Contacts of the helix formed by residues 40 - 54 (chain A) in PDB entry 3IEQ
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 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.3 21.2 - - + +
22A ILE* 3.4 2.6 - - - -
23A GLY 2.8 20.8 + - - -
24A GLY* 2.7 31.0 + - - -
38A ASP* 3.1 20.0 + - - +
39A ALA* 1.3 71.6 - - - +
41A VAL* 1.3 63.2 + - - +
42A LEU 3.4 3.1 + - - -
43A LEU* 3.2 23.3 + - - +
44A HIS* 3.1 29.3 + - - -
75A SER* 3.6 11.2 - - - -
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP* 3.2 48.1 - - + +
11A VAL* 3.8 2.9 - - - +
12A HIS* 4.0 9.2 - - + -
21A ILE 4.4 0.2 + - - -
22A ILE* 4.6 11.4 - - + -
33A LEU* 3.8 20.5 - - + +
39A ALA 2.9 6.8 + - - -
40A ASP* 1.3 73.1 + - - +
42A LEU* 1.3 66.7 + - - +
44A HIS 3.5 0.2 + - - -
45A ALA* 3.1 23.9 + - - +
100A ILE* 5.2 0.7 - - + -
148A ILE* 3.6 33.9 - - + +
150A ALA* 3.6 11.7 - - + +
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Residues in contact with LEU 42 (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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22A ILE* 3.8 16.2 - - + -
23A GLY* 3.8 20.4 - - - +
40A ASP* 3.3 4.3 + - - +
41A VAL* 1.3 80.1 - - - +
43A LEU* 1.3 64.2 + - - +
45A ALA* 3.2 2.8 + - - +
46A ILE* 3.0 37.0 + - + +
98A SER* 3.5 33.2 - - - +
99A THR 4.8 0.4 - - - +
100A ILE* 4.0 14.6 - - + -
114A MET* 3.9 21.1 - - - -
118A ILE* 3.9 14.8 - - + -
131A VAL* 4.0 11.4 - - + -
150A ALA* 3.7 15.0 - - + -
151A GLN 4.8 0.7 - - - +
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Residues in contact with LEU 43 (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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23A GLY* 3.8 11.2 - - - -
24A GLY 3.7 4.0 - - - +
40A ASP* 3.2 35.6 + - + +
42A LEU* 1.3 77.2 - - - +
44A HIS* 1.3 55.4 + - - +
46A ILE* 3.4 4.8 + - + +
47A THR* 2.6 38.2 + - - +
75A SER* 3.9 12.6 - - - +
76A ARG* 3.4 45.3 - - + +
79A LEU* 4.1 15.7 - - + +
117A ASN* 6.0 0.7 - - + -
118A ILE* 3.5 34.5 - - + -
121A ASP* 4.9 1.6 - - - +
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Residues in contact with HIS 44 (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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9A TYR 5.4 0.2 - - - -
10A ASP* 3.0 21.5 + - - +
12A HIS* 3.5 5.1 + + - -
37A SER* 3.2 22.5 + - - -
39A ALA* 4.0 1.6 - - - -
40A ASP 3.1 24.5 + - - +
43A LEU* 1.3 75.0 - - - +
45A ALA* 1.3 58.1 + - - +
47A THR* 3.5 1.7 + - - -
48A ASP* 3.0 31.9 + - - +
59A ILE* 3.9 33.1 - - + +
75A SER* 2.7 33.0 + - - -
78A LEU* 4.8 4.7 - - + +
163A ZN 2.1 32.6 - - - -
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Residues in contact with ALA 45 (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 GLY* 3.4 12.6 - - - -
9A TYR 4.2 8.1 - - - +
10A ASP* 4.0 10.9 - - - +
41A VAL 3.1 17.5 + - - +
42A LEU* 3.6 5.2 - - + +
44A HIS* 1.3 78.0 - - - +
46A ILE* 1.3 56.7 + - - +
48A ASP* 3.4 1.5 + - - -
49A ALA 3.0 22.0 + - - -
150A ALA* 3.8 31.6 - - + +
151A GLN 4.3 1.3 - - - +
152A ALA* 3.5 14.0 - - + +
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Residues in contact with ILE 46 (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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42A LEU* 3.0 31.6 + - + +
43A LEU* 3.4 7.4 + - + +
44A HIS 3.3 0.2 - - - -
45A ALA* 1.3 72.2 - - - +
47A THR* 1.3 66.1 + - - +
49A ALA* 3.2 3.7 + - + +
50A LEU* 3.0 32.2 + - + +
79A LEU* 4.0 17.7 - - + -
96A VAL* 4.0 33.4 - - + -
98A SER* 4.3 4.5 - - - +
118A ILE* 3.6 35.4 - - + -
122A LEU* 4.5 5.2 - - + -
152A ALA* 3.7 19.3 - - + -
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Residues in contact with THR 47 (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 LEU* 2.6 23.7 + - - +
44A HIS* 3.6 5.6 - - - -
45A ALA 3.4 0.2 - - - -
46A ILE* 1.3 74.2 - - - +
48A ASP* 1.3 63.6 + - - +
50A LEU 3.2 1.6 + - - -
51A PHE* 3.0 52.2 + - + -
59A ILE* 3.7 23.6 - - + +
63A PHE* 4.5 4.9 - - + -
75A SER 5.0 1.0 + - - -
78A LEU* 4.8 2.4 - - - +
79A LEU* 3.5 23.1 + - - +
82A CYS* 3.7 21.0 - - + -
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Residues in contact with ASP 48 (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 GLY* 4.1 5.8 - - - -
9A TYR 4.1 5.7 + - - +
44A HIS 3.0 15.4 + - - +
45A ALA* 3.6 7.0 - - - +
47A THR* 1.3 77.5 - - - +
49A ALA* 1.3 56.1 + - - +
51A PHE* 3.9 2.1 - - - +
52A GLY 2.9 24.3 + - - -
58A ASP* 3.3 9.6 - - - +
59A ILE* 2.8 42.2 + - - +
99B THR* 5.1 0.7 + - - -
132B LYS* 3.3 35.9 - - - +
134B LYS* 3.8 26.7 - - - +
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Residues in contact with ALA 49 (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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6A GLY* 3.3 16.6 - - - +
7A GLN* 3.6 30.0 + - - -
8A GLY 3.7 2.0 - - - +
45A ALA 3.0 15.3 + - - +
46A ILE* 3.2 9.1 + - + +
48A ASP* 1.3 76.0 - - - +
50A LEU* 1.3 58.4 + - - +
52A GLY 3.4 0.2 + - - -
53A ALA* 3.0 24.8 + - - +
152A ALA* 4.0 14.1 - - + +
153A ALA 4.3 0.4 - - - -
154A ALA* 4.1 13.4 - - + +
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Residues in contact with LEU 50 (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 ILE* 3.0 26.4 + - + +
49A ALA* 1.3 72.2 - - - +
51A PHE* 1.3 66.5 + - - +
52A GLY 3.1 1.3 - - - -
53A ALA* 3.3 6.5 + - - +
54A ALA* 3.2 23.2 + - - +
79A LEU* 3.8 14.1 - - + -
82A CYS* 3.7 18.6 - - - -
83A ALA* 5.3 1.6 - - + -
86A VAL* 3.8 11.8 - - + +
93A ILE* 3.8 37.2 - - + -
96A VAL* 4.5 2.5 - - + -
122A LEU* 3.8 28.5 - - + -
154A ALA* 3.8 21.8 - - + -
156A VAL* 4.4 6.5 - - + -
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Residues in contact with PHE 51 (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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47A THR* 3.0 42.8 + - + +
48A ASP 3.9 2.9 - - - +
50A LEU* 1.3 75.6 - - - +
52A GLY* 1.3 56.1 + - - +
54A ALA 3.3 2.1 + - - -
55A ALA 3.1 8.0 + - - -
56A LEU* 2.8 42.8 + - + +
57A GLY 3.8 17.3 - - - +
58A ASP* 3.9 3.1 - - - -
59A ILE* 3.9 18.6 - - - -
62A HIS* 3.4 51.4 - + + -
63A PHE* 3.8 14.4 - + - -
82A CYS* 3.6 34.3 - - + -
85A ARG* 4.4 8.3 - - + -
86A VAL* 4.6 2.7 - - + -
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Residues in contact with GLY 52 (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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5A ILE 4.3 0.3 - - - +
48A ASP 2.9 15.5 + - - -
51A PHE* 1.3 75.1 - - - +
53A ALA* 1.3 63.8 + - - +
55A ALA* 3.2 9.7 + - - +
95B ASN* 4.6 2.6 + - - -
97B ASP* 3.3 36.7 - - - +
130B ASN* 3.5 24.4 - - - +
132B LYS* 4.3 0.4 - - - -
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Residues in contact with ALA 53 (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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4A ARG* 3.2 32.1 + - - +
5A ILE* 3.5 15.5 - - - -
6A GLY* 3.5 19.2 - - - +
49A ALA 3.0 13.5 + - - +
50A LEU* 3.3 5.8 + - - +
52A GLY* 1.3 75.5 - - - +
54A ALA* 1.3 58.6 + - - +
55A ALA* 3.2 1.6 + - - +
154A ALA 4.3 3.4 - - - +
156A VAL* 3.8 29.2 - - + -
95B ASN* 4.3 3.1 + - - -
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Residues in contact with ALA 54 (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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4A ARG* 5.4 0.2 - - - -
50A LEU 3.2 15.9 + - - +
51A PHE 3.9 0.4 - - - +
53A ALA* 1.3 74.5 - - - +
55A ALA* 1.3 69.2 + - - +
56A LEU* 3.4 30.5 + - + +
86A VAL* 4.2 11.0 - - + -
89A ALA* 5.1 0.2 - - - +
91A PHE* 3.7 43.8 - - + -
156A VAL* 5.1 0.9 - - + -
127B ASP* 4.9 2.3 - - - +
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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