Contacts of the helix formed by residues 61 - 79 (chain A) in PDB entry 2QMR
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 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLU* 1.3 101.0 - - - +
62A GLU* 1.3 58.3 + - - +
63A PRO* 3.3 23.4 - - - +
64A THR* 2.5 48.4 + - - +
65A ARG* 3.4 3.4 + - - -
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Residues in contact with GLU 62 (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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60A GLU* 3.9 6.0 - - + +
61A ASP* 1.3 72.8 - - - +
63A PRO* 1.4 64.3 - - + +
64A THR 3.1 0.2 + - - -
65A ARG* 3.1 15.1 + - - +
66A SER* 2.8 33.6 + - - -
103A SER* 3.3 32.1 + - - +
104A PRO* 5.7 0.9 - - - +
105A LEU* 4.4 18.5 - - + +
106A ILE* 3.8 17.8 - - + +
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Residues in contact with PRO 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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61A ASP* 3.3 27.6 - - - +
62A GLU* 1.4 92.4 - - + +
64A THR* 1.3 54.1 + - - +
66A SER* 3.9 2.6 + - - +
67A LEU* 3.1 30.2 + - - +
105A LEU* 4.4 12.5 - - + -
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Residues in contact with THR 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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15A ILE* 5.0 6.5 - - + +
18A LEU* 4.4 23.8 + - + +
19A LEU* 4.9 14.0 - - + +
51A ILE* 4.8 10.1 - - + -
59A SER* 5.1 6.5 - - - +
60A GLU 4.2 7.0 - - - +
61A ASP* 2.5 31.7 + - - +
63A PRO* 1.3 76.1 - - - +
65A ARG* 1.3 67.0 + - - +
67A LEU* 3.2 9.3 + - - +
68A SER* 3.0 21.1 + - - -
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Residues in contact with ARG 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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51A ILE* 3.3 21.9 + - + +
52A PHE* 3.1 47.4 + - + +
53A VAL* 4.5 9.9 + - - +
55A THR 3.7 12.9 + - - -
56A LYS* 4.0 29.2 + - - +
59A SER 3.9 16.8 - - - +
60A GLU* 4.4 10.9 - - - +
61A ASP 3.4 4.7 + - - +
62A GLU* 3.1 14.1 + - - +
64A THR* 1.3 78.5 - - - +
66A SER* 1.3 64.3 + - - +
68A SER* 3.1 19.2 + - - -
69A GLY 3.2 0.3 + - - -
101A ASP* 5.0 4.9 + - - -
106A ILE* 3.4 40.2 - - + +
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Residues in contact with SER 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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52A PHE* 4.2 4.9 - - - -
62A GLU 2.8 19.3 + - - -
63A PRO* 3.9 4.3 + - - +
65A ARG* 1.3 73.2 - - - +
67A LEU* 1.3 57.9 + - - +
69A GLY 3.5 0.2 + - - -
70A LEU* 3.0 43.4 + - - +
105A LEU* 3.8 29.1 - - - +
106A ILE* 5.1 3.3 - - - +
109A THR* 3.3 28.0 + - - +
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Residues in contact with LEU 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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18A LEU* 4.1 21.3 - - + +
21A GLU* 4.4 14.8 - - + +
22A SER* 4.2 19.5 - - - +
63A PRO 3.1 20.6 + - - +
64A THR* 3.6 7.0 - - - +
65A ARG 3.2 0.2 - - - -
66A SER* 1.3 75.4 + - - +
68A SER* 1.3 59.2 + - - +
70A LEU* 4.1 12.6 - - + -
71A ILE* 2.8 53.4 + - + +
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Residues in contact with SER 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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18A LEU* 5.7 6.7 - - - +
48A ASN* 2.7 46.4 + - - +
51A ILE* 3.5 33.0 - - - +
52A PHE* 3.8 0.8 - - - +
64A THR 3.0 9.0 + - - -
65A ARG 3.1 11.0 - - - -
67A LEU* 1.3 77.8 - - - +
69A GLY* 1.3 61.1 + - - +
71A ILE* 3.4 6.4 + - - +
72A LEU* 3.2 21.0 + - - +
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Residues in contact with GLY 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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52A PHE* 4.0 18.8 - - - +
65A ARG 3.2 7.5 + - - -
66A SER 3.8 3.1 - - - -
68A SER* 1.3 79.1 + - - +
70A LEU* 1.3 57.5 + - - +
72A LEU* 3.6 15.6 + - - +
73A LYS* 3.0 21.3 + - - +
109A THR* 4.0 11.2 - - - +
113A LEU* 3.5 15.2 - - - +
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Residues in contact with LEU 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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66A SER* 3.0 36.6 + - - +
67A LEU* 3.1 13.7 + - + +
69A GLY* 1.3 75.6 - - - +
71A ILE* 1.3 64.9 + - - +
72A LEU 3.2 1.1 - - - -
73A LYS* 3.3 38.8 + - + +
74A ASN* 3.0 18.7 + - - +
105A LEU* 5.7 2.9 - - + -
109A THR* 3.8 13.0 - - + +
112A ILE* 4.2 20.2 - - + -
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Residues in contact with ILE 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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18A LEU* 5.7 7.4 - - + -
21A GLU* 4.8 13.2 - - + -
36A LYS* 5.3 17.9 - - + +
48A ASN* 5.2 6.7 - - - +
67A LEU* 2.8 51.4 + - + +
68A SER* 4.0 5.6 - - - +
70A LEU* 1.3 72.8 - - - +
72A LEU* 1.3 56.6 + - - +
74A ASN* 3.1 24.3 + - + +
75A ASN* 2.9 29.4 + - - +
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Residues in contact with LEU 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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45A ASP* 4.2 24.7 - - + +
48A ASN* 3.5 30.9 - - + +
49A TYR* 3.0 55.0 - - + +
68A SER 3.2 12.3 + - - +
69A GLY* 3.7 16.4 - - - +
70A LEU 3.2 0.2 - - - -
71A ILE* 1.3 76.0 - - - +
73A LYS* 1.3 63.0 + - - +
75A ASN* 3.2 8.3 + - - +
76A VAL* 3.0 37.6 + - + +
83A PHE* 4.7 0.2 - - + -
91A ILE* 4.2 4.0 - - + -
113A LEU* 3.9 5.2 - - + -
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Residues in contact with LYS 73 (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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69A GLY 3.0 15.3 + - - +
70A LEU* 3.3 33.4 - - + +
71A ILE 3.3 0.2 - - - -
72A LEU* 1.3 76.0 - - - +
74A ASN* 1.3 68.5 + - - +
76A VAL* 3.3 8.9 + - - +
77A LYS* 3.0 50.9 + - - +
112A ILE* 4.0 32.8 - - + +
113A LEU* 3.7 17.5 - - + -
116A THR* 4.0 20.7 - - - +
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Residues in contact with ASN 74 (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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70A LEU 3.0 21.3 + - - -
71A ILE* 3.1 16.3 + - + +
73A LYS* 1.3 96.9 + - - +
75A ASN* 1.3 60.7 + - - +
77A LYS* 3.1 14.9 + - + +
78A ALA* 3.0 31.0 + - - +
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Residues in contact with ASN 75 (chain A).
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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36A LYS 5.5 2.6 + - - -
37A LEU* 6.0 1.2 - - - -
40A LEU* 3.5 35.4 - - + +
44A PRO* 5.4 1.2 - - - +
45A ASP* 3.7 27.1 + - - +
48A ASN* 4.7 4.6 - - - +
71A ILE* 2.9 24.2 + - - +
72A LEU* 3.3 13.9 - - - +
74A ASN* 1.3 78.4 - - - +
76A VAL* 1.3 57.9 + - - +
79A HIS* 3.0 43.2 + - - +
83A PHE* 4.3 3.4 - - + -
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Residues in contact with VAL 76 (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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49A TYR* 5.4 0.2 - - - +
72A LEU* 3.0 29.7 + - + +
73A LYS* 3.4 11.9 - - - +
74A ASN 3.2 0.2 - - - -
75A ASN* 1.3 77.4 - - - +
77A LYS* 1.3 61.4 + - - +
80A PHE* 3.1 45.3 - - + +
83A PHE* 4.2 18.4 - - + -
91A ILE* 5.5 2.0 - - + -
113A LEU* 4.9 3.1 - - + -
116A THR* 4.6 8.7 - - + -
117A ILE* 3.9 40.2 - - + +
120A LYS* 3.6 8.7 - - + +
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Residues in contact with LYS 77 (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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73A LYS* 3.0 43.7 + - - +
74A ASN* 3.1 18.6 + - + +
76A VAL* 1.3 78.4 - - - +
78A ALA* 1.3 61.1 + - + +
80A PHE 5.2 0.2 + - - -
116A THR* 3.7 19.7 - - + -
120A LYS* 3.3 33.9 + - - +
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Residues in contact with ALA 78 (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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74A ASN 3.0 13.9 + - - +
77A LYS* 1.3 80.2 - - + +
79A HIS* 1.3 85.3 + - + +
80A PHE 3.8 1.7 + - - -
81A GLN* 5.9 0.9 + - - -
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Residues in contact with HIS 79 (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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37A LEU* 4.9 3.6 + - - +
40A LEU* 3.5 44.6 - - + +
75A ASN* 3.0 21.7 + - - +
78A ALA* 1.3 96.1 + - + +
80A PHE* 1.3 59.1 + - - +
81A GLN 3.7 1.3 - - - +
82A ASN* 4.4 26.7 + - + +
83A PHE* 3.0 20.3 + - - -
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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