Contacts of the helix formed by residues 64 - 83 (chain A) in PDB entry 4QYD
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 ASN 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.5 16.0 - - - -
62A TYR 3.4 2.4 + - - -
63A LEU* 1.3 88.2 + - - +
65A PHE* 1.3 61.7 + - - +
66A ASP* 3.1 15.7 + - - +
67A ASP* 2.9 58.5 + - - +
68A PHE* 3.7 9.9 + - - +
116A ILE* 5.3 6.7 - - + -
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Residues in contact with PHE 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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8A PHE* 3.6 7.7 - + + -
11A LEU* 5.0 2.0 - - + -
12A LEU* 3.9 27.4 - - + -
15A THR* 4.9 1.3 - - - -
64A ASN* 1.3 74.1 - - - +
66A ASP* 1.3 67.5 + - - +
68A PHE* 3.3 9.3 + + - +
69A GLU* 3.0 50.3 + - + +
104A LEU* 3.8 17.0 - - + -
107A ALA* 3.6 35.7 - - + -
108A ARG* 3.6 35.2 - - + +
111A ALA* 4.1 24.5 - - + -
116A ILE* 4.4 16.5 - - + +
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Residues in contact with ASP 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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64A ASN* 3.1 12.8 + - - +
65A PHE* 1.3 79.3 + - - +
67A ASP* 1.3 61.0 + - - +
69A GLU* 3.3 5.0 + - - +
70A GLU* 2.9 30.4 + - - +
108A ARG* 3.0 32.8 + - - +
116A ILE* 6.0 1.7 - - - +
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Residues in contact with ASP 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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61A ARG 4.6 9.1 - - - +
62A TYR* 3.6 25.1 - - + -
63A LEU 5.1 1.0 + - - -
64A ASN* 2.9 37.7 + - - +
66A ASP* 1.3 79.0 - - - +
68A PHE* 1.3 62.9 + - - +
70A GLU* 3.4 17.3 + - - +
71A ASP* 3.3 18.7 + - - +
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Residues in contact with PHE 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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12A LEU* 3.8 51.1 - - + -
15A THR* 3.6 28.7 - - + -
16A LEU* 4.0 17.3 - - + -
19A LEU* 4.1 10.8 - - + -
53A MET* 3.5 28.9 - - + +
57A LEU* 4.7 4.0 - - + -
62A TYR* 3.7 31.4 - + + -
64A ASN 3.7 9.2 + - - +
65A PHE* 3.3 17.5 + + - +
66A ASP 3.3 0.2 - - - -
67A ASP* 1.3 76.4 - - - +
69A GLU* 1.3 66.1 + - - +
71A ASP 3.3 2.6 + - - -
72A PHE* 3.2 18.0 + - + +
104A LEU* 3.9 13.2 - - + -
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Residues in contact with GLU 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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65A PHE* 3.0 39.6 + - + +
66A ASP* 3.6 8.5 - - - +
68A PHE* 1.3 78.5 - - - +
70A GLU* 1.3 58.3 + - - +
72A PHE* 3.3 2.2 + - - +
73A ASN* 2.9 45.2 + - - +
104A LEU* 3.8 34.0 - - + +
108A ARG* 2.8 33.9 + - - -
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Residues in contact with GLU 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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46A LYS* 4.5 9.7 + - - -
66A ASP 2.9 17.0 + - - +
67A ASP* 3.7 17.2 - - - +
68A PHE 3.2 0.4 - - - -
69A GLU* 1.3 77.5 - - - +
71A ASP* 1.3 67.1 + - - +
73A ASN* 3.5 7.7 + - - +
74A LEU* 3.1 34.9 + - + +
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Residues in contact with ASP 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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46A LYS* 3.6 21.6 + - - -
48A MET* 3.3 34.7 - - + +
53A MET* 3.9 6.7 - - + -
56A ASN* 3.6 10.6 + - - -
62A TYR* 2.5 40.2 + - - +
67A ASP 3.3 5.0 + - - +
68A PHE 3.3 7.8 + - - +
69A GLU 3.2 0.2 - - - -
70A GLU* 1.3 82.2 - - - +
72A PHE* 1.3 65.0 + - - +
74A LEU* 3.2 16.6 + - - +
75A ILE* 3.2 9.4 + - - +
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Residues in contact with PHE 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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19A LEU* 3.8 30.1 - - + -
50A PHE* 3.9 19.5 - + - -
53A MET* 3.7 15.9 - - + -
68A PHE* 3.2 13.6 + - + +
69A GLU* 3.3 5.8 + - - +
71A ASP* 1.3 75.0 - - - +
73A ASN* 1.3 73.8 + - - +
75A ILE* 3.0 22.2 + - + +
76A VAL* 3.4 19.7 + - + +
96A LEU* 3.7 46.4 - - + -
97A ARG* 5.2 2.2 - - - -
100A GLY* 4.0 16.8 - - - -
101A GLY* 4.7 1.6 - - - -
104A LEU* 3.4 30.7 - - + -
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Residues in contact with ASN 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 GLU* 2.9 33.9 + - - +
70A GLU* 3.8 6.8 - - - +
72A PHE* 1.3 92.3 - - - +
74A LEU* 1.3 57.0 + - - +
76A VAL* 3.4 6.1 + - - +
77A SER* 2.8 33.8 + - - -
97A ARG* 5.2 1.6 + - - +
104A LEU* 4.4 6.3 - - - +
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Residues in contact with LEU 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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46A LYS* 3.6 46.4 - - + +
48A MET* 3.9 10.8 - - + -
70A GLU* 3.1 22.9 + - + +
71A ASP* 3.4 25.8 - - - +
72A PHE 3.2 0.2 - - - -
73A ASN* 1.3 72.9 - - - +
75A ILE* 1.3 66.7 + - - +
77A SER* 3.5 9.0 - - - +
78A ASN* 2.8 49.1 + - - +
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Residues in contact with ILE 75 (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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28A PHE* 3.4 39.1 - - + -
48A MET* 3.7 29.2 - - + +
49A ASP* 3.6 24.7 - - - +
50A PHE* 3.8 20.4 - - + +
53A MET* 3.8 22.4 - - - -
71A ASP 3.6 8.7 - - - +
72A PHE* 3.0 10.8 + - + +
74A LEU* 1.3 79.3 - - - +
76A VAL* 1.3 62.8 + - + +
78A ASN* 4.2 2.6 - - - +
79A CYS* 3.5 20.1 + - - +
96A LEU* 4.5 7.9 - - + -
12B ALY 5.7 0.3 - - - +
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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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28A PHE* 5.3 0.7 - - - -
72A PHE* 3.4 37.2 + - + +
73A ASN* 3.4 8.9 + - - +
74A LEU 3.2 0.2 - - - -
75A ILE* 1.3 75.6 - - - +
77A SER* 1.3 65.4 + - - +
79A CYS* 3.2 4.2 + - - +
80A LEU* 3.1 26.7 + - + +
93A ALA* 3.6 24.8 - - + +
96A LEU* 4.0 21.5 - - + -
97A ARG* 3.7 38.8 - - + +
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Residues in contact with SER 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 ASN* 2.8 23.2 + - - -
74A LEU* 3.5 17.2 - - - +
76A VAL* 1.3 71.0 - - - +
78A ASN* 1.3 68.8 + - - +
80A LEU* 3.4 5.4 + - - +
81A LYS* 2.9 25.4 + - - +
97A ARG* 4.2 17.7 - - - +
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Residues in contact with ASN 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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40A TYR* 3.5 16.3 + - - +
44A ILE* 3.5 28.5 - - + +
45A LYS 5.3 0.5 + - - -
46A LYS 2.8 27.4 + - - +
47A PRO* 3.5 14.8 - - - +
48A MET 3.7 9.0 + - - +
74A LEU* 2.8 38.0 + - - +
75A ILE* 4.2 3.1 - - - +
77A SER* 1.3 79.9 + - - +
79A CYS* 1.3 58.5 + - - +
81A LYS* 4.5 3.0 - - - +
82A TYR* 2.9 33.1 + - - +
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Residues in contact with CYS 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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28A PHE* 3.6 23.1 - - + -
40A TYR* 5.2 0.2 - - - -
75A ILE 3.5 16.4 + - - +
76A VAL 3.2 5.1 + - - +
77A SER 3.2 0.6 - - - -
78A ASN* 1.3 79.0 - - - +
80A LEU* 1.3 64.6 + - - +
83A ASN* 3.0 51.5 + - - +
89A PHE* 3.2 33.9 - - - -
90A TYR* 4.8 1.0 - - - -
93A ALA* 3.8 5.2 - - + -
12B ALY 3.7 13.9 - - + +
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Residues in contact with LEU 80 (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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76A VAL* 3.1 23.4 + - + +
77A SER* 3.9 4.5 - - - +
79A CYS* 1.3 78.0 - - - +
81A LYS* 1.3 57.8 + - - +
83A ASN 3.5 1.7 - - - +
90A TYR* 3.7 33.4 - - + +
93A ALA* 3.7 10.5 - - + +
94A VAL* 3.7 31.4 - - + +
97A ARG* 3.4 41.7 - - - +
8B LYS* 3.0 27.2 + - - -
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Residues in contact with LYS 81 (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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43A HIS* 3.2 33.7 + - + +
44A ILE* 3.8 13.2 - - + +
45A LYS* 5.2 4.9 - - - +
77A SER 2.9 19.6 + - - +
78A ASN* 3.8 5.6 - - - +
80A LEU* 1.3 78.3 - - - +
82A TYR* 1.3 61.1 + - - +
7B GLY 5.5 0.2 - - - +
8B LYS* 3.5 23.1 - - - +
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Residues in contact with TYR 82 (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 VAL* 3.3 14.1 - - + +
39A ASP* 2.6 30.4 + - - -
40A TYR* 3.7 39.0 - + + -
43A HIS* 4.0 21.5 - + + -
44A ILE* 4.2 6.1 - - + -
78A ASN 2.9 16.9 + - - +
81A LYS* 1.3 79.0 - - - +
83A ASN* 1.3 76.7 + - - +
84A ALA 4.0 0.3 + - - -
8B LYS* 3.4 20.7 - - - +
9B GLY* 3.5 22.7 + - - +
11B GLY* 3.0 40.2 + - - -
12B ALY 3.9 15.7 - - + -
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Residues in contact with ASN 83 (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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79A CYS* 3.0 33.0 + - - +
80A LEU 3.5 3.6 - - - +
82A TYR* 1.3 93.3 - - - +
84A ALA* 1.3 58.8 + - - +
87A THR* 3.5 16.9 - - + +
89A PHE* 3.6 27.2 - - + +
90A TYR* 3.5 7.0 - - + +
8B LYS* 2.7 30.1 + - - -
11B GLY* 5.1 2.6 - - - -
12B ALY 2.9 39.3 + - - +
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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