Contacts of the helix formed by residues 77 - 88 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24Q ILE* 3.9 16.6 - - + -
27Q PHE 4.1 2.5 - - - -
28Q LYS* 3.5 48.9 - - + -
31Q PHE* 3.6 36.3 - + + -
40Q GLY 4.0 0.6 + - - -
76Q ASN* 1.3 75.3 - - - +
78Q THR* 1.3 64.2 + - + +
80Q PHE* 3.3 4.1 + + + +
81Q LEU* 3.0 64.8 + - + +
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Residues in contact with THR 78 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Q ASN* 2.8 19.0 + - - +
77Q PHE* 1.3 83.6 - - + +
79Q VAL* 1.3 63.6 + - - +
81Q LEU* 3.4 10.9 + - + +
82Q THR* 3.0 38.8 + - - +
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Residues in contact with VAL 79 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71Q ALA* 4.1 14.4 - - + -
72Q SER 5.5 0.4 - - - +
73Q GLY* 4.3 7.6 - - - +
74Q PRO* 3.5 25.6 - - + +
75Q ILE* 4.0 19.3 - - + -
76Q ASN* 3.0 24.8 + - - +
78Q THR* 1.3 77.6 - - - +
80Q PHE* 1.3 60.0 + - - +
82Q THR* 2.9 19.6 + - - +
83Q MET* 3.0 18.7 + - + +
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Residues in contact with PHE 80 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831P TRP* 3.9 33.7 - + - -
27Q PHE* 4.6 13.7 - + + -
30Q ALA* 4.9 4.3 - - + -
31Q PHE* 3.7 41.1 - + + -
34Q ILE* 4.4 7.2 - - + -
42Q ILE* 4.6 3.8 - - + -
75Q ILE* 3.7 23.3 - - + +
76Q ASN 3.0 16.7 + - - +
77Q PHE* 3.6 7.2 - + + +
78Q THR 3.3 0.2 - - - -
79Q VAL* 1.3 77.4 - - - +
81Q LEU* 1.3 58.7 + - + +
83Q MET* 3.4 21.5 + - + +
84Q PHE* 3.0 64.0 + + - +
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Residues in contact with LEU 81 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Q PHE* 4.5 11.0 - - + -
24Q ILE* 4.4 17.0 - - + -
27Q PHE* 4.0 31.2 - - + -
77Q PHE* 3.0 62.6 + - + +
78Q THR* 3.7 11.2 - - + +
79Q VAL 3.3 0.2 - - - -
80Q PHE* 1.3 79.1 - - + +
82Q THR* 1.3 57.5 + - + +
84Q PHE* 3.4 4.6 + - + +
85Q GLY* 2.8 26.2 + - - -
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Residues in contact with THR 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78Q THR* 3.0 20.5 + - - +
79Q VAL* 2.9 21.7 + - - +
81Q LEU* 1.3 76.0 - - + +
83Q MET* 1.3 59.1 + - - +
85Q GLY* 3.7 1.5 - - - -
86Q GLU* 3.0 50.9 + - - +
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Residues in contact with MET 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829P TRP* 3.2 30.1 - - + -
831P TRP* 4.9 5.2 - - + +
67Q MET 4.6 3.8 - - - +
70Q GLU* 3.7 46.2 - - + +
71Q ALA* 4.6 3.4 - - + -
75Q ILE* 4.9 12.6 - - + -
79Q VAL* 3.0 19.1 + - + +
80Q PHE* 3.7 27.8 - - + +
81Q LEU 3.3 0.2 - - - -
82Q THR* 1.3 79.8 + - - +
84Q PHE* 1.3 60.7 + - + +
86Q GLU* 3.3 8.7 + - - +
87Q LYS* 3.2 38.8 + - + +
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Residues in contact with PHE 84 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829P TRP* 2.7 43.1 - + - -
831P TRP* 4.0 15.0 - - + -
832P MET* 3.3 25.6 - - - -
835P PHE* 5.6 3.8 - + + -
19Q PHE* 4.3 4.0 - - + -
27Q PHE* 4.3 31.9 - + + -
80Q PHE* 3.0 57.2 + + - +
81Q LEU* 3.9 4.3 - - + +
83Q MET* 1.3 77.2 - - + +
85Q GLY* 1.3 56.3 + - - +
87Q LYS* 3.2 4.7 + - - +
88Q LEU* 2.9 56.4 + - + +
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Residues in contact with GLY 85 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Q PHE* 3.5 27.9 - - - -
81Q LEU 2.8 14.8 + - - -
82Q THR* 3.3 2.9 + - - -
83Q MET 3.3 0.2 - - - -
84Q PHE* 1.3 75.4 - - - +
86Q GLU* 1.3 61.3 + - - +
88Q LEU* 3.2 15.5 + - - -
89Q LYS* 3.2 15.0 - - - +
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Residues in contact with GLU 86 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82Q THR* 3.0 34.7 + - - +
83Q MET* 3.3 7.3 + - - +
85Q GLY* 1.3 75.7 - - - +
87Q LYS* 1.3 62.1 + - + +
89Q LYS* 3.5 24.8 - - + +
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Residues in contact with LYS 87 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822P SER* 4.0 10.6 + - - +
825P ASN* 4.6 9.8 + - + +
826P VAL* 3.6 22.1 - - + +
829P TRP* 2.1 79.4 - - + +
70Q GLU* 5.5 2.2 - - + +
83Q MET* 3.2 26.9 + - + +
84Q PHE* 3.2 13.1 + - - +
86Q GLU* 1.3 80.2 - - + +
88Q LEU* 1.3 62.2 + - - +
89Q LYS* 3.5 4.0 + - - -
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Residues in contact with LEU 88 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822P SER* 3.3 15.7 - - - +
823P PHE* 5.1 0.4 - - - +
826P VAL* 3.0 39.7 - - + -
832P MET* 4.1 17.5 - - + -
19Q PHE* 5.2 9.6 - - + -
23Q GLU* 5.8 1.1 - - - +
27Q PHE* 4.5 11.9 - - + -
84Q PHE* 2.9 44.3 + - + +
85Q GLY* 3.4 7.8 - - - +
87Q LYS* 1.3 78.0 - - + +
89Q LYS* 1.3 56.8 + - - +
90Q GLY 3.1 10.0 + - - -
91Q ALA* 3.2 27.2 + - + +
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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