Contacts of the helix formed by residues 93 - 105 (chain N) 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 PRO 93 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20N ASP* 4.4 17.9 - - - +
23N GLU* 5.8 4.3 - - - +
91N ALA 4.1 4.3 - - - +
92N ASP* 1.3 98.3 - - - +
94N GLU* 1.3 66.9 + - - +
95N ASP* 4.4 8.5 - - + +
96N VAL* 3.0 29.8 + - + -
97N ILE* 3.1 11.7 - - - +
158N THR* 4.2 8.1 - - + +
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Residues in contact with GLU 94 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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839M MLY 4.4 9.7 - - - -
93N PRO* 1.3 72.4 - - - +
95N ASP* 1.3 61.5 + - - +
97N ILE* 3.2 10.3 + - - +
98N MET* 2.9 43.0 + - - +
154N CYS* 3.4 15.5 - - + +
155N TYR* 3.2 39.9 - - - -
158N THR* 3.2 25.7 + - + +
159N HIS* 3.3 14.6 + - - -
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Residues in contact with ASP 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93N PRO* 3.1 5.9 + - + +
94N GLU* 1.3 83.1 + - - +
96N VAL* 1.3 63.2 + - + +
98N MET* 3.6 9.1 + - - +
99N GLY* 3.0 22.9 + - - -
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Residues in contact with VAL 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815M CYS* 4.1 12.5 - - - -
92N ASP* 3.1 28.3 - - - +
93N PRO* 3.0 22.7 + - + +
95N ASP* 1.3 81.0 - - + +
97N ILE* 1.3 58.1 + - - +
99N GLY* 3.3 2.3 + - - +
100N ALA* 3.0 27.4 + - - +
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Residues in contact with ILE 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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815M CYS* 6.1 0.4 - - - -
816M ILE* 5.8 4.5 - - + -
819M ASN* 5.8 1.3 - - + -
92N ASP* 3.1 41.1 - - + +
93N PRO 3.1 11.2 + - - +
94N GLU* 3.2 4.9 + - - +
96N VAL* 1.3 77.9 - - - +
98N MET* 1.3 56.5 + - - +
100N ALA* 3.3 7.0 + - - +
101N PHE* 3.0 58.5 + - + -
154N CYS* 3.5 31.0 - - + +
157N ILE* 3.9 29.8 - - + -
158N THR* 4.0 0.2 - - - +
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Residues in contact with MET 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94N GLU* 2.9 29.4 + - - +
95N ASP* 4.0 8.7 - - - +
97N ILE* 1.3 74.8 - - - +
99N GLY* 1.3 58.0 - - - +
101N PHE* 3.7 6.5 - - - +
102N LYS* 2.9 31.4 + - - +
150N TYR* 5.8 1.1 - - + -
151N LYS* 4.5 31.4 - - + +
154N CYS* 3.6 22.2 - - - -
155N TYR* 5.2 11.4 - - - -
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Residues in contact with GLY 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95N ASP 3.0 15.7 + - - -
96N VAL* 3.3 6.2 + - - -
97N ILE 3.3 0.4 - - - -
98N MET* 1.3 74.7 - - - +
100N ALA* 1.3 62.1 + - - +
102N LYS* 3.1 16.9 + - - +
103N VAL* 3.1 20.6 + - - +
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Residues in contact with ALA 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812M SER* 4.8 17.0 - - - +
815M CYS* 5.9 3.4 - - - -
816M ILE* 3.6 32.8 - - + -
96N VAL 3.0 12.7 + - - +
97N ILE* 3.3 8.5 + - - +
99N GLY* 1.3 73.5 - - - +
101N PHE* 1.3 57.6 + - - +
103N VAL* 3.2 11.3 + - - +
104N LEU* 3.0 32.2 + - + +
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Residues in contact with PHE 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816M ILE* 4.5 16.8 - - + -
97N ILE* 3.0 42.0 + - + +
98N MET* 3.9 5.6 - - - +
99N GLY 3.3 0.4 - - - -
100N ALA* 1.3 76.1 - - - +
102N LYS* 1.3 57.2 + - - +
104N LEU* 3.4 26.1 + - + +
105N ASP 2.9 21.7 + - - -
117N LEU* 5.2 14.4 - - + -
150N TYR* 3.1 54.3 + + + -
151N LYS 5.5 0.7 - - - -
153N ILE* 5.0 22.4 - - + -
154N CYS* 3.6 20.4 - - - -
157N ILE* 6.0 0.9 - - + -
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Residues in contact with LYS 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98N MET 2.9 17.8 + - - +
99N GLY* 3.4 7.2 - - - +
101N PHE* 1.3 75.4 - - - +
103N VAL* 1.3 61.9 + - + +
105N ASP* 3.0 29.5 - - - +
106N PRO* 3.2 9.3 - - + +
108N GLY* 3.6 28.7 - - - +
109N LYS* 3.7 11.1 - - - +
150N TYR* 4.9 5.2 - - + +
151N LYS* 5.4 8.4 - - - +
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Residues in contact with VAL 103 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812M SER* 5.7 9.4 - - - +
99N GLY 3.1 17.0 + - - +
100N ALA* 3.2 11.2 + - - +
102N LYS* 1.3 80.3 - - + +
104N LEU* 1.3 64.7 + - + +
106N PRO* 3.7 17.9 - - - +
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Residues in contact with LEU 104 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816M ILE* 4.6 10.3 - - + -
100N ALA 3.0 13.1 + - - +
101N PHE* 3.7 37.9 - - + +
103N VAL* 1.3 84.5 - - + +
105N ASP* 1.3 56.9 + - - +
106N PRO* 3.3 7.5 - - - +
112N ILE* 3.3 32.2 - - + +
116N PHE* 5.0 5.2 - - + -
117N LEU* 4.2 15.7 - - + -
120N LEU* 3.7 28.5 - - + -
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Residues in contact with ASP 105 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101N PHE 2.9 6.2 + - - +
102N LYS* 3.0 14.5 - - + +
104N LEU* 1.3 77.6 - - - +
106N PRO* 1.3 58.2 - - - +
107N ASP* 3.1 13.0 - - - +
108N GLY* 3.0 38.1 + - - +
109N LYS 3.8 0.3 + - - -
110N GLY* 2.9 29.7 - - - +
111N SER 4.9 0.5 - - - -
112N ILE* 4.8 10.4 + - + +
150N TYR* 2.9 25.6 + - + +
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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