Contacts of the helix formed by residues 30 - 45 (chain B) in PDB entry 1MJO
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 LEU 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A GLU 4.3 11.7 - - - +
20A GLN* 3.0 16.3 + - + +
22A LYS* 3.6 47.1 - - + +
28B ILE 3.5 1.2 + - - -
29B PRO* 1.3 71.8 - - - +
31B LYS* 1.3 64.7 + - - +
33B LEU* 3.1 11.8 + - + +
34B LYS* 2.9 27.5 + - + +
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Residues in contact with LYS 31 (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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8A ILE* 5.0 17.9 - - + -
9A SER 5.5 2.0 - - - +
29B PRO* 3.2 4.8 - - + +
30B LEU* 1.3 80.1 - - - +
32B VAL* 1.3 67.8 - - + +
34B LYS* 3.5 6.8 + - + +
35B ILE* 3.3 31.0 + - + +
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 5.3 0.9 - - + -
9A SER 4.0 17.5 - - - +
10A PRO* 4.4 4.0 - - + +
58A CYS* 4.4 13.9 - - + +
61A PHE* 4.0 21.7 - - + -
62A LEU* 4.2 20.6 - - + -
28B ILE* 3.7 19.7 - - + -
29B PRO* 3.0 30.0 + - + +
31B LYS* 1.3 76.9 - - + +
33B LEU* 1.3 59.8 + - - +
35B ILE* 3.3 10.2 + - - +
36B LEU* 2.8 29.8 + - - +
57B LEU* 6.4 0.2 - - + -
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS* 3.7 34.8 - - + -
24A ILE* 3.7 26.0 - - + -
28B ILE* 3.5 22.6 - - + +
29B PRO 2.9 12.5 + - - +
30B LEU* 3.1 14.1 + - + +
32B VAL* 1.3 76.6 - - - +
34B LYS* 1.3 52.2 + - - +
36B LEU* 3.5 4.6 - - + +
37B THR* 2.7 53.3 + - - +
53B ASN* 4.0 13.2 - - - +
3F A 5.4 1.3 - - - +
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Residues in contact with LYS 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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30B LEU* 2.9 17.0 + - + +
31B LYS* 3.6 7.6 - - + +
33B LEU* 1.3 77.7 - - - +
35B ILE* 1.3 58.3 + - + +
37B THR* 3.3 5.0 + - - -
38B ASP* 2.8 73.9 + - - +
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Residues in contact with ILE 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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8A ILE* 4.1 29.8 - - + -
61A PHE* 3.6 13.4 - - + -
62A LEU* 4.2 15.5 - - + -
65A PHE* 3.5 38.9 - - + -
31B LYS* 3.3 22.0 + - + +
32B VAL 3.3 5.7 + - - +
34B LYS* 1.3 80.9 - - + +
36B LEU* 1.3 63.0 + - - +
38B ASP* 3.8 6.4 - - - +
39B GLU* 3.2 22.7 + - - +
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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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24A ILE* 4.3 2.7 - - + -
61A PHE* 3.4 37.2 - - + -
28B ILE* 4.0 20.4 - - + -
32B VAL 2.8 17.9 + - - +
33B LEU* 3.5 7.2 - - + +
35B ILE* 1.3 78.3 - - - +
37B THR* 1.3 56.9 + - - +
39B GLU* 3.2 5.2 + - - +
40B ARG 3.0 22.2 + - - -
53B ASN* 3.4 39.7 - - + +
56B LEU* 3.7 22.4 - - + +
57B LEU* 4.0 23.6 - - + -
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Residues in contact with THR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 2.7 37.3 + - - +
34B LYS* 3.7 5.4 - - - -
36B LEU* 1.3 71.5 - - - +
38B ASP* 1.3 62.6 + - - +
40B ARG* 3.2 23.4 + - - +
41B THR* 2.9 34.5 + - - +
53B ASN* 3.4 22.0 + - - -
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Residues in contact with ASP 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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65A PHE* 6.5 0.4 - - + -
34B LYS* 2.8 62.3 + - - +
35B ILE* 3.8 6.3 - - - +
37B THR* 1.3 76.9 - - - +
39B GLU* 1.3 58.8 + - - +
41B THR* 3.2 9.6 + - - +
42B ARG* 2.8 27.7 + - - +
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Residues in contact with GLU 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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61A PHE* 4.7 2.7 - - + -
65A PHE* 3.3 36.7 - - + -
35B ILE 3.2 11.7 + - - +
36B LEU 3.6 7.9 - - - +
38B ASP* 1.3 76.4 - - - +
40B ARG* 1.3 66.1 + - - +
42B ARG* 3.0 40.6 + - - +
43B ARG* 3.0 30.1 + - - +
56B LEU* 3.8 23.8 - - + -
200B SAM 3.0 25.6 + - - +
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Residues in contact with ARG 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 3.0 6.6 + - - +
37B THR* 3.2 28.8 + - - +
39B GLU* 1.3 76.7 - - - +
41B THR* 1.3 60.3 + - - +
43B ARG* 3.1 8.6 + - - +
44B LYS* 2.9 54.6 + - - +
51B ALA* 3.6 13.0 - - - +
52B THR* 3.8 2.2 - - - +
53B ASN* 3.2 42.6 + - - +
56B LEU* 3.6 11.6 - - + +
2F G 2.8 48.1 + - - -
3F A 4.9 4.9 + - - -
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Residues in contact with THR 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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37B THR* 2.9 22.0 + - - +
38B ASP* 3.4 13.1 + - - +
40B ARG* 1.3 80.7 + - - +
42B ARG* 1.3 56.9 + - - +
44B LYS* 3.0 14.9 + - + +
45B VAL* 2.8 42.2 + - + +
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Residues in contact with ARG 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 ASP 2.8 13.6 + - - +
39B GLU* 3.0 45.2 + - - +
41B THR* 1.3 77.8 - - - +
43B ARG* 1.3 65.2 + - - +
45B VAL* 3.5 4.4 + - - -
46B ASN* 2.8 46.1 + - - +
48B LEU* 4.2 11.8 - - - +
73B ASP* 2.9 41.2 + - - -
76B LEU* 5.6 0.6 - - - +
200B SAM 3.7 11.2 + - - -
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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 GLU* 3.0 24.6 + - - +
40B ARG 3.4 8.1 - - - +
42B ARG* 1.3 79.6 - - - +
44B LYS* 1.3 62.0 + - - +
46B ASN 3.6 0.3 + - - -
47B ASN 3.2 2.9 + - - -
48B LEU* 2.9 53.4 + - + +
49B ARG 4.0 5.8 - - - -
50B HIS* 2.8 41.3 + - - +
51B ALA* 3.7 13.9 - - + +
56B LEU* 3.3 25.3 - - - +
59B GLU* 2.8 41.0 + - - -
71B PRO* 3.9 2.2 - - - +
76B LEU* 3.5 20.5 - - - +
200B SAM 3.0 28.7 + - - -
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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 ARG* 2.9 44.0 + - + +
41B THR* 3.0 16.1 + - + +
43B ARG* 1.3 77.3 - - - +
45B VAL* 1.3 65.0 + - + +
47B ASN* 3.0 20.9 + - - +
48B LEU 5.3 0.2 - - - -
51B ALA* 3.0 29.7 + - + +
52B THR* 5.2 2.4 - - - +
2F G 5.3 1.2 + - - -
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Residues in contact with VAL 45 (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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41B THR* 2.8 38.3 + - + +
42B ARG* 3.9 3.1 - - - +
44B LYS* 1.3 73.4 - - + +
46B ASN* 1.3 70.1 + - - +
47B ASN* 3.1 7.1 + - - +
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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
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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