Contacts of the helix formed by residues 77 - 88 (chain E) 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 PHE 77 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24E ILE* 3.9 15.3 - - + -
27E PHE 4.1 2.9 - - - -
28E LYS* 3.5 50.5 - - + -
31E PHE* 3.6 36.5 - + + -
40E GLY 4.0 0.8 + - - -
76E ASN* 1.3 74.9 - - - +
78E THR* 1.3 64.8 + - + +
80E PHE* 3.3 4.0 + + + +
81E LEU* 3.0 64.8 + - + +
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Residues in contact with THR 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ASN* 2.8 18.4 + - - +
77E PHE* 1.3 84.5 - - + +
79E VAL* 1.3 64.1 + - - +
81E LEU* 3.7 10.6 - - + +
82E THR* 3.0 37.6 + - - +
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Residues in contact with VAL 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E ALA* 4.1 15.0 - - + -
72E SER 5.5 0.4 - - - +
73E GLY* 4.3 7.9 - - - +
74E PRO* 3.5 25.4 - - + +
75E ILE* 4.0 18.8 - - + -
76E ASN* 3.0 24.1 + - - +
78E THR* 1.3 77.8 - - - +
80E PHE* 1.3 59.9 + - - +
82E THR* 2.9 20.1 + - - +
83E MET* 3.0 19.0 + - + +
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Residues in contact with PHE 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829D TRP* 4.6 9.0 - + - -
831D TRP* 6.4 0.2 - + - -
27E PHE* 4.6 13.0 - + + -
30E ALA* 4.9 4.3 - - + -
31E PHE* 3.7 40.4 - + + -
34E ILE* 4.4 19.5 - - + -
42E ILE* 4.6 6.1 - - + -
75E ILE* 3.7 24.2 - - + +
76E ASN 3.0 15.8 + - - +
77E PHE* 3.6 7.2 - + + +
79E VAL* 1.3 77.8 - - - +
81E LEU* 1.3 58.0 + - + +
83E MET* 3.4 21.1 + - + +
84E PHE* 3.0 64.9 + + - +
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Residues in contact with LEU 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E PHE* 4.5 11.3 - - + -
24E ILE* 4.4 17.9 - - + -
27E PHE* 4.0 30.3 - - + -
77E PHE* 3.0 64.1 + - + +
78E THR* 3.7 10.5 - - + +
80E PHE* 1.3 78.5 - - + +
82E THR* 1.3 59.2 + - + +
84E PHE* 3.4 4.1 + - + +
85E GLY* 2.8 26.7 + - - -
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Residues in contact with THR 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E THR* 3.0 21.5 + - - +
79E VAL* 2.9 21.0 + - - +
81E LEU* 1.3 75.7 - - + +
83E MET* 1.3 57.9 + - - +
85E GLY* 3.3 1.9 + - - -
86E GLU* 3.0 49.5 + - - +
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Residues in contact with MET 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829D TRP* 5.1 6.7 - - + -
67E MET 4.6 4.5 - - - +
70E GLU* 3.7 51.6 - - + +
71E ALA* 4.6 3.1 - - + -
75E ILE* 4.9 12.8 - - + -
79E VAL* 3.0 18.8 + - + +
80E PHE* 3.7 33.4 - - + +
82E THR* 1.3 79.0 + - - +
84E PHE* 1.3 66.7 + - + +
86E GLU* 3.3 8.3 + - - +
87E LYS* 3.2 48.8 + - + +
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Residues in contact with PHE 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826D VAL* 5.6 4.3 - - + -
829D TRP* 3.0 44.4 - + - -
832D MET* 4.7 14.1 - - - -
19E PHE* 4.3 4.5 - - + -
27E PHE* 4.3 34.5 - + + -
80E PHE* 3.0 52.5 + + - +
81E LEU* 3.9 5.4 - - + +
83E MET* 1.3 81.4 - - + +
85E GLY* 1.3 55.4 + - - +
87E LYS* 3.2 19.7 + - - +
88E LEU* 2.9 60.2 + - + +
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Residues in contact with GLY 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E PHE* 3.5 28.1 - - - -
81E LEU 2.8 15.4 + - - -
82E THR* 3.3 2.7 + - - -
83E MET 3.3 0.2 - - - -
84E PHE* 1.3 75.8 - - - +
86E GLU* 1.3 61.2 + - - +
88E LEU 3.2 15.8 + - - +
89E LYS* 3.2 14.7 - - - +
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Residues in contact with GLU 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E THR* 3.0 33.3 + - - +
83E MET* 3.3 7.8 + - - +
85E GLY* 1.3 76.0 - - - +
87E LYS* 1.3 62.6 + - + +
89E LYS* 3.5 25.5 - - + +
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Residues in contact with LYS 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822D SER* 4.1 7.4 + - - -
825D ASN* 6.1 4.5 - - + +
826D VAL* 5.4 9.2 - - + +
829D TRP* 5.2 6.0 - - - -
70E GLU* 5.2 10.8 - - + +
83E MET* 3.2 45.1 + - + +
84E PHE* 3.7 37.3 - - - +
86E GLU* 1.3 80.2 - - + +
88E LEU* 1.3 68.6 + - + +
89E LYS* 3.5 4.1 + - - +
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Residues in contact with LEU 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822D SER* 2.0 48.0 - - - +
826D VAL* 4.6 13.0 - - + -
19E PHE* 5.2 9.9 - - + -
23E GLU* 5.8 1.8 - - - +
27E PHE* 4.5 14.4 - - + -
84E PHE* 2.9 46.9 + - + +
85E GLY* 3.4 7.5 - - - +
87E LYS* 1.3 83.8 - - + +
89E LYS* 1.3 55.7 + - - +
90E GLY 3.1 9.5 + - - +
91E ALA* 3.2 26.0 + - + +
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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