Contacts of the helix formed by residues 64 - 83 (chain B) in PDB entry 4QYL
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B PHE* 3.4 14.9 - - - -
62B TYR* 3.6 1.3 - - - +
63B LEU* 1.3 81.1 + - - +
65B PHE* 1.3 62.7 + - - +
66B ASP* 3.2 14.4 + - - +
67B ASP* 2.9 48.0 + - - +
68B PHE* 3.6 4.5 + - - +
116B ILE 4.7 0.4 - - - -
117B ASP 3.2 16.6 - - - +
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.8 8.0 - + + -
11B LEU* 4.7 4.3 - - + -
12B LEU* 4.0 25.4 - - + -
15B THR* 4.4 6.3 - - + -
64B ASN* 1.3 69.4 - - - +
66B ASP* 1.4 65.7 + - - +
68B PHE* 3.1 9.3 + + - +
69B GLU* 2.9 35.4 + - + -
104B LEU* 3.9 24.9 - - + -
107B ALA* 3.6 35.0 - - + -
108B ARG* 3.6 42.2 - - + +
111B ALA* 4.1 13.7 - - + -
117B ASP* 2.8 28.7 + - + +
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Residues in contact with ASP 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASN* 3.2 13.4 + - - +
65B PHE* 1.4 78.8 - - - +
67B ASP* 1.4 53.1 - - - +
69B GLU* 3.3 2.2 + - - +
70B GLU* 2.9 36.2 + - - +
108B ARG* 2.8 42.2 + - - +
117B ASP 4.3 2.4 + - - -
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Residues in contact with ASP 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG 4.4 4.2 - - - +
62B TYR* 3.6 27.0 - - + -
63B LEU* 3.1 28.8 + - - +
64B ASN* 2.9 38.0 + - - +
66B ASP* 1.4 75.8 - - - +
68B PHE* 1.3 62.0 + - - +
70B GLU* 3.6 13.7 + - - +
71B ASP* 3.4 17.3 + - - +
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Residues in contact with PHE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.8 41.7 - - + -
15B THR* 3.8 22.4 - - + -
16B LEU* 4.0 31.6 - - + -
19B LEU* 4.0 18.8 - - + -
53B MET* 3.5 29.1 - - + +
57B LEU* 4.5 5.2 - - + -
62B TYR* 3.8 30.5 - + + -
64B ASN 3.6 5.1 + - - +
65B PHE* 3.1 13.4 + + - +
67B ASP* 1.3 80.0 - - - +
69B GLU* 1.3 68.1 + - - +
71B ASP 3.2 10.4 + - - -
72B PHE* 3.2 10.2 + - + +
104B LEU* 4.2 8.7 - - + -
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 2.9 27.9 + - + +
66B ASP* 3.8 4.0 - - - +
68B PHE* 1.3 81.9 - - - +
70B GLU* 1.3 57.1 + - - +
72B PHE* 3.2 6.6 + - - +
73B ASN* 2.9 43.5 + - - +
104B LEU* 4.0 31.3 - - + +
108B ARG* 2.8 38.1 + - - +
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Residues in contact with GLU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS* 4.9 7.1 + - - -
66B ASP 2.9 18.1 + - - +
67B ASP* 3.7 12.6 - - - +
68B PHE 3.2 0.2 - - - -
69B GLU* 1.3 75.7 - - - +
71B ASP* 1.3 65.3 + - - +
73B ASN* 3.3 11.1 + - - +
74B LEU* 3.0 32.0 + - + +
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Residues in contact with ASP 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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46B LYS* 3.6 21.1 + - - -
48B MET* 3.5 31.0 - - + +
53B MET* 4.0 7.2 - - + -
56B ASN* 3.5 10.9 + - - -
62B TYR* 2.5 39.9 + - - +
67B ASP 3.4 5.3 + - - +
68B PHE 3.2 8.5 + - - +
70B GLU* 1.3 82.6 - - - +
72B PHE* 1.3 64.4 + - - +
74B LEU* 3.1 20.3 + - - +
75B ILE* 3.1 10.4 + - - +
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Residues in contact with PHE 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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19B LEU* 3.9 29.4 - - + -
50B PHE* 4.2 14.4 - + - -
53B MET* 3.8 14.8 - - + -
68B PHE 3.2 10.1 + - - +
69B GLU* 3.2 11.2 + - - +
71B ASP* 1.3 75.5 - - - +
73B ASN* 1.3 75.3 + - - +
75B ILE* 3.1 17.3 + - + +
76B VAL* 3.3 22.1 + - + +
96B LEU* 3.6 54.3 - - + -
97B ARG* 4.8 6.1 - - + -
100B GLY* 3.9 14.6 - - - -
101B GLY* 4.8 0.7 - - - -
104B LEU* 3.4 30.5 - - + -
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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
----------------------------------------------------------
69B GLU* 2.9 38.1 + - - +
70B GLU* 3.5 9.5 - - - +
71B ASP 3.2 0.2 - - - -
72B PHE* 1.3 94.5 - - - +
74B LEU* 1.3 58.1 + - - +
76B VAL* 3.4 6.7 + - - +
77B SER* 2.8 32.1 + - - -
104B LEU* 4.6 2.6 - - - +
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Residues in contact with LEU 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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46B LYS* 3.7 45.5 - - + +
48B MET* 3.9 11.0 - - + -
70B GLU* 3.0 20.0 + - + +
71B ASP* 3.1 25.1 + - - +
73B ASN* 1.3 74.2 - - - +
75B ILE* 1.3 61.0 + - - +
77B SER* 3.5 9.0 - - - +
78B ASN* 2.8 54.4 + - - +
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Residues in contact with ILE 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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28B PHE* 3.5 37.0 - - + -
48B MET* 3.8 22.4 - - + +
49B ASP 3.6 30.1 - - - +
50B PHE* 3.8 19.5 - - + +
53B MET* 3.6 22.9 - - - -
71B ASP 3.5 9.4 - - - +
72B PHE* 3.1 9.6 + - + +
74B LEU* 1.3 78.7 - - - +
76B VAL* 1.3 65.3 + - + +
78B ASN* 4.1 2.3 - - - +
79B CYS* 3.4 19.1 + - - +
96B LEU* 4.3 10.3 - - + -
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PHE* 5.6 0.4 - - - -
72B PHE* 3.3 34.7 + - + +
73B ASN* 3.6 8.7 - - - +
74B LEU 3.1 0.4 - - - -
75B ILE* 1.3 81.5 - - - +
77B SER* 1.3 65.5 + - - +
79B CYS* 3.2 4.7 + - - +
80B LEU* 3.0 46.4 + - + +
93B ALA* 4.0 12.1 - - + +
96B LEU* 4.1 16.2 - - + -
97B ARG* 3.8 36.8 - - + +
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Residues in contact with SER 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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73B ASN* 2.8 23.2 + - - -
74B LEU* 3.5 18.2 - - - +
76B VAL* 1.3 76.7 - - - +
78B ASN* 1.3 66.1 + - - +
80B LEU* 3.4 8.8 + - - +
81B LYS* 3.0 25.7 + - - +
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Residues in contact with ASN 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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40B TYR* 3.6 16.2 + - - +
44B ILE* 3.5 26.1 - - + +
45B LYS 5.3 0.9 + - - -
46B LYS 2.8 28.6 + - - +
47B PRO* 3.5 15.2 - - - +
48B MET 3.5 8.7 + - - +
74B LEU* 2.8 41.3 + - - +
75B ILE* 4.1 2.5 - - - +
77B SER* 1.3 76.4 + - - +
79B CYS* 1.3 56.3 + - - +
81B LYS* 3.3 2.3 + - - +
82B TYR* 3.0 32.1 + - - +
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Residues in contact with CYS 79 (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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28B PHE* 3.7 21.5 - - + -
40B TYR* 5.2 1.3 - - - -
75B ILE 3.4 16.8 + - - +
76B VAL 3.2 5.6 + - - +
78B ASN* 1.3 78.4 - - - +
80B LEU* 1.3 62.1 + - - +
82B TYR* 5.0 0.2 - - - -
83B ASN* 3.0 53.1 + - - +
89B PHE* 3.2 32.3 - - - -
90B TYR* 4.2 1.1 - - - -
93B ALA* 3.7 10.1 - - + -
5F ALY 3.9 11.4 - - + +
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Residues in contact with LEU 80 (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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76B VAL* 3.0 34.1 + - + +
77B SER* 3.9 7.2 - - - +
78B ASN 3.3 0.2 - - - -
79B CYS* 1.3 76.3 - - - +
81B LYS* 1.3 60.9 + - - +
83B ASN 3.4 7.1 - - - +
90B TYR* 3.4 68.0 - - + +
93B ALA* 3.6 10.3 - - + +
94B VAL* 3.8 9.2 - - + -
97B ARG* 3.4 31.9 - - - +
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Residues in contact with LYS 81 (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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43B HIS* 2.9 36.3 + - + +
44B ILE* 3.9 12.4 - - + +
45B LYS* 5.2 3.8 - - - +
77B SER 3.0 17.3 + - - +
78B ASN* 3.7 5.8 - - - +
79B CYS 3.2 0.2 - - - -
80B LEU* 1.3 77.5 - - - +
82B TYR* 1.4 65.6 + - - +
1F SER* 3.6 17.8 + - - -
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Residues in contact with TYR 82 (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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37B VAL* 3.3 15.8 - - + +
39B ASP* 2.6 31.5 + - - -
40B TYR* 3.6 37.2 - + + -
43B HIS* 4.0 19.7 - + + -
44B ILE* 4.2 5.4 - - + -
78B ASN 3.0 17.2 + - - +
81B LYS* 1.4 77.0 - - - +
83B ASN* 1.4 74.2 + - - +
1F SER* 2.6 27.3 - - - +
2F GLY* 3.1 26.8 + - - +
4F GLY* 3.1 38.9 + - - -
5F ALY 4.0 13.7 - - + -
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Residues in contact with ASN 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B CYS* 3.0 35.2 + - - +
80B LEU 3.4 6.6 - - - +
81B LYS 4.4 0.2 - - - +
82B TYR* 1.4 96.2 - - - +
84B ALA* 1.3 64.6 + - - +
85B LYS 3.7 0.2 + - - -
87B THR* 3.5 18.0 - - + +
89B PHE* 3.8 13.8 - - - +
90B TYR* 3.4 20.7 - - + +
1F SER* 3.8 3.4 - - - -
4F GLY* 5.0 1.8 - - - -
5F ALY 2.9 45.4 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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