Contacts of the helix formed by residues 62 - 72 (chain A) in PDB entry 4RQO
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 GLY 62 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A PRO* 5.5 0.9 - - - -
20A THR* 4.5 2.5 - - - +
58A GLY 2.8 5.0 + - - -
59A LYS 2.9 11.2 + - - -
60A GLY 3.3 1.2 + - - -
61A HIS* 1.3 79.9 - - - +
63A THR* 1.3 59.1 + - - +
64A ASP* 3.2 11.9 - - - -
65A LYS* 3.3 21.3 + - - +
66A ALA* 2.9 29.0 + - - +
84A MSE 5.0 0.3 - - - +
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS* 2.6 34.0 + - - +
23A PRO* 3.9 11.4 - - + -
50A LEU* 3.8 21.3 - - + -
54A LEU* 3.9 6.1 - - + +
58A GLY* 2.7 37.2 + - - -
61A HIS 3.2 1.2 - - - -
62A GLY* 1.3 72.3 - - - +
64A ASP* 1.3 56.0 + - - +
66A ALA* 3.6 2.9 - - - +
67A ILE* 2.9 48.3 + - + +
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Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 5.2 0.2 - - - +
58A GLY 4.3 0.8 + - - -
59A LYS* 3.8 31.9 - - - +
62A GLY* 3.6 14.3 - - - -
63A THR* 1.3 76.4 - - - +
65A LYS* 1.3 83.8 + - - +
67A ILE* 3.1 2.4 + - - +
68A LEU* 3.0 33.4 + - + +
88A MSE 4.0 18.3 - - - +
92A LEU* 6.1 0.3 - - - +
113A PHE* 3.6 32.2 - - + -
115A PHE* 4.4 12.8 - - + -
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PRO* 6.6 0.4 - - - -
20A THR* 6.6 0.2 - - - -
62A GLY* 3.4 19.3 - - - +
64A ASP* 1.3 86.3 + - - +
66A ALA* 1.3 63.5 + - - +
68A LEU* 3.9 1.1 - - - +
69A ASN* 3.0 31.0 + - - +
84A MSE 3.4 45.7 - - + +
85A ILE* 3.3 43.5 - - + +
88A MSE 3.9 24.2 - - + -
281A ALA 5.6 3.4 + - - -
282A GLY* 5.9 4.0 - - - -
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS 5.1 0.2 - - - +
20A THR* 3.5 38.6 - - + +
23A PRO* 5.3 0.2 - - + -
24A MSE 3.4 22.7 - - + +
62A GLY 2.9 17.9 + - - +
63A THR* 3.6 5.4 - - - +
65A LYS* 1.3 78.2 - - - +
67A ILE* 1.3 63.2 + - + +
69A ASN 3.6 0.5 + - - -
70A GLY 3.0 17.7 + - - -
84A MSE 3.9 12.3 - - + +
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Residues in contact with ILE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PRO* 3.8 26.9 - - + +
27A ALA* 3.8 5.0 - - + +
48A VAL* 3.8 25.1 - - + -
50A LEU* 3.5 32.3 - - + -
63A THR* 2.9 29.8 + - + +
64A ASP 3.1 2.4 + - - +
66A ALA* 1.3 72.4 - - - +
68A LEU* 1.3 52.0 + - - +
70A GLY* 3.1 1.6 + - - -
71A LEU* 2.7 38.6 + - + +
113A PHE* 4.0 11.4 - - + -
128A MSE 4.4 7.9 - - - -
130A PHE* 3.8 25.1 - - + -
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ASP* 3.0 24.2 + - + +
65A LYS* 4.0 3.4 - - - +
67A ILE* 1.3 77.1 - - - +
69A ASN* 1.3 63.1 + - - +
71A LEU* 3.4 14.4 + - + +
72A GLU* 3.3 24.9 + - - +
88A MSE 4.2 21.1 - - + -
91A ILE* 4.0 23.0 - - + +
92A LEU* 3.9 28.5 - - + -
97A LEU* 4.1 8.3 - - + +
107A PHE* 3.7 31.9 - - + -
113A PHE* 4.1 17.0 - - + -
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Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A MSE 4.1 9.4 - - + -
65A LYS* 3.0 30.3 + - - +
68A LEU* 1.3 77.2 - - - +
70A GLY* 1.3 57.4 + - - +
72A GLU* 3.1 13.8 + - - +
74A LYS* 2.8 51.0 + - + +
79A VAL* 5.4 1.1 - - - -
83A SER* 4.4 4.3 + - - +
84A MSE 3.3 42.4 + - - +
87A ARG* 3.2 30.9 - - - +
88A MSE 4.6 4.9 - - - +
91A ILE* 5.8 0.2 - - - -
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A MSE 4.0 7.8 - - - +
27A ALA* 3.6 11.4 - - - -
28A ASN* 3.0 24.1 + - - -
31A LEU* 3.4 7.6 - - - +
66A ALA 3.0 15.1 + - - -
67A ILE 3.1 4.2 + - - -
69A ASN* 1.3 74.0 - - - +
71A LEU* 1.3 60.3 + - - +
72A GLU 3.2 0.7 - - - -
73A ASN 3.1 9.0 + - - -
74A LYS 3.4 15.3 - - - -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 3.7 20.2 - - + +
30A PHE* 4.7 3.4 - - + -
31A LEU* 3.3 25.0 - - + +
46A VAL* 3.9 26.9 - - + -
48A VAL* 4.1 19.1 - - + -
67A ILE* 2.7 26.8 + - + +
68A LEU* 3.7 13.7 - - + +
69A ASN 3.4 0.2 - - - -
70A GLY* 1.3 71.5 - - - +
72A GLU* 1.3 58.0 + - - +
73A ASN 3.2 0.7 - - - -
97A LEU* 4.1 23.1 - - + -
99A LEU* 3.6 9.7 - - + +
100A ALA 2.7 21.1 + - - -
107A PHE* 5.2 1.3 - - + -
130A PHE* 3.9 14.1 - - + -
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU 3.3 14.5 + - - +
69A ASN* 3.1 11.5 + - - +
71A LEU* 1.3 77.6 - - - +
73A ASN* 1.3 67.6 + - - +
74A LYS* 3.2 17.9 + - + +
87A ARG* 2.7 52.3 + - - +
91A ILE* 3.2 15.5 - - - +
97A LEU* 3.7 5.1 - - + +
98A ASN* 3.1 38.3 + - + +
101A GLY* 3.5 16.1 + - - +
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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