Contacts of the helix formed by residues 39 - 48 (chain J) in PDB entry 2IUO
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 ALA 39 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A PHE* 2.8 54.8 + - + +
38J LEU* 1.3 73.5 - - - +
40J GLU* 1.3 66.5 + - - +
41J ALA* 4.1 4.3 - - + +
42J PHE* 3.0 3.2 + - - +
43J VAL* 2.9 21.5 + - - +
128J LEU 5.8 0.2 - - - +
1159J SO4 3.5 20.0 - - - +
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Residues in contact with GLU 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111I LEU* 3.0 32.5 - - + +
114I GLU* 3.4 16.6 - - - +
115I LYS* 3.7 26.2 + - - -
29J PHE 4.1 7.0 - - - +
30J ALA* 3.7 30.2 + - - +
33J ALA* 4.0 11.7 - - + -
38J LEU 3.7 0.2 + - - -
39J ALA* 1.3 73.2 - - - +
41J ALA* 1.3 55.1 + - - +
43J VAL* 4.1 0.3 - - - +
44J THR* 2.5 38.9 + - - +
1159J SO4 2.9 30.8 + - - +
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Residues in contact with ALA 41 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PHE* 4.4 8.5 - - + -
104I TYR* 3.9 5.1 - - + -
107I THR* 3.7 7.9 - - + +
111I LEU* 4.0 18.5 - - + +
39J ALA* 3.2 2.1 - - + +
40J GLU* 1.3 79.9 - - - +
42J PHE* 1.3 57.8 + - - +
45J ALA* 3.1 29.5 + - - +
128J LEU* 3.6 40.4 - - + +
129J ASP* 5.2 2.5 - - - -
1159J SO4 4.6 1.0 + - - -
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Residues in contact with PHE 42 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ASP* 6.2 0.2 - - - -
153A THR* 5.0 2.7 - - + -
154A LYS 4.0 6.1 - - - -
155A PRO* 3.5 39.0 - - + -
156A PHE* 3.6 48.9 - + + +
104I TYR* 4.3 1.6 - - - -
38J LEU* 4.0 22.7 - - + -
39J ALA 3.0 5.1 + - - +
41J ALA* 1.3 77.7 - - - +
43J VAL* 1.3 67.7 + - - +
45J ALA* 3.4 5.8 + - - +
46J ALA* 3.1 19.2 + - - +
51J GLN* 3.7 37.9 - - + +
52J ALA 3.4 26.9 - - - -
53J LEU* 4.4 5.4 - - + -
54J PRO* 4.7 0.2 - - + -
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Residues in contact with VAL 43 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J PHE 5.8 0.2 - - - +
32J ILE* 4.5 4.9 - - + -
33J ALA* 3.9 22.9 - - + -
36J THR* 3.5 32.8 - - + +
38J LEU* 3.5 14.1 - - + -
39J ALA 2.9 15.0 + - - +
40J GLU 4.2 0.2 - - - +
42J PHE* 1.3 75.1 - - - +
44J THR* 1.3 64.1 + - - +
46J ALA* 3.2 3.8 + - - +
47J LEU* 3.0 29.9 + - + +
53J LEU* 4.3 19.5 - - + -
61J VAL* 4.2 25.6 - - + -
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Residues in contact with THR 44 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I THR* 3.8 22.9 - - + -
110I ALA* 4.2 8.7 - - + -
111I LEU* 3.9 6.6 - - + +
29J PHE* 3.5 42.7 + - + +
40J GLU* 2.5 25.1 + - - +
43J VAL* 1.3 75.2 - - - +
45J ALA* 1.3 65.1 + - - +
47J LEU* 3.1 12.3 + - - +
48J LEU* 2.9 44.6 + - + +
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Residues in contact with ALA 45 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103I VAL 4.9 0.2 - - - +
104I TYR* 3.7 20.2 - - + -
107I THR* 3.1 18.5 + - - +
41J ALA 3.1 20.2 + - - +
42J PHE 3.6 4.5 - - - +
43J VAL 3.3 0.2 - - - -
44J THR* 1.3 73.8 - - - +
46J ALA* 1.3 61.0 + - - +
48J LEU* 3.2 6.0 + - - -
49J GLY 3.1 5.9 + - - -
50J GLN* 2.9 33.7 + - + +
51J GLN* 3.8 12.6 - - + -
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Residues in contact with ALA 46 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J ARG* 2.8 24.2 + - - +
42J PHE* 3.1 11.3 + - + +
43J VAL 3.5 8.3 - - - +
44J THR 3.2 0.4 - - - -
45J ALA* 1.3 73.5 - - - +
47J LEU* 1.3 65.9 + - - +
49J GLY 3.0 3.6 + - - -
51J GLN* 3.4 30.2 - - + +
53J LEU* 3.6 35.2 - - + +
75J LEU* 3.7 5.1 - - + +
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Residues in contact with LEU 47 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J ARG* 4.7 1.6 + - - +
14J LEU* 5.5 0.7 - - - +
15J ALA* 3.3 23.9 + - - +
18J ILE* 3.9 35.4 - - + +
29J PHE* 4.0 28.9 - - + -
32J ILE* 3.9 28.0 - - + -
43J VAL* 3.0 22.1 + - + +
44J THR* 3.1 8.3 + - - +
46J ALA* 1.3 75.6 - - - +
48J LEU* 1.3 65.3 + - + +
49J GLY* 3.3 2.4 + - - -
53J LEU* 4.8 2.9 - - + -
61J VAL* 3.9 29.4 - - + -
65J LEU* 4.2 8.1 - - + -
75J LEU* 4.2 9.8 - - + +
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Residues in contact with LEU 48 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 4.0 26.4 - - + +
106I THR* 3.6 45.8 + - - +
107I THR* 3.9 3.6 - - - +
110I ALA* 4.2 6.5 - - + -
12J LEU* 3.5 12.7 - - - +
15J ALA* 3.9 9.6 - - + -
18J ILE* 6.1 0.2 - - + -
19J LEU* 4.1 28.0 - - + -
29J PHE* 4.8 3.6 - - + -
44J THR* 2.9 37.2 + - + +
45J ALA* 3.4 9.0 - - - +
46J ALA 3.1 0.4 - - - -
47J LEU* 1.3 82.4 - - + +
49J GLY* 1.3 53.8 + - - +
50J GLN* 3.4 18.1 + - + +
83J CYS* 5.5 0.2 - - - +
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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