Contacts of the helix formed by residues 76 - 89 (chain W) in PDB entry 5A0Q
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 VAL 76 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41W ILE* 3.7 7.6 - - + -
75W ARG* 1.3 75.0 - - - +
77W VAL* 1.3 58.5 + - - +
79W ALA* 3.1 5.9 + - - +
80W ASN* 3.0 37.4 + - - +
100W LEU* 3.4 24.2 - - + -
102W GLY* 3.4 43.1 - - - +
103W VAL* 3.7 4.9 - - - +
104W ASP* 3.8 15.9 - - + +
109W HIS* 3.3 36.1 + - + +
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Residues in contact with VAL 77 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105O TYR 3.6 3.0 - - - +
106O GLY* 4.3 20.2 - - - +
107O TYR* 4.9 6.7 - - + -
75W ARG* 4.3 13.0 - - + -
76W VAL* 1.3 76.7 - - - +
78W THR* 1.3 63.3 + - - +
79W ALA 3.3 0.2 - - - -
80W ASN* 3.4 10.7 + - - +
81W ARG* 2.8 33.4 + - - +
106W THR* 5.6 1.1 - - - +
109W HIS* 4.0 22.4 - - + +
111W TYR* 3.6 20.4 - - - +
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Residues in contact with THR 78 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104O LYS 4.3 0.9 - - - +
105O TYR* 3.1 31.8 + - + +
107O TYR* 3.4 27.0 - - - -
63W LEU* 5.6 1.1 - - + -
66W HIS* 3.8 15.9 - - + +
74W PRO* 5.3 4.3 - - + -
75W ARG* 3.4 24.5 + - - +
77W VAL* 1.3 73.2 - - - +
79W ALA* 1.3 64.0 + - - +
81W ARG* 3.3 1.6 + - - +
82W MET* 3.1 47.4 + - + +
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Residues in contact with ALA 79 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41W ILE* 4.1 9.6 - - + -
59W ILE* 4.6 0.9 - - - +
63W LEU* 3.4 34.3 - - + +
75W ARG 3.6 0.8 + - - +
76W VAL 3.1 10.5 + - - +
78W THR* 1.3 79.2 - - - +
80W ASN* 1.3 58.1 + - - +
82W MET* 3.4 7.6 - - - +
83W LEU* 3.1 31.9 + - - +
100W LEU* 3.6 25.6 - - + -
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Residues in contact with ASN 80 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76W VAL* 3.0 24.5 + - - +
77W VAL* 3.5 8.1 - - - +
79W ALA* 1.3 76.4 - - - +
81W ARG* 1.3 54.1 + - - +
83W LEU* 3.2 6.3 + - - +
84W LYS* 2.7 35.6 + - - +
100W LEU* 3.8 16.7 - - - +
111W TYR* 2.5 65.3 - - + +
113W ILE* 3.6 13.4 - - - +
119W THR* 3.7 12.8 - - + +
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Residues in contact with ARG 81 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102O LYS* 2.2 26.5 + - - +
103O TYR* 1.8 78.5 + - - +
104O LYS* 3.5 20.0 - - - +
105O TYR 3.3 20.9 - - - +
106O GLY* 3.6 12.1 - - - -
57V ASP* 5.2 14.7 + - - +
77W VAL 2.8 12.8 + - - +
78W THR 3.3 1.5 + - - +
80W ASN* 1.3 69.5 - - - +
82W MET* 1.3 63.1 + - - +
84W LYS* 3.4 23.1 + - - +
85W GLN* 3.2 31.4 + - - +
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Residues in contact with MET 82 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104O LYS* 4.0 7.2 + - + +
105O TYR* 4.2 16.6 - - + -
59W ILE* 3.8 16.6 - - + +
62W ASN* 4.0 19.1 - - + +
63W LEU* 2.8 38.4 - - + -
66W HIS* 5.0 2.5 - - + +
78W THR* 3.1 43.4 + - + +
79W ALA 3.4 10.5 - - - +
81W ARG* 1.3 77.3 - - - +
83W LEU* 1.4 59.8 + - - +
85W GLN* 3.7 11.1 + - - +
86W MET* 2.9 32.7 + - + +
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Residues in contact with LEU 83 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37W ILE* 4.6 4.9 - - + -
43W CYS* 4.5 4.5 - - - -
55W THR* 4.3 7.2 - - + -
56W THR* 6.3 0.2 - - - -
59W ILE* 3.7 26.5 - - + -
79W ALA 3.1 17.3 + - - +
80W ASN 3.2 6.2 + - - +
82W MET* 1.4 74.3 - - - +
84W LYS* 1.3 62.8 + - - +
86W MET* 4.2 1.6 - - + -
87W LEU* 3.1 36.4 + - + +
98W LEU* 3.5 32.5 - - + -
100W LEU* 3.4 34.1 - - + -
113W ILE* 3.5 27.1 - - + -
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Residues in contact with LYS 84 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53V GLN* 3.2 56.7 - - + +
54V ALA* 6.2 0.2 - - - -
57V ASP* 4.5 13.2 + - + +
80W ASN 2.7 18.0 + - - +
81W ARG* 3.5 26.0 - - - +
82W MET 3.3 0.4 - - - -
83W LEU* 1.3 70.7 - - - +
85W GLN* 1.4 62.5 + - + +
87W LEU 3.9 1.0 - - - -
88W PHE* 3.1 30.2 + - + +
113W ILE* 4.9 0.7 - - - -
117W GLY* 3.9 15.3 - - - +
119W THR* 3.2 34.7 + - + +
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Residues in contact with GLN 85 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103O TYR* 2.9 59.0 + - - +
104O LYS* 4.0 19.4 - - - +
81W ARG* 3.2 24.8 + - - +
82W MET* 3.9 8.5 - - - +
84W LYS* 1.4 79.8 - - + +
86W MET* 1.3 64.2 + - + +
88W PHE* 3.6 6.4 - - - +
89W ARG* 3.0 31.6 + - - +
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Residues in contact with MET 86 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55W THR* 4.0 26.0 - - + +
58W LEU* 3.6 31.0 - - + -
59W ILE* 4.1 19.1 - - + -
62W ASN* 4.7 6.1 - - - +
82W MET* 2.9 22.6 + - + +
83W LEU* 3.9 6.7 - - + +
84W LYS 3.4 0.2 - - - -
85W GLN* 1.3 77.4 - - - +
87W LEU* 1.4 60.0 + - + +
88W PHE 3.7 0.2 + - - -
89W ARG* 3.8 22.6 + - - +
90W TYR* 3.1 54.6 - - + -
94W ILE* 6.0 0.2 - - + -
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Residues in contact with LEU 87 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55W THR* 4.3 17.3 - - + -
83W LEU* 3.1 26.4 + - + +
84W LYS 3.9 2.5 - - - +
86W MET* 1.4 74.2 - - + +
88W PHE* 1.3 61.7 + - - +
89W ARG 3.6 0.2 - - - -
90W TYR* 4.7 3.3 + - - +
91W GLN* 4.5 5.9 + - - -
92W GLY 4.8 0.3 + - - -
94W ILE* 3.4 34.0 - - + +
96W ALA 3.9 11.2 - - - +
98W LEU* 4.4 10.5 - - + -
113W ILE* 3.5 37.2 - - + +
114W TYR 3.9 8.1 - - - +
115W PRO* 2.9 32.6 - - + +
116W HIS* 3.6 6.3 - - - -
117W GLY* 4.2 4.9 - - - -
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Residues in contact with PHE 88 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50V ALA* 3.3 29.2 - - + -
51V ASP* 3.6 23.3 - - - -
53V GLN* 5.9 0.9 - - + -
54V ALA* 3.4 30.3 - - + +
93V ASP 5.4 1.8 - - - -
94V LEU* 6.3 0.7 - - + -
84W LYS* 3.1 19.4 + - + +
85W GLN* 3.2 8.5 + - - +
87W LEU* 1.3 78.4 - - - +
89W ARG* 1.3 72.4 + - + +
90W TYR 3.2 0.7 - - - -
91W GLN* 3.0 42.6 + - + +
116W HIS 3.6 14.4 - - - +
117W GLY* 4.9 1.6 - - - +
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Residues in contact with ARG 89 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58W LEU* 5.9 0.4 - - - +
85W GLN* 3.0 14.1 + - - +
86W MET* 3.8 37.8 + - - +
87W LEU 3.6 0.6 - - - -
88W PHE* 1.3 86.5 - - + +
90W TYR* 1.3 93.3 + - + +
91W GLN* 3.4 9.9 + - - +
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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