Contacts of the helix formed by residues 77 - 89 (chain V) in PDB entry 3MQT
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 GLU 77 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122N TYR* 3.9 4.0 - - - -
123N LYS* 3.2 43.6 + - + +
126N GLY 3.2 18.4 - - - +
127N GLY* 3.5 20.9 - - - -
128N ALA* 3.8 12.4 + - - +
73V ARG* 5.8 2.8 - - - +
74V ASP* 3.0 27.2 + - + +
75V PRO 3.2 1.0 - - - -
76V LEU* 1.3 75.9 - - - +
78V PHE* 1.3 63.4 + - - +
80V ALA* 3.4 10.9 + - + +
81V ASN* 2.9 29.6 + - - +
84V ARG* 4.8 5.7 + - - -
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Residues in contact with PHE 78 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126N GLY* 3.6 5.0 + - - -
75V PRO 3.4 21.1 - - - -
76V LEU* 3.1 31.7 + - + -
77V GLU* 1.3 70.2 - - - +
79V ARG* 1.3 58.3 + - + +
81V ASN* 3.9 3.8 - - - +
82V TYR* 2.9 33.3 + - - +
106V ASP* 4.6 2.3 - - - +
109V LEU* 3.9 9.9 - - + -
110V TYR* 3.4 74.5 - + - +
113V ALA* 4.1 4.9 - - + -
124V LEU* 3.9 35.9 - - + -
290V THR* 3.6 9.5 + - + +
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Residues in contact with ARG 79 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79N ARG* 4.8 12.7 - - - +
125N MET 4.0 20.8 + - - -
126N GLY* 3.3 13.3 + - - +
129N GLN* 3.9 13.9 - - - +
293N LEU* 4.4 21.9 + - - +
294N ARG* 6.2 0.8 - - - +
296N MET* 4.3 18.7 - - - +
297N ASP* 3.3 38.4 + - - -
326N VAL* 5.3 0.7 - - - -
78V PHE* 1.3 79.6 - - + +
80V ALA* 1.3 57.8 + - - +
82V TYR* 3.6 1.5 - - - +
83V ASN* 2.9 39.0 + - - +
290V THR* 4.3 15.2 - - + +
294V ARG* 4.2 16.9 - - - +
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Residues in contact with ALA 80 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126N GLY 3.0 16.7 + - - +
127N GLY* 3.9 7.0 - - - +
128N ALA 3.7 12.8 - - - +
129N GLN* 3.6 31.9 + - + +
77V GLU* 3.9 11.7 - - + +
79V ARG* 1.3 75.7 - - - +
81V ASN* 1.3 57.9 + - - +
83V ASN* 4.0 1.0 - - - +
84V ARG* 3.0 40.7 + - - +
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Residues in contact with ASN 81 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7V ILE* 5.1 1.0 - - - +
69V ALA 4.5 0.6 + - - -
70V VAL* 4.2 12.4 - - + +
73V ARG* 3.7 19.8 - - - +
74V ASP 3.1 25.0 + - - +
75V PRO* 4.0 8.1 - - - +
77V GLU* 2.9 29.8 + - - +
78V PHE* 3.9 3.3 - - - +
80V ALA* 1.3 69.9 - - - +
82V TYR* 1.3 65.2 + - - +
84V ARG* 3.2 26.4 + - - +
85V MET* 2.9 29.4 + - - +
109V LEU* 4.2 20.8 - - + +
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Residues in contact with TYR 82 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78V PHE 2.9 23.0 + - - +
79V ARG* 3.6 2.9 - - - +
81V ASN* 1.3 72.9 - - - +
83V ASN* 1.3 71.9 + - - +
85V MET* 3.1 11.4 + - - +
86V TYR* 2.9 46.9 + + + +
99V LEU* 3.5 21.1 - - - +
102V ILE* 3.6 20.1 - - + +
106V ASP* 4.2 10.9 + - - +
264V ARG* 4.7 7.4 - - - -
287V GLY 3.2 29.2 - - - -
290V THR* 3.9 20.2 - - + -
291V GLU* 3.5 39.2 + - + +
294V ARG* 6.5 0.4 - - - -
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Residues in contact with ASN 83 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129N GLN* 2.8 33.6 + - - +
300N GLU* 6.1 0.2 - - - -
328N HIS* 3.9 19.2 + - + -
79V ARG* 2.9 25.2 + - - +
80V ALA 4.1 1.6 - - - +
82V TYR* 1.3 85.8 - - - +
84V ARG* 1.3 58.2 + - - +
86V TYR* 3.4 4.4 + - - +
87V ASP* 2.9 46.1 + - - +
264V ARG* 5.2 6.9 + - - -
294V ARG* 6.0 0.5 + - - -
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Residues in contact with ARG 84 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128N ALA 4.6 6.1 + - - -
129N GLN* 5.9 0.2 - - - +
68V GLU 5.4 0.2 - - - -
69V ALA* 2.9 39.2 + - + +
73V ARG* 3.6 44.1 - - - +
77V GLU* 4.8 4.8 + - - -
80V ALA* 3.0 34.4 + - - +
81V ASN* 3.2 25.6 - - - +
82V TYR 3.2 0.4 - - - -
83V ASN* 1.3 77.4 - - - +
85V MET* 1.3 61.7 + - - +
87V ASP* 4.8 3.1 - - - -
88V THR* 2.9 43.2 + - + +
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Residues in contact with MET 85 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66V ILE* 4.1 14.6 - - + +
69V ALA* 3.8 11.9 - - + -
70V VAL* 3.7 20.6 - - + -
81V ASN 2.9 22.6 + - - +
82V TYR* 3.7 12.6 - - - +
84V ARG* 1.3 76.0 - - - +
86V TYR* 1.3 62.1 + - - +
88V THR* 3.6 1.8 + - - -
89V THR* 2.8 30.2 + - - +
102V ILE* 4.0 37.4 - - + +
105V ILE* 3.6 50.0 - - + -
106V ASP* 4.1 10.1 - - + +
109V LEU* 4.4 7.2 - - + -
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Residues in contact with TYR 86 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239M ASP* 2.6 30.8 + - - -
82V TYR* 2.9 41.1 + + + +
83V ASN* 3.6 6.7 - - - +
85V MET* 1.3 79.9 - - - +
87V ASP* 1.3 76.1 + - - +
89V THR* 3.4 2.4 + - - -
90V LYS* 3.0 38.9 + - + -
94V MET* 3.2 30.8 + - - +
95V ARG* 3.1 20.8 + - - -
99V LEU* 4.3 3.4 - - + -
102V ILE* 3.8 19.0 - - + +
263V THR* 4.2 12.3 - - + -
264V ARG* 6.4 0.2 - - - -
265V PHE* 3.7 8.9 - + - -
291V GLU* 6.0 0.4 - - - -
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Residues in contact with ASP 87 (chain V).
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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61V LYS 4.3 0.2 - - - +
62V TRP* 3.8 14.6 - - + -
83V ASN* 2.9 34.0 + - - +
84V ARG* 4.2 3.2 - - + +
86V TYR* 1.3 81.9 - - - +
88V THR* 1.3 65.3 + - + +
89V THR 3.1 1.1 + - - -
90V LYS* 2.7 49.3 + - + +
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Residues in contact with THR 88 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61V LYS 4.1 5.2 - - - +
62V TRP 3.3 6.3 - - - -
64V ASN* 2.9 53.9 + - - +
65V ASN 5.1 2.1 + - - -
66V ILE 5.3 0.5 + - - -
69V ALA* 3.7 14.7 + - + +
84V ARG* 2.9 39.0 + - + +
85V MET* 3.6 4.2 + - - -
87V ASP* 1.3 76.9 - - + +
89V THR* 1.3 64.8 + - - +
90V LYS 3.7 0.2 - - - -
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Residues in contact with THR 89 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53V PHE* 5.1 5.9 - - + -
62V TRP 3.2 3.8 - - - -
64V ASN 3.4 24.5 - - - +
66V ILE* 4.0 27.7 - - + +
85V MET 2.8 22.5 + - - +
86V TYR* 3.3 4.7 + - - -
87V ASP 3.1 0.4 - - - -
88V THR* 1.3 82.3 - - - +
90V LYS* 1.3 64.3 + - - +
91V TRP 3.2 3.1 - - - -
92V ILE* 2.9 19.6 + - + +
93V GLY* 2.7 27.0 + - - -
94V MET 5.3 0.3 + - - -
98V GLY 5.6 0.7 + - - -
102V ILE* 4.3 10.2 - - - +
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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