Contacts of the helix formed by residues 77 - 88 (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 PHE 77 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24N ILE* 3.9 16.6 - - + -
27N PHE 4.1 2.2 - - - -
28N LYS* 3.5 49.8 - - + -
31N PHE* 3.6 35.8 - + + -
40N GLY 4.0 0.8 + - - +
76N ASN* 1.3 74.2 - - - +
78N THR* 1.3 64.5 + - + +
80N PHE* 3.3 4.5 + + + +
81N LEU* 3.0 65.0 + - + +
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Residues in contact with THR 78 (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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76N ASN* 2.8 19.1 + - - +
77N PHE* 1.3 84.3 - - + +
79N VAL* 1.3 63.0 + - - +
81N LEU* 3.4 10.6 + - + +
82N THR* 3.0 38.4 + - - +
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Residues in contact with VAL 79 (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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71N ALA* 4.1 14.6 - - + -
72N SER 5.5 0.7 - - - +
73N GLY* 4.3 7.4 - - - +
74N PRO* 3.5 26.5 - - + +
75N ILE* 4.0 18.8 - - + -
76N ASN* 3.0 24.5 + - - +
78N THR* 1.3 77.8 - - - +
80N PHE* 1.3 60.4 + - - +
82N THR* 2.9 20.0 + - - +
83N MET* 3.0 18.7 + - + +
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Residues in contact with PHE 80 (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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831M TRP* 3.6 38.4 - + - -
27N PHE* 4.6 13.0 - + + -
30N ALA* 4.9 4.3 - - + -
31N PHE* 3.7 41.3 - + + -
34N ILE* 4.4 5.6 - - + -
42N ILE* 4.6 2.7 - - + -
75N ILE* 3.7 23.3 - - + +
76N ASN 3.0 16.7 + - - +
77N PHE* 3.6 7.0 - + + +
79N VAL* 1.3 77.8 - - - +
81N LEU* 1.3 57.5 + - + +
83N MET* 3.4 21.3 + - + +
84N PHE* 3.0 62.8 + + - +
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Residues in contact with LEU 81 (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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19N PHE* 4.5 11.4 - - + -
24N ILE* 4.4 17.0 - - + -
27N PHE* 4.0 31.0 - - + -
77N PHE* 3.0 62.4 + - + +
78N THR* 3.7 11.7 - - + +
80N PHE* 1.3 79.3 - - + +
82N THR* 1.3 59.3 + - + +
84N PHE* 3.4 4.1 + - + +
85N GLY* 2.8 26.3 + - - -
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Residues in contact with THR 82 (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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78N THR* 3.0 20.9 + - - +
79N VAL* 2.9 21.0 + - - +
81N LEU* 1.3 75.3 - - + +
83N MET* 1.3 58.8 + - - +
85N GLY* 3.3 2.0 + - - -
86N GLU* 3.0 50.1 + - - +
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Residues in contact with MET 83 (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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829M TRP* 3.0 33.4 - - + -
831M TRP* 4.6 5.8 - - + +
67N MET 4.6 3.6 - - - +
70N GLU* 3.7 44.9 - - + +
71N ALA* 4.6 2.7 - - + -
75N ILE* 4.9 12.6 - - + -
79N VAL* 3.0 18.7 + - + +
80N PHE* 3.8 27.4 - - + +
81N LEU 3.3 0.2 - - - -
82N THR* 1.3 78.6 + - - +
84N PHE* 1.3 61.4 + - - +
86N GLU* 3.3 8.8 + - - +
87N LYS* 3.2 38.0 + - + +
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Residues in contact with PHE 84 (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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829M TRP* 2.7 44.4 - + - -
831M TRP* 3.8 17.9 - - + -
832M MET* 3.2 24.2 - - - -
835M PHE* 5.5 3.8 - - + -
19N PHE* 4.3 4.3 - - + -
27N PHE* 4.3 31.4 - + + -
80N PHE* 3.0 56.7 + + - +
81N LEU* 3.9 4.7 - - - +
83N MET* 1.3 77.2 - - - +
85N GLY* 1.3 55.7 + - - +
87N LYS* 3.2 4.5 + - - +
88N LEU* 2.9 55.9 + - + +
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Residues in contact with GLY 85 (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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19N PHE* 3.5 28.3 - - - -
81N LEU 2.8 15.0 + - - -
82N THR* 3.3 2.4 + - - -
83N MET 3.3 0.2 - - - -
84N PHE* 1.3 75.8 - - - +
86N GLU* 1.3 62.6 + - - +
88N LEU 3.2 15.8 + - - -
89N LYS* 3.2 14.1 - - - +
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Residues in contact with GLU 86 (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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82N THR* 3.0 33.9 + - - +
83N MET* 3.3 8.2 + - - +
85N GLY* 1.3 76.5 - - - +
87N LYS* 1.3 60.9 + - + +
89N LYS* 3.5 24.1 - - + +
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Residues in contact with LYS 87 (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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822M SER* 4.0 10.7 + - - +
825M ASN* 4.4 11.3 + - + +
826M VAL* 3.5 23.0 - - + +
829M TRP* 1.9 85.5 - - + +
70N GLU* 5.6 2.0 - - + +
83N MET* 3.2 24.1 + - + +
84N PHE* 3.7 11.4 - - - +
86N GLU* 1.3 81.2 - - + +
88N LEU* 1.3 60.3 + - - +
89N LYS* 3.5 3.9 + - - -
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Residues in contact with LEU 88 (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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822M SER* 3.3 16.2 - - - +
823M PHE* 5.0 0.9 - - - +
826M VAL* 2.8 40.8 - - + -
832M MET* 4.0 18.6 - - + -
19N PHE* 5.2 10.1 - - + -
23N GLU* 5.8 1.6 - - - +
27N PHE* 4.5 11.4 - - + -
84N PHE* 2.9 44.9 + - + +
85N GLY* 3.2 7.9 + - - +
87N LYS* 1.3 79.1 - - + +
89N LYS* 1.3 55.6 + - - +
90N GLY 3.1 10.1 + - - -
91N ALA* 3.2 27.9 + - + +
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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