Contacts of the helix formed by residues 40 - 54 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ILE* 3.5 23.9 - - + +
22C ILE* 3.4 3.5 - - - -
23C GLY 2.8 21.0 + - - -
24C GLY* 2.7 28.8 + - - -
38C ASP* 3.2 10.8 + - - +
39C ALA* 1.3 71.1 - - - +
41C VAL* 1.3 63.3 + - - +
42C LEU 3.4 4.0 + - - -
43C LEU* 3.2 22.9 + - - +
44C HIS* 3.0 26.9 + - - -
75C SER* 3.6 23.7 + - - -
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ASP* 3.4 42.4 - - - +
11C VAL* 3.7 4.5 - - - +
12C HIS* 3.9 10.5 - - + -
21C ILE 4.6 0.2 + - - -
22C ILE* 4.7 9.4 - - + -
33C LEU* 3.8 17.8 - - + +
39C ALA 3.0 5.7 + - - -
40C ASP* 1.3 70.0 + - - +
42C LEU* 1.3 67.5 + - + +
44C HIS 3.6 0.2 + - - -
45C ALA* 3.1 18.7 + - - +
100C ILE* 5.1 1.1 - - + -
148C ILE* 3.3 45.3 - - + +
149C GLU 4.7 0.2 - - - +
150C ALA* 3.5 16.2 - - + +
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.8 11.0 - - + -
23C GLY* 3.9 13.0 - - - +
40C ASP* 3.3 8.3 + - - +
41C VAL* 1.3 80.0 - - - +
43C LEU* 1.3 63.4 + - - +
45C ALA* 3.3 3.9 + - + +
46C ILE* 3.1 32.4 + - + +
98C SER* 3.5 33.7 - - - +
99C THR 4.7 0.7 - - - +
100C ILE* 3.8 35.0 - - + -
114C MET* 3.9 16.4 - - - -
118C ILE* 4.0 11.9 - - + -
131C VAL* 3.9 9.2 - - + -
150C ALA* 3.6 15.3 - - + -
151C GLN 4.8 0.4 - - - +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C GLY* 3.8 12.6 - - - -
24C GLY* 4.0 3.4 - - - +
40C ASP* 3.2 34.0 + - - +
42C LEU* 1.3 76.5 - - - +
44C HIS* 1.3 55.4 + - - +
46C ILE* 3.5 5.3 + - + +
47C THR* 2.7 37.6 + - - -
75C SER* 3.9 17.0 - - - +
76C ARG* 3.6 42.8 - - + +
79C LEU* 4.0 17.8 - - + +
117C ASN* 6.1 0.4 - - + -
118C ILE* 3.7 33.0 - - + -
121C ASP* 5.4 0.7 - - - +
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Residues in contact with HIS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 6.0 0.7 - - - +
9C TYR 5.6 0.2 - - - -
10C ASP* 3.1 19.3 + - - +
12C HIS* 3.3 8.8 + + - -
37C SER* 3.2 22.5 + - - -
39C ALA* 3.8 9.9 - - - -
40C ASP 3.0 13.0 + - - +
41C VAL 3.9 0.4 - - - +
43C LEU* 1.3 74.0 - - - +
45C ALA* 1.3 60.4 + - - +
47C THR* 3.2 2.5 + - - -
48C ASP* 2.9 30.7 + - - +
59C ILE* 4.0 31.0 - - + +
75C SER* 2.8 30.5 + - - -
78C LEU* 5.1 6.5 - - + +
163C ZN 2.3 32.5 - - - -
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Residues in contact with ALA 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C GLY* 3.4 14.7 - - - -
9C TYR 4.3 6.1 - - - +
10C ASP* 4.1 11.1 - - - +
41C VAL 3.1 17.7 + - - +
42C LEU* 3.3 5.1 + - + +
44C HIS* 1.3 77.0 - - - +
46C ILE* 1.3 63.6 + - - +
48C ASP* 3.4 1.0 + - - -
49C ALA 3.1 17.7 + - - -
150C ALA* 3.6 31.0 - - + +
151C GLN 4.3 0.4 - - - +
152C ALA* 3.6 14.3 - - + +
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Residues in contact with ILE 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 3.1 32.7 + - + +
43C LEU* 3.9 5.6 - - + +
45C ALA* 1.3 74.6 - - - +
47C THR* 1.3 63.2 + - - +
49C ALA* 3.2 4.4 + - + +
50C LEU* 3.0 33.8 + - + +
79C LEU* 3.8 18.2 - - + -
96C VAL* 3.8 33.9 - - + -
98C SER* 4.2 6.7 - - - +
118C ILE* 3.6 35.2 - - + -
122C LEU* 4.5 4.9 - - + -
130C ASN 5.7 0.2 - - - +
152C ALA* 3.6 20.4 - - + -
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Residues in contact with THR 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C LEU 2.7 25.9 + - - -
44C HIS* 3.4 6.7 - - - -
46C ILE* 1.3 75.2 - - - +
48C ASP* 1.3 56.8 + - - +
50C LEU 3.2 1.2 + - - -
51C PHE* 2.9 55.7 + - + -
59C ILE* 3.7 22.8 - - + +
63C PHE* 4.4 5.4 - - + -
75C SER 5.1 0.7 + - - -
78C LEU* 4.7 2.2 - - - +
79C LEU* 3.4 23.5 + - - +
82C CYS* 3.5 20.4 - - + -
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Residues in contact with ASP 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A THR* 4.9 0.9 + - - -
132A LYS* 3.4 37.1 - - - +
134A LYS* 3.5 27.1 - - - +
8C GLY* 4.1 6.5 - - - -
9C TYR 4.3 4.0 + - - +
44C HIS 2.9 15.1 + - - +
45C ALA* 3.7 6.1 - - - +
47C THR* 1.3 75.4 - - - +
49C ALA* 1.3 53.6 + - - +
51C PHE* 3.7 2.8 - - - +
52C GLY* 2.8 30.1 + - - -
58C ASP* 3.4 9.4 - - - +
59C ILE* 2.9 40.6 + - - +
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLY* 3.3 16.6 - - - +
7C GLN 3.6 14.1 - - - +
8C GLY* 3.5 19.4 - - - +
45C ALA 3.1 10.7 + - - +
46C ILE* 3.2 8.5 + - - +
48C ASP* 1.3 76.7 - - - +
50C LEU* 1.3 58.0 + - - +
53C ALA* 2.9 24.9 + - - +
152C ALA* 3.8 17.3 - - + +
154C ALA* 4.0 12.6 - - + +
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Residues in contact with LEU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ILE* 3.0 32.2 + - + +
47C THR 3.2 0.2 + - - -
49C ALA* 1.3 74.6 - - - +
51C PHE* 1.3 64.2 + - - +
53C ALA* 3.4 3.7 + - - +
54C ALA* 3.1 23.7 + - - +
79C LEU* 4.2 2.9 - - + -
82C CYS* 3.6 24.9 - - - -
83C ALA* 5.3 0.9 - - - +
86C VAL* 3.8 11.7 - - + +
93C ILE* 3.7 36.3 - - + -
96C VAL* 4.2 2.9 - - + -
122C LEU* 3.6 31.6 - - + -
154C ALA* 3.7 22.4 - - + -
156C VAL* 4.3 8.1 - - + +
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Residues in contact with PHE 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C THR* 2.9 46.0 + - + +
48C ASP 3.8 3.1 - - - +
50C LEU* 1.3 76.3 - - - +
52C GLY* 1.3 61.0 + - - +
54C ALA* 3.4 2.1 + - - -
55C ALA 3.1 3.8 + - - -
56C LEU* 2.9 41.4 + - + -
57C GLY 3.7 18.6 - - - +
58C ASP* 4.1 1.8 - - - -
59C ILE* 4.0 19.1 - - - -
62C HIS* 3.5 53.2 - + + -
63C PHE* 3.8 14.1 - + - -
82C CYS* 3.9 29.6 - - - -
85C ARG* 4.3 11.9 - - + -
86C VAL* 5.0 0.7 - - + -
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Residues in contact with GLY 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ASN* 4.7 2.8 + - - -
96A VAL 5.0 0.2 - - - +
97A ASP* 3.3 29.9 - - - +
130A ASN* 3.4 25.1 - - - +
132A LYS* 4.2 0.7 - - - -
5C ILE 4.3 0.3 - - - +
48C ASP 2.8 18.4 + - - -
49C ALA 3.4 0.9 + - - -
51C PHE* 1.3 74.2 - - - +
53C ALA* 1.3 57.5 + - - +
55C ALA* 3.0 19.1 + - - +
57C GLY 4.1 0.2 + - - -
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Residues in contact with ALA 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASN* 4.5 2.3 + - - -
4C ARG* 3.2 29.7 + - - +
5C ILE 3.5 14.6 - - - -
6C GLY* 3.5 16.2 - - - +
49C ALA 2.9 17.2 + - - +
50C LEU* 3.4 5.6 + - - +
52C GLY* 1.3 76.0 - - - +
54C ALA* 1.3 58.7 + - - +
55C ALA* 3.4 1.9 + - - +
154C ALA 4.0 5.8 - - - +
156C VAL* 3.8 30.9 - - + +
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Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ASP 4.8 0.7 - - - +
4C ARG* 5.5 0.2 - - - -
50C LEU 3.1 15.8 + - - +
51C PHE 4.0 0.7 - - - +
53C ALA* 1.3 75.1 - - - +
55C ALA* 1.3 69.3 + - - +
56C LEU* 3.3 31.9 + - + +
86C VAL* 4.2 12.3 - - + -
89C ALA* 5.0 0.3 - - - +
91C PHE* 3.9 39.9 - - + -
156C VAL* 4.5 0.8 - - + +
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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