Contacts of the helix formed by residues 29 - 44 (chain B) in PDB entry 3IMO
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 VAL 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ALA* 4.5 6.3 - - + -
26B ALA* 3.5 16.6 - - + +
27B GLY 3.1 0.2 - - - -
28B ASN* 1.3 84.5 - - - +
30B GLU* 1.3 66.9 + - - +
32B ILE* 3.5 6.0 + - + +
33B ALA* 3.1 24.3 + - + +
75B TYR* 3.8 24.5 - - + -
80B GLU 3.4 22.7 - - - +
82B ILE* 3.8 26.0 - - + +
97B PHE 3.9 18.2 - - - +
98B ASP* 3.9 1.3 - - + -
99B ASN* 3.2 7.4 - - - -
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B MET* 3.5 49.8 - - + +
22B ALA* 3.9 24.2 - - + -
23B ASP* 3.8 19.0 - - - +
26B ALA 3.8 1.2 + - - -
27B GLY* 3.6 16.7 + - - +
29B VAL* 1.3 80.4 - - - +
31B GLU* 1.3 65.9 + - + +
33B ALA* 3.6 5.0 + - - +
34B LEU* 4.1 0.7 + - - +
99B ASN* 3.4 2.3 + - - +
42D TRP* 4.9 1.2 - - - -
107D VAL* 4.6 12.1 - - + +
111D LYS* 3.1 38.3 + - - +
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLU* 1.3 80.2 - - + +
32B ILE* 1.3 63.6 + - - +
33B ALA 3.1 0.9 + - - -
34B LEU* 3.2 19.2 + - - +
35B ALA 4.0 0.3 + - - -
99B ASN* 2.9 36.6 + - + +
103D LEU* 3.3 29.8 - - + +
104D SER* 3.0 40.4 + - - -
107D VAL* 3.9 27.1 - - + -
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Residues in contact with ILE 32 (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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29B VAL* 3.6 12.1 - - - +
31B GLU* 1.3 78.9 - - - +
33B ALA* 1.3 58.7 + - - +
35B ALA* 3.2 2.5 + - - +
36B LEU* 2.9 29.4 + - + +
82B ILE* 4.2 13.9 - - + -
97B PHE* 4.2 10.8 - - + -
98B ASP* 3.3 41.3 - - - +
99B ASN* 3.2 5.9 + - - +
101B THR* 3.5 32.3 - - - +
103B LEU* 4.1 15.5 - - + -
106B LEU* 3.8 27.1 - - + -
103D LEU* 3.9 6.9 - - + +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 4.3 18.8 - - + -
19B MET* 4.1 12.6 - - - -
22B ALA* 5.8 0.7 - - + -
29B VAL* 3.1 20.2 + - + +
30B GLU* 3.6 9.2 - - - +
31B GLU 3.1 0.6 - - - -
32B ILE* 1.3 79.6 - - - +
34B LEU* 1.3 57.2 + - - +
36B LEU* 3.4 7.5 + - - +
37B ALA* 3.0 27.0 + - - +
82B ILE* 4.5 11.4 - - + -
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Residues in contact with LEU 34 (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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15B ILE* 4.5 4.9 - - + -
19B MET* 3.5 35.0 - - + -
31B GLU 3.2 7.3 + - - +
32B ILE 3.2 0.4 - - - -
33B ALA* 1.3 78.2 - - - +
35B ALA* 1.3 64.0 + - - +
37B ALA* 3.3 8.0 + - - +
38B GLY 3.2 16.3 + - - -
34D LEU 3.6 1.7 - - - +
35D ALA* 4.0 15.7 - - + +
38D GLY* 3.4 28.7 - - - +
39D ALA* 3.9 20.0 - - + +
42D TRP* 3.9 22.0 - - + -
103D LEU* 5.9 0.4 - - + -
106D LEU* 5.1 4.3 - - + -
107D VAL* 3.7 31.2 - - + -
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Residues in contact with ALA 35 (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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31B GLU 4.0 0.8 + - - -
32B ILE* 3.2 11.6 + - + +
34B LEU* 1.3 75.3 - - - +
36B LEU* 1.3 60.8 + - - +
38B GLY* 3.2 1.6 + - - -
39B ALA* 2.9 28.8 + - - +
103B LEU* 3.5 31.9 - - + -
106B LEU* 4.0 13.7 - - + +
34D LEU* 4.1 6.7 - - + +
35D ALA* 3.9 23.2 - - + +
103D LEU* 4.6 2.9 - - + -
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Residues in contact with LEU 36 (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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32B ILE* 2.9 18.6 + - + +
33B ALA* 3.7 4.9 - - - +
35B ALA* 1.3 74.7 - - - +
37B ALA* 1.3 65.9 + - - +
39B ALA* 3.8 2.4 - - - +
40B ILE* 2.9 37.9 + - + +
73B PHE* 4.2 9.6 - - + -
82B ILE* 3.8 43.3 - - + -
97B PHE* 3.9 30.7 - - + -
106B LEU* 4.1 13.0 - - + -
110B PHE* 3.7 33.7 - - + -
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Residues in contact with ALA 37 (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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11B LEU* 6.3 0.2 - - + -
15B ILE* 4.1 27.1 - - + -
33B ALA 3.0 13.4 + - - +
34B LEU* 3.3 11.2 - - - +
36B LEU* 1.3 76.5 - - - +
38B GLY* 1.3 62.5 + - - +
40B ILE* 3.9 6.1 - - - +
41B LEU* 3.1 33.2 + - + +
38D GLY* 4.0 13.2 - - - -
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Residues in contact with GLY 38 (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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34B LEU 3.2 8.1 + - - -
35B ALA 3.2 0.6 + - - -
37B ALA* 1.3 79.9 - - - +
39B ALA* 1.3 57.2 + - - +
41B LEU* 3.3 7.3 + - - +
42B TRP* 2.8 29.8 + - - +
15D ILE* 4.3 2.6 - - - +
34D LEU* 3.5 27.7 - - - +
37D ALA* 4.1 15.9 - - - -
38D GLY 4.4 1.1 - - - +
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Residues in contact with ALA 39 (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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35B ALA 2.9 17.1 + - - +
36B LEU* 3.8 3.4 - - - +
38B GLY* 1.3 77.9 - - - +
40B ILE* 1.3 61.8 + - - +
42B TRP* 3.3 9.1 - - - +
43B ARG* 3.2 18.7 + - - +
106B LEU* 3.7 17.9 - - + -
110B PHE* 3.5 38.6 - - + -
34D LEU* 3.9 12.9 - - + +
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Residues in contact with ILE 40 (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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36B LEU* 2.9 29.3 + - + +
37B ALA* 3.9 4.7 - - - +
39B ALA* 1.3 74.3 - - - +
41B LEU* 1.3 66.2 + - + +
43B ARG* 3.4 0.3 + - - +
44B LYS* 3.0 25.3 + - - +
49B ILE* 4.2 17.0 - - + -
62B LEU* 4.5 12.8 - - + -
64B VAL* 4.0 29.8 - - + +
66B ILE* 5.0 2.8 - - - +
73B PHE* 3.8 47.3 - - + -
110B PHE* 3.9 11.9 - - + -
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Residues in contact with LEU 41 (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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11B LEU* 3.7 28.9 - - + -
37B ALA* 3.1 25.3 + - + +
38B GLY* 3.7 4.5 - - - +
40B ILE* 1.3 76.3 - - + +
42B TRP* 1.3 63.3 + - - +
44B LYS* 3.7 6.1 - - + +
49B ILE* 4.3 17.9 - - + -
8D VAL* 4.0 21.3 - - + -
11D LEU* 4.3 7.0 - - + -
12D SER* 2.7 34.5 + - - +
15D ILE* 3.8 15.5 - - + -
41D LEU* 3.2 35.2 - - + -
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Residues in contact with TRP 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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38B GLY 2.8 18.0 + - - +
39B ALA* 3.3 7.2 - - - +
41B LEU* 1.3 80.4 - - - +
43B ARG* 1.3 82.9 + - + +
44B LYS 3.9 1.9 + - - +
107B VAL* 4.2 7.0 - - + -
110B PHE* 4.0 11.2 - - + -
111B LYS* 3.8 52.5 - - + -
12D SER* 4.4 1.2 - - - +
15D ILE* 3.8 15.2 - - + +
16D SER* 3.1 40.6 + - - +
19D MET* 3.6 47.0 - - + +
30D GLU* 5.6 0.4 - - - -
34D LEU* 3.9 23.6 - - + -
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Residues in contact with ARG 43 (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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39B ALA 3.2 13.3 + - - +
42B TRP* 1.3 118.8 + - + +
44B LYS* 1.3 66.7 + - - +
45B ASP* 3.6 1.2 + - - -
66B ILE* 3.6 42.0 - - + +
67B ASN* 4.5 10.9 + - - +
110B PHE* 2.8 43.2 + - + +
111B LYS* 3.6 10.1 + - - +
113B LEU* 3.1 28.5 + - - +
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Residues in contact with LYS 44 (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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40B ILE 3.0 19.6 + - - +
41B LEU* 3.7 5.7 - - - +
42B TRP 3.6 2.1 - - - +
43B ARG* 1.3 80.3 - - - +
45B ASP* 1.3 81.7 + - - +
46B ASP* 5.3 0.3 - - - +
47B THR 2.9 21.9 + - - -
48B ASN* 4.6 2.8 + - - +
49B ILE* 3.7 33.4 - - + +
64B VAL* 3.4 16.8 - - + -
65B THR 3.5 6.5 - - - -
66B ILE* 3.9 3.8 - - - +
8D VAL* 4.1 17.3 - - + +
9D ASN* 3.5 19.2 + - - -
12D SER* 3.5 29.0 + - - +
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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