Contacts of the helix formed by residues 64 - 76 (chain R) 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 THR 64 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23R ALA 4.3 4.5 - - - -
24R LYS* 4.4 16.6 - - - -
25R ILE 5.7 0.4 - - - -
62R ALA* 6.1 0.7 - - + -
63R ILE* 1.3 102.7 - - - +
65R PHE* 1.3 64.7 - - - +
66R GLU* 3.1 24.9 + - - +
67R GLU* 2.9 33.8 + - - +
68R PHE* 3.2 3.5 + - - +
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Residues in contact with PHE 65 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10R PHE* 5.6 1.3 - - + -
11R LYS* 3.9 34.5 - - + -
14R PHE* 3.4 39.5 - + + -
23R ALA* 4.3 11.3 + - + +
64R THR* 1.3 74.5 - - - +
66R GLU* 1.3 75.0 + - + +
67R GLU 3.2 0.4 - - - -
68R PHE* 4.3 5.8 - - - -
69R LEU* 3.0 60.2 + - + +
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Residues in contact with GLU 66 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64R THR* 3.1 23.4 + - - +
65R PHE* 1.3 97.0 + - + +
67R GLU* 1.3 62.3 + - + +
69R LEU* 5.1 1.3 - - - -
70R PRO* 3.3 20.2 - - - +
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Residues in contact with GLU 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55R LYS* 4.6 19.8 + - - +
62R ALA 5.0 0.3 - - - +
63R ILE* 3.9 15.1 - - + +
64R THR* 2.9 39.2 + - - +
66R GLU* 1.3 80.8 - - + +
68R PHE* 1.3 66.0 + - - +
69R LEU 3.4 0.9 - - - -
70R PRO* 3.3 5.8 - - - +
71R MET* 3.1 35.0 + - + +
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Residues in contact with PHE 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R PHE* 3.8 29.2 - + + -
25R ILE* 3.6 46.7 - - + -
30R VAL* 3.7 39.3 - - + -
33R ILE* 3.5 29.8 - - + -
34R ALA* 4.8 6.7 - - + -
37R LEU* 5.0 3.1 - - + -
63R ILE* 4.2 6.3 - - + -
64R THR 3.2 12.6 + - - +
65R PHE* 4.0 6.5 - - - +
67R GLU* 1.3 78.7 - - - +
69R LEU* 1.3 65.1 + - - +
71R MET* 3.2 10.9 + - + -
72R LEU* 3.0 29.4 + - + +
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Residues in contact with LEU 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10R PHE* 4.9 20.9 - - + -
14R PHE* 4.8 5.3 - - + -
65R PHE* 3.0 47.8 + - + +
66R GLU* 5.1 1.6 - - - -
68R PHE* 1.3 78.4 - - - +
70R PRO* 1.3 69.4 - - + +
72R LEU* 3.0 17.0 + - + +
73R GLN* 3.1 41.5 + - + +
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Residues in contact with PRO 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66R GLU* 3.3 24.2 - - - +
67R GLU* 3.3 14.1 - - - +
69R LEU* 1.3 93.6 - - + +
71R MET* 1.3 55.9 + - + +
73R GLN* 3.2 15.8 + - + +
74R ALA* 2.9 28.6 + - - +
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Residues in contact with MET 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30R VAL* 3.9 25.8 - - + -
49R ILE* 5.5 14.7 - - + +
50R LEU* 4.7 18.8 - - + -
53R PRO* 6.2 0.9 - - - -
55R LYS* 3.7 27.1 - - - +
63R ILE* 4.0 21.1 - - + -
67R GLU* 3.1 24.1 + - + +
68R PHE* 3.2 18.3 + - + +
70R PRO* 1.3 77.0 - - + +
72R LEU* 1.3 57.8 + - - +
74R ALA* 3.3 6.3 + - - +
75R ALA* 3.0 28.5 + - - +
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Residues in contact with LEU 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10R PHE* 4.0 31.2 - - + -
14R PHE* 5.0 3.4 - - + -
34R ALA* 4.1 27.4 - - + -
37R LEU* 3.6 31.6 - - + -
39R GLN* 4.0 21.8 - - + -
68R PHE* 3.0 20.4 + - + +
69R LEU* 3.0 15.0 + - + +
71R MET* 1.3 75.8 - - - +
73R GLN* 1.3 60.1 + - + +
75R ALA* 3.3 4.5 + - + +
76R ALA* 3.0 28.9 + - + +
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Residues in contact with GLN 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3R SER* 4.5 16.8 - - - +
69R LEU* 3.1 49.6 + - + +
70R PRO* 3.2 14.8 - - + +
71R MET 3.3 0.2 - - - -
72R LEU* 1.3 81.1 - - + +
74R ALA* 1.3 58.3 + - - +
75R ALA 3.7 0.2 + - - -
76R ALA* 3.7 13.1 + - - +
77R ASN* 3.2 19.8 + - - +
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Residues in contact with ALA 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49R ILE* 5.6 13.9 - - + +
70R PRO 2.9 16.4 + - - +
71R MET* 3.7 7.6 - - - +
73R GLN* 1.3 77.3 - - - +
75R ALA* 1.3 59.9 + - - +
76R ALA 3.3 0.2 - - - -
77R ASN* 3.2 18.9 + - - +
78R ASN* 3.4 13.6 + - - +
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Residues in contact with ALA 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34R ALA* 5.4 2.7 - - + -
39R GLN* 3.0 18.6 - - + +
41R PRO* 4.2 27.8 - - + +
45R GLU* 5.0 0.9 - - - +
49R ILE* 5.6 7.0 - - + -
71R MET 3.0 16.1 + - - +
72R LEU* 3.7 8.5 - - + +
74R ALA* 1.3 75.0 - - - +
76R ALA* 1.3 58.6 + - - +
77R ASN 3.2 2.2 - - - -
78R ASN* 3.0 33.0 + - - +
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Residues in contact with ALA 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39R GLN* 3.3 20.4 - - + +
72R LEU* 3.0 16.4 + - + +
73R GLN* 3.8 12.1 - - - +
74R ALA 3.3 0.8 - - - -
75R ALA* 1.3 77.2 - - - +
77R ASN* 1.3 59.2 + - - +
78R ASN 3.2 0.4 - - - -
79R LYS* 3.1 30.2 - - + +
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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