2 23.0 - - - +
89A GLU* 3.4 14.0 - - + +
90A ARG 2.8 30.3 + - - -
91A LEU 3.3 19.9 + - - +
92A ALA* 4.8 0.4 - - - -
93A SER* 4.1 10.3 - - - +
95A HIS 2.9 15.9 + - - +
96A MSE 3.4 5.4 + - - +
98A ASP* 1.3 77.1 - - - +
100A LEU* 1.3 60.1 + - + +
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A VAL* 4.2 8.7 - - + -
87A ARG 4.8 2.7 - - - +
88A THR* 3.8 37.5 - - + +
90A ARG* 3.0 30.3 + - - +
96A MSE 3.1 45.7 + - + +
97A LYS 3.4 2.9 - - - +
98A ASP 3.4 0.3 - - - +
99A LEU* 1.3 84.7 - - + +
101A SER* 1.3 63.0 + - - +
104A ASP* 3.9 20.2 - - + +
107A PHE* 6.2 0.9 - - + -
108A VAL* 3.9 14.6 - - + -
114A ARG* 4.0 22.4 - - + -
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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