Contacts of the helix formed by residues 40 - 54 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.5 18.4 - - + +
22B ILE* 3.5 2.3 - - - -
23B GLY 2.8 20.7 + - - -
24B GLY* 2.7 31.0 + - - -
38B ASP* 3.1 11.9 + - - +
39B ALA* 1.3 71.3 - - - +
41B VAL* 1.3 62.8 + - - +
42B LEU 3.3 3.6 + - - -
43B LEU* 3.2 24.3 + - - +
44B HIS* 3.1 27.5 + - - -
75B SER* 3.6 21.8 + - - +
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 3.3 16.4 - - + +
11B VAL* 3.8 4.9 - - - +
12B HIS* 3.4 35.2 - - + +
22B ILE* 4.5 12.6 - - + -
33B LEU* 3.9 16.8 - - + -
39B ALA 2.9 7.4 + - - +
40B ASP* 1.3 71.8 + - - +
42B LEU* 1.3 65.8 + - - +
45B ALA* 3.1 19.9 + - - +
100B ILE* 5.2 0.7 - - + -
148B ILE* 3.6 39.0 - - + +
149B GLU 4.9 0.2 - - - +
150B ALA* 3.4 23.9 - - + +
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Residues in contact with LEU 42 (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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22B ILE* 3.7 17.0 - - + -
23B GLY* 3.8 14.8 - - - +
40B ASP* 3.2 4.7 + - - +
41B VAL* 1.3 82.5 - - - +
43B LEU* 1.3 63.8 + - - +
45B ALA* 3.4 2.0 + - + +
46B ILE* 3.1 29.5 + - + +
98B SER* 3.5 32.1 - - - +
99B THR 5.0 0.4 - - - +
100B ILE* 4.1 16.6 - - + -
114B MET* 3.9 11.2 - - - -
118B ILE* 3.8 22.9 - - + -
131B VAL* 3.9 19.5 - - + -
150B ALA* 3.7 11.2 - - + -
151B GLN 4.9 0.9 - - - +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY* 3.6 18.4 - - - -
24B GLY 3.8 3.4 - - - +
40B ASP* 3.2 32.0 + - - +
42B LEU* 1.3 73.0 - - - +
44B HIS* 1.3 61.8 + - - +
46B ILE* 3.4 6.6 + - + +
47B THR* 2.8 34.5 + - - +
75B SER* 3.9 16.4 - - - +
76B ARG* 3.4 45.3 - - + +
79B LEU* 4.4 13.2 - - + +
117B ASN* 6.0 1.1 - - + -
118B ILE* 3.7 28.0 - - + -
121B ASP* 5.0 1.6 - - - +
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Residues in contact with HIS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TYR 5.3 0.7 - - - -
10B ASP* 3.1 19.1 + - - +
12B HIS* 3.8 3.1 + + - -
38B ASP* 4.7 0.2 - - - -
39B ALA* 4.2 5.6 - - - -
40B ASP 3.1 22.5 + - - +
41B VAL 3.8 0.2 - - - +
43B LEU* 1.3 76.1 - - - +
45B ALA* 1.3 57.1 + - - +
47B THR* 3.2 3.0 + - - -
48B ASP* 2.9 32.7 + - - +
59B ILE* 3.8 30.4 - - + +
75B SER* 3.0 32.8 + - - -
78B LEU* 4.9 7.5 - - + +
164B ZN 2.4 32.2 - - - -
134C LYS* 5.1 3.8 - - - +
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY* 3.3 20.7 - - - -
9B TYR 4.1 12.3 - - - +
10B ASP* 4.1 3.7 - - - +
41B VAL 3.1 18.1 + - - +
42B LEU* 3.6 4.7 - - + +
44B HIS* 1.3 75.2 - - - +
46B ILE* 1.3 57.9 + - - +
48B ASP* 3.5 0.6 + - - -
49B ALA* 3.0 24.1 + - - +
150B ALA* 3.9 28.9 - - + +
151B GLN 4.3 0.4 - - - +
152B ALA* 3.7 10.5 - - + -
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Residues in contact with ILE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.1 33.0 + - + +
43B LEU* 3.9 6.3 - - + +
45B ALA* 1.3 72.1 - - - +
47B THR* 1.3 67.5 + - - +
49B ALA* 3.2 2.8 + - + +
50B LEU* 2.9 33.4 + - + +
79B LEU* 3.9 18.2 - - + -
96B VAL* 3.8 33.7 - - + -
98B SER* 4.5 4.5 - - - +
118B ILE* 3.7 35.0 - - + -
122B LEU* 4.4 5.4 - - + -
129B VAL* 5.9 0.2 - - + -
131B VAL* 5.4 0.2 - - + -
152B ALA* 3.7 20.2 - - + -
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Residues in contact with THR 47 (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 LEU 2.8 25.1 + - - -
44B HIS* 3.5 5.8 - - - -
46B ILE* 1.3 75.1 - - - +
48B ASP* 1.3 58.4 + - - +
50B LEU* 3.2 5.0 + - - +
51B PHE* 3.0 54.1 + - + -
59B ILE* 3.7 23.4 - - + +
63B PHE* 4.3 5.4 - - + -
75B SER 4.8 1.4 + - - -
78B LEU* 4.7 1.6 - - - +
79B LEU* 3.4 25.4 + - - +
82B CYS* 3.6 18.1 - - + -
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Residues in contact with ASP 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLY* 4.1 7.0 - - - -
9B TYR 4.2 4.3 + - - +
44B HIS 2.9 13.0 + - - +
45B ALA* 3.7 6.1 - - - +
47B THR* 1.3 77.3 - - - +
49B ALA* 1.3 56.8 + - - +
51B PHE* 3.3 3.3 + - - +
52B GLY 2.8 26.2 + - - -
58B ASP* 3.3 11.4 - - - +
59B ILE* 2.7 42.7 + - - +
99C THR* 5.3 0.3 + - - -
132C LYS* 3.4 31.3 - - - +
134C LYS* 3.6 28.4 + - - +
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLY* 3.3 14.5 - - - +
7B GLN* 3.5 30.0 + - - +
8B GLY 3.7 2.2 - - - +
45B ALA 3.0 18.2 + - - +
46B ILE* 3.2 6.5 + - + +
48B ASP* 1.3 74.8 - - - +
50B LEU* 1.3 57.9 + - - +
53B ALA* 2.9 26.0 + - - +
152B ALA* 4.0 15.5 - - + +
154B ALA* 4.1 14.0 - - + +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 2.9 24.7 + - + +
47B THR 3.2 6.9 + - - +
49B ALA* 1.3 74.4 - - - +
51B PHE* 1.3 63.5 - - - +
53B ALA* 3.4 4.0 + - - +
54B ALA* 3.2 23.7 + - - +
79B LEU* 3.9 14.1 - - + -
82B CYS* 3.6 15.3 - - - -
83B ALA* 5.4 1.1 - - - +
86B VAL* 3.8 12.0 - - + +
93B ILE* 3.7 36.1 - - + -
96B VAL* 4.6 2.0 - - + -
122B LEU* 3.6 31.0 - - + -
154B ALA* 4.0 20.2 - - + -
156B VAL* 4.4 8.0 - - + +
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Residues in contact with PHE 51 (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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47B THR* 3.0 43.4 + - + +
48B ASP 3.8 3.4 - - - +
50B LEU* 1.3 77.0 - - - +
52B GLY* 1.3 57.3 + - - +
54B ALA* 3.4 2.7 + - - -
55B ALA 2.9 9.2 + - - -
56B LEU* 2.9 40.7 + - + -
57B GLY 3.9 16.4 - - - +
58B ASP* 3.9 2.9 - - - -
59B ILE* 3.9 19.1 - - - -
62B HIS* 3.5 51.4 - + + -
63B PHE* 3.8 13.7 - + - -
82B CYS* 3.6 33.9 - - + -
85B ARG* 4.4 7.4 - - + -
86B VAL* 4.8 1.8 - - + -
130C ASN* 4.3 0.2 + - - -
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Residues in contact with GLY 52 (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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5B ILE 4.3 0.5 - - - +
48B ASP 2.8 14.8 + - - -
51B PHE* 1.3 76.6 - - - +
53B ALA* 1.3 62.0 + - - +
55B ALA* 3.1 13.5 + - - +
57B GLY 4.3 0.4 + - - -
95C ASN* 4.7 2.6 + - - -
97C ASP* 3.2 37.5 - - - +
130C ASN* 3.4 17.8 - - - +
132C LYS* 4.2 0.9 - - - -
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Residues in contact with ALA 53 (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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4B ARG* 3.2 28.7 + - - +
5B ILE 3.5 14.6 - - - -
6B GLY* 3.4 19.6 - - - +
49B ALA 2.9 14.6 + - - +
50B LEU* 3.8 6.1 - - - +
51B PHE 3.4 0.2 - - - -
52B GLY* 1.3 75.8 - - - +
54B ALA* 1.3 60.8 + - - +
55B ALA* 3.2 2.1 + - - +
154B ALA 4.1 5.4 - - - +
156B VAL* 3.7 30.1 - - + -
95C ASN* 4.4 2.9 + - - -
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Residues in contact with ALA 54 (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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50B LEU 3.2 16.2 + - - +
51B PHE 3.9 1.3 - - - +
53B ALA* 1.3 74.7 - - - +
55B ALA* 1.3 70.4 + - - +
56B LEU* 3.7 29.3 - - + +
86B VAL* 4.2 13.7 - - + -
89B ALA* 5.1 0.3 - - - +
91B PHE* 3.9 39.6 - - + -
156B VAL* 4.6 0.4 - - + +
127C ASP* 4.6 1.1 - - - +
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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