Contacts of the helix formed by residues 63 - 78 (chain B) in PDB entry 4QOZ
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 ASP 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B PHE 3.0 3.0 + - - +
62B SER* 1.3 78.1 - - - +
64B PRO* 1.3 85.6 - - - +
65B VAL* 3.0 32.6 + - + +
66B TYR* 2.8 37.5 + - + +
67B LYS* 3.8 3.9 + - - +
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Residues in contact with PRO 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B SER 3.9 5.6 - - - +
63B ASP* 1.3 91.6 - - - +
65B VAL* 1.3 59.3 + - - +
67B LYS* 2.9 40.3 + - + +
68B GLU* 3.0 16.8 + - - +
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ASP* 3.0 31.9 + - + +
64B PRO* 1.3 78.3 - - - +
66B TYR* 1.3 62.2 + - + +
68B GLU* 3.2 28.4 - - - +
69B ILE* 3.0 25.5 + - + +
114B LYS* 3.7 33.4 - - + +
115B LEU* 4.0 22.2 - - + -
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A U 3.3 58.1 - + - +
61B PHE* 3.5 43.1 - + - +
63B ASP* 2.8 20.5 + - + +
65B VAL* 1.3 84.4 - - + +
67B LYS* 1.3 61.0 + - - +
69B ILE* 3.6 20.6 - - + +
70B ALA* 2.9 29.3 + - - +
111B LYS* 4.4 9.2 - - - -
115B LEU* 3.7 29.1 - - + +
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Residues in contact with LYS 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A U 5.0 5.8 + - - -
13A U 5.0 3.0 - - - +
14A U 3.4 30.4 + - - +
62B SER* 5.8 3.8 + - - +
63B ASP 3.8 2.9 + - - +
64B PRO* 2.9 28.6 + - + +
66B TYR* 1.3 73.9 - - - +
68B GLU* 1.3 66.9 + - - +
70B ALA* 3.4 1.9 + - - +
71B ILE* 3.1 34.2 + - + +
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Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B PRO 3.0 16.5 + - - +
65B VAL* 3.2 32.3 - - - +
67B LYS* 1.3 77.6 - - - +
69B ILE* 1.3 56.4 + - - +
71B ILE* 3.4 7.9 + - - +
72B THR* 3.0 33.5 + - - -
114B LYS* 4.1 21.8 - - + +
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Residues in contact with ILE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A U 3.5 15.5 - - + +
65B VAL 3.0 17.1 + - - +
66B TYR* 3.6 23.3 - - + +
67B LYS 3.2 0.4 - - - -
68B GLU* 1.3 74.6 - - - +
70B ALA* 1.3 60.3 + - - +
72B THR* 3.2 6.7 + - - -
73B ASN* 2.8 52.8 + - - +
110B TYR* 5.4 0.7 - - + -
111B LYS* 4.0 39.5 - - + +
114B LYS* 4.1 22.7 - - + +
115B LEU* 4.1 20.0 - - + -
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A U 3.5 28.7 + - - +
14A U 3.8 14.4 - - - +
15A C 3.0 10.0 + - + +
16A A 3.3 29.9 - - - +
66B TYR 2.9 12.6 + - - +
67B LYS 3.8 4.0 - - - +
69B ILE* 1.3 74.5 - - - +
71B ILE* 1.3 64.5 + - + +
73B ASN* 3.4 0.6 + - - +
74B GLY 3.0 17.3 + - - -
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A U 5.9 0.7 - - - +
15A C 3.8 46.2 + - + +
67B LYS* 3.1 19.6 + - + +
68B GLU* 3.7 9.2 - - - +
70B ALA* 1.3 79.4 - - + +
72B THR* 1.3 65.3 + - - +
74B GLY* 3.0 11.3 + - - -
75B CYS* 3.0 21.6 + - - -
78B ARG* 5.1 1.6 + - - -
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B GLU 3.0 10.2 + - - -
69B ILE* 3.7 4.7 - - - -
71B ILE* 1.3 73.7 - - - +
73B ASN* 1.3 61.1 + - - +
75B CYS* 3.0 13.1 + - + +
76B ILE* 2.9 37.7 + - + +
110B TYR* 4.0 31.6 - - + -
114B LYS* 2.5 33.8 + - - +
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Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A U 3.5 11.5 + - - +
16A A 3.3 39.0 + - - +
17A G 3.8 11.4 - - - +
69B ILE* 2.8 32.3 + - - +
70B ALA 3.4 6.3 - - - +
72B THR* 1.3 72.1 - - - +
74B GLY* 1.3 58.3 + - - +
76B ILE* 3.1 6.2 + - - +
77B ASN* 2.9 33.1 + - - +
107B LYS* 3.4 37.5 - - + +
110B TYR* 6.0 1.0 - - - +
111B LYS* 6.0 0.2 - - - +
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Residues in contact with GLY 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A C 3.1 25.6 - - - -
16A A 3.5 11.9 + - - -
70B ALA 3.0 10.5 + - - -
71B ILE 3.0 2.4 + - - -
73B ASN* 1.3 78.9 - - - +
75B CYS* 1.3 60.6 + - - +
77B ASN* 3.4 13.3 + - - +
78B ARG* 3.4 25.1 + - - +
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Residues in contact with CYS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ILE* 3.0 24.4 + - - -
72B THR* 3.0 14.8 + - + +
74B GLY* 1.3 74.8 - - - +
76B ILE* 1.3 65.8 + - + +
78B ARG* 3.0 33.7 + - - +
79B MET* 3.5 15.8 + - + +
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B THR* 2.9 25.3 + - + +
73B ASN* 3.1 7.2 + - - +
75B CYS* 1.3 76.9 - - + +
77B ASN* 1.3 59.6 + - - +
78B ARG 3.1 1.2 + - - -
79B MET* 3.2 20.0 + - - +
84B LEU* 4.0 19.2 - - + +
103B LYS* 2.9 32.3 + - + +
106B LEU* 3.9 14.1 - - + -
107B LYS* 3.6 45.5 - - + +
110B TYR* 3.7 31.4 - - + -
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Residues in contact with ASN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A A 3.0 38.4 + - - +
17A G 4.6 4.8 + - - -
73B ASN 2.9 16.1 + - - -
74B GLY 3.5 9.4 - - - +
75B CYS 3.2 0.2 - - - -
76B ILE* 1.3 76.6 - - - +
78B ARG* 1.3 60.0 + - + +
79B MET 4.6 0.2 - - - +
99B LYS* 5.7 0.2 - - - -
103B LYS* 3.2 26.7 + - - +
107B LYS* 2.8 30.3 + - - +
188C LYS* 5.2 4.8 - - - +
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A C 2.5 38.5 + - - -
16A A 5.8 1.9 + - - +
71B ILE 5.1 0.4 + - - -
74B GLY* 3.4 23.8 + - - +
75B CYS* 3.0 35.6 + - - +
77B ASN* 1.3 80.9 - - + +
79B MET* 1.3 62.6 + - - +
80B SER 4.0 0.3 + - - -
83B GLU* 4.7 2.1 - - - +
192C VAL* 4.4 19.1 - - + +
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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