Contacts of the helix formed by residues 55 - 71 (chain E) in PDB entry 4Q96
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 ARG 55 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LEU 2.7 29.7 + - - -
14E SER* 3.6 16.3 + - - +
16E LEU* 3.3 29.7 + - - +
51E ALA* 4.0 23.5 - - + +
52E LYS* 2.9 23.2 + - - +
54E ASN* 1.3 97.8 - - - +
56E LYS* 1.3 65.9 + - - +
57E LEU 3.3 2.5 - - - -
58E THR* 3.3 21.6 + - - +
59E PHE* 3.3 24.5 - - - -
201E UNX 4.3 15.2 + - - -
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Residues in contact with LYS 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1615C TYR* 6.1 0.9 - - + -
48E LEU* 2.9 45.4 + - + +
49E ARG 2.9 15.0 + - - -
51E ALA* 3.0 18.4 + - + +
52E LYS 3.7 8.3 - - - +
53E SER* 3.6 17.7 + - - +
55E ARG* 1.3 76.0 - - - +
57E LEU* 1.3 67.3 + - - +
59E PHE* 3.0 23.9 + - - +
60E LEU 3.7 1.9 + - - -
91E HIS* 2.9 34.7 + - + +
92E VAL* 4.2 13.9 - - + +
95E GLU* 3.7 34.8 - - + -
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Residues in contact with LEU 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1615C TYR* 4.1 19.6 - - + -
1616C SER 3.7 18.2 - - - +
1618C THR 3.6 27.1 - - - +
1619C SER* 5.4 0.2 - - - -
103D PRO* 3.8 23.3 - - + -
104D LEU* 3.6 31.4 - - + -
107D LEU* 5.1 0.4 - - + -
18E ASN* 5.8 0.7 - - - +
53E SER 4.9 1.6 + - - -
54E ASN 5.1 4.7 + - - +
55E ARG 3.3 0.6 - - - -
56E LYS* 1.3 77.5 - - - +
58E THR* 1.3 63.3 + - - +
60E LEU* 2.9 21.7 + - + +
61E TYR* 3.4 31.8 + - + -
92E VAL* 4.4 8.0 - - - +
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Residues in contact with THR 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1620C PRO* 5.1 0.7 - - + -
16E LEU* 3.6 22.0 - - + -
17E SER 3.5 25.4 - - - +
18E ASN* 2.8 34.8 + - - +
23E VAL* 3.9 13.5 - - + -
54E ASN 4.8 2.4 + - - -
55E ARG* 3.3 18.5 + - - -
56E LYS 3.2 0.8 - - - -
57E LEU* 1.3 78.6 - - - +
59E PHE* 1.3 62.2 + - - +
61E TYR* 3.1 8.4 + - - +
62E LEU* 2.9 21.0 + - - +
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Residues in contact with PHE 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E LEU* 4.1 31.9 - - + -
16E LEU* 4.5 9.9 - - + -
44E TRP* 3.1 41.8 + + + +
47E GLU* 3.8 24.9 - - + -
48E LEU* 3.6 37.9 - - + -
51E ALA* 3.8 19.3 - - + -
55E ARG* 3.3 33.2 - - - -
56E LYS* 3.0 16.1 + - - +
58E THR* 1.3 78.6 - - - +
60E LEU* 1.3 58.0 + - - +
62E LEU* 3.2 6.1 + - - +
63E ALA 3.0 23.6 + - - -
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Residues in contact with LEU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D LEU* 3.6 30.5 - - + -
107D LEU* 3.8 17.4 - - + +
111D TRP* 4.8 3.5 - - - -
44E TRP* 3.8 26.5 - - + -
48E LEU* 4.5 2.7 - - + -
56E LYS 4.3 0.7 - - - +
57E LEU* 2.9 12.7 + - + +
59E PHE* 1.3 77.1 - - - +
61E TYR* 1.3 57.6 + - - +
63E ALA* 3.4 4.6 + - + +
64E ASN* 2.9 25.3 + - - +
85E LEU* 5.0 2.0 - - + -
88E ALA* 4.1 16.2 - - + -
89E PHE* 4.1 32.3 - - + -
92E VAL* 3.8 29.6 - - + -
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Residues in contact with TYR 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1619C SER* 3.4 23.4 - - - -
1620C PRO* 3.5 38.6 - - + -
103D PRO* 3.5 21.9 + - + +
106D ARG* 3.7 15.0 + - + +
107D LEU* 4.0 29.8 - - + +
110D ILE* 6.3 1.6 - - + -
20E GLN* 5.9 1.3 - - - +
23E VAL* 3.9 8.4 - - + +
57E LEU* 3.4 43.1 + - + -
58E THR* 3.1 8.5 + - - +
60E LEU* 1.3 75.2 - - - +
62E LEU* 1.3 59.9 + - - +
64E ASN* 3.1 13.6 + - - +
65E ASP* 3.0 28.1 + - - +
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Residues in contact with LEU 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E LEU* 3.7 19.1 - - + -
16E LEU* 4.0 13.9 - - + -
23E VAL* 3.4 36.4 - - + +
26E LEU* 3.6 30.5 - - + -
27E SER* 3.8 19.3 - - - +
30E LEU* 4.4 10.3 - - + -
44E TRP* 4.2 13.0 - - + +
58E THR 2.9 12.5 + - - +
59E PHE* 3.3 10.3 - - - +
61E TYR* 1.3 72.7 - - - +
63E ALA* 1.3 65.7 + - - +
65E ASP* 3.2 2.4 + - - +
66E VAL* 3.0 31.1 + - + +
81E PHE* 6.3 0.2 - - + -
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Residues in contact with ALA 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D TRP* 5.3 2.2 - - + -
44E TRP* 3.7 18.3 - - + +
59E PHE 3.0 6.1 + - - -
60E LEU* 3.5 9.9 - - - +
62E LEU* 1.3 75.6 - - - +
64E ASN* 1.3 63.3 + - - +
66E VAL* 3.3 0.4 + - - -
67E ILE* 2.9 36.6 + - + +
81E PHE* 3.5 39.9 - - + -
85E LEU* 4.8 6.1 - - + -
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Residues in contact with ASN 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D LEU* 3.6 31.5 - - + +
110D ILE* 4.8 8.3 - - - +
111D TRP* 3.0 24.4 + - + +
60E LEU 2.9 9.8 + - - +
61E TYR* 3.1 17.7 + - - +
63E ALA* 1.3 76.5 - - - +
65E ASP* 1.3 65.2 + - - +
67E ILE* 4.0 1.2 - - - +
68E GLN* 2.9 53.1 + - - +
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Residues in contact with ASP 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E GLN* 4.0 6.6 + - - -
23E VAL* 4.0 10.5 - - + +
24E GLN* 3.2 33.9 + - - +
27E SER* 2.6 28.5 + - - +
61E TYR 3.0 12.5 + - - +
62E LEU 3.7 6.5 - - - +
64E ASN* 1.3 80.0 - - - +
66E VAL* 1.3 62.8 + - - +
68E GLN* 4.2 1.5 - - - -
69E ASN* 2.7 56.3 + - - +
206E UNX 3.0 8.4 + - - -
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Residues in contact with VAL 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E SER* 3.5 24.5 - - - +
30E LEU* 3.8 27.4 - - + -
31E ILE* 4.2 6.7 - - + +
62E LEU* 3.0 24.2 + - + +
63E ALA* 3.7 3.8 - - - +
65E ASP* 1.3 76.7 - - - +
67E ILE* 1.3 57.5 + - - +
69E ASN 3.8 0.3 - - - -
70E SER* 2.9 34.3 + - - -
77E PHE* 3.7 43.5 - - + -
81E PHE* 3.8 13.9 - - + -
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Residues in contact with ILE 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D TRP* 4.5 9.6 - - + +
116D VAL* 3.7 26.0 - - + -
117D TYR* 3.6 22.4 - - + +
63E ALA* 2.9 26.5 + - + +
64E ASN* 4.0 2.9 - - - +
66E VAL* 1.3 76.4 - - - +
68E GLN* 1.3 63.8 + - + +
70E SER* 3.2 16.4 + - - -
71E LYS* 3.3 15.1 - - - +
77E PHE* 4.6 4.0 - - - +
78E THR* 3.5 22.3 + - - +
81E PHE* 3.4 36.1 - - + -
85E LEU* 4.2 10.1 - - + -
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Residues in contact with GLN 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ILE* 3.4 27.1 - - - +
111D TRP* 4.2 4.9 - - - +
114D ARG* 3.0 34.6 + - - +
116D VAL* 3.9 21.7 - - + +
64E ASN* 2.9 40.9 + - - +
65E ASP* 4.4 2.5 - - - +
67E ILE* 1.3 78.6 - - + +
69E ASN* 1.3 65.7 + - - +
70E SER 3.4 0.3 + - - -
71E LYS* 3.5 22.3 + - + +
72E ARG* 4.8 0.9 + - - +
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Residues in contact with ASN 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E GLN* 5.3 2.0 - - - +
31E ILE* 3.4 22.0 - - + +
65E ASP* 2.7 53.2 + - - +
68E GLN* 1.3 78.9 - - - +
70E SER* 1.3 60.1 + - - +
71E LYS 3.4 0.2 - - - -
72E ARG* 3.7 36.6 + - - +
73E LYS* 4.5 3.6 - - - +
206E UNX 3.9 8.8 + - - -
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Residues in contact with SER 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ILE* 4.2 12.8 - - - -
34E ARG* 5.8 1.6 - - - -
66E VAL 2.9 22.6 + - - -
67E ILE 3.2 8.7 + - - -
68E GLN 3.3 0.2 - - - -
69E ASN* 1.3 74.6 - - - +
71E LYS* 1.3 55.2 + - - +
72E ARG 3.2 3.4 - - - -
73E LYS* 2.7 32.6 + - - +
74E GLY 3.0 18.3 + - - +
77E PHE* 3.4 38.2 - - - +
78E THR* 4.7 2.9 + - - -
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Residues in contact with LYS 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D ARG 5.4 2.0 - - - +
115D SER 4.5 4.0 - - - -
116D VAL* 3.6 52.0 - - + +
67E ILE 3.3 16.2 - - - +
68E GLN* 3.7 13.0 - - - +
69E ASN 3.4 0.8 - - - -
70E SER* 1.3 78.5 + - - +
72E ARG* 1.3 58.5 + - - +
73E LYS 3.2 3.3 + - - -
74E GLY* 3.7 15.1 + - - +
75E PRO* 5.8 0.7 - - - -
78E THR* 4.1 16.6 - - - +
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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