Contacts of the helix formed by residues 30 - 45 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C GLU 3.2 27.8 - - - +
20C GLN* 2.7 22.8 + - + +
22C LYS* 3.4 33.0 - - + +
28D ILE 3.4 3.3 + - - -
29D PRO* 1.3 69.8 - - - +
31D LYS* 1.3 57.3 + - - +
33D LEU* 3.2 9.8 + - + +
34D LYS* 2.9 31.2 + - - +
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Residues in contact with LYS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 3.6 33.8 - - + +
9C SER* 4.4 10.6 + - - +
104C TYR* 3.7 22.6 + - - +
29D PRO* 3.0 4.2 + - + -
30D LEU* 1.3 78.6 - - - +
32D VAL* 1.3 64.7 + - + +
34D LYS* 3.5 7.0 - - - +
35D ILE* 3.3 30.5 + - + +
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Residues in contact with VAL 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C SER 4.2 17.0 - - - +
10C PRO* 4.3 6.1 - - + +
58C CYS* 4.5 13.7 - - + +
61C PHE* 4.1 12.9 - - + -
62C LEU* 4.0 30.1 - - + -
28D ILE* 3.9 19.5 - - + -
29D PRO* 2.8 35.8 + - + +
31D LYS* 1.3 73.7 - - + +
33D LEU* 1.3 63.7 + - - +
35D ILE* 3.3 10.6 + - - +
36D LEU* 3.0 21.3 + - - +
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Residues in contact with LEU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LYS* 4.1 28.5 - - + -
24C ILE* 3.8 27.4 - - + -
28D ILE* 3.7 20.8 - - + +
29D PRO 3.0 10.3 + - - +
30D LEU* 3.6 12.1 - - + +
32D VAL* 1.3 73.0 - - - +
34D LYS* 1.3 60.5 + - - +
36D LEU* 4.1 10.8 - - + -
37D THR* 2.8 50.6 + - - +
53D ASN* 4.0 10.5 - - - +
3G A 5.4 0.2 - - - +
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Residues in contact with LYS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU 2.9 17.0 + - - +
31D LYS* 3.5 8.5 - - - +
33D LEU* 1.3 76.8 - - - +
35D ILE* 1.3 71.2 + - + +
37D THR* 3.8 4.2 - - - -
38D ASP* 2.6 61.5 + - - +
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Residues in contact with ILE 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 4.4 16.4 - - + -
61C PHE* 3.7 11.7 - - + -
62C LEU* 4.2 20.4 - - + -
65C PHE* 3.5 40.9 - - + -
31D LYS* 3.3 29.4 - - + +
32D VAL* 3.6 5.6 - - - +
34D LYS* 1.3 85.6 - - + +
36D LEU* 1.3 56.7 + - - +
38D ASP* 3.7 6.7 - - - +
39D GLU* 3.1 26.9 + - - +
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Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 4.4 2.0 - - + -
61C PHE* 3.3 40.1 - - + -
28D ILE* 4.0 22.9 - - + -
32D VAL 3.0 16.3 + - - +
33D LEU* 3.7 7.0 - - + +
35D ILE* 1.3 72.9 - - - +
37D THR* 1.3 61.0 + - - +
39D GLU* 3.2 4.3 + - - +
40D ARG 3.0 22.0 + - - -
53D ASN* 3.3 43.9 - - + +
56D LEU* 3.6 26.6 - - + +
57D LEU* 3.9 20.0 - - + -
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Residues in contact with THR 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 2.8 33.6 + - - +
34D LYS* 3.9 3.8 - - - -
36D LEU* 1.3 73.6 - - - +
38D ASP* 1.3 60.6 + - - +
40D ARG* 3.3 28.4 + - - +
41D THR* 2.9 35.7 + - - +
53D ASN* 3.3 23.4 + - - -
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Residues in contact with ASP 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LYS* 2.6 58.3 + - - +
35D ILE* 3.7 6.7 - - - +
37D THR* 1.3 79.0 - - - +
39D GLU* 1.3 61.3 + - - +
41D THR* 3.4 11.0 + - - +
42D ARG* 3.0 25.1 + - - +
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Residues in contact with GLU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C PHE* 4.7 1.3 - - + -
65C PHE* 3.7 27.6 - - + -
200C SAM 2.9 33.3 + - + +
35D ILE 3.1 17.0 + - - +
36D LEU* 3.2 7.2 + - - +
38D ASP* 1.3 76.3 - - - +
40D ARG* 1.3 64.0 + - - +
42D ARG* 3.0 35.4 + - - +
43D ARG* 3.1 28.0 + - - +
56D LEU* 3.8 24.7 - - + -
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Residues in contact with ARG 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU 3.0 6.0 + - - +
37D THR* 3.5 28.3 + - - +
38D ASP 3.3 0.2 - - - -
39D GLU* 1.3 73.6 - - - +
41D THR* 1.3 69.8 + - - +
43D ARG* 3.2 6.8 + - - +
44D LYS* 3.0 45.5 + - - +
51D ALA 3.3 21.5 - - - +
52D THR* 3.7 3.8 - - - +
53D ASN* 3.2 44.2 - - - +
56D LEU* 3.7 10.9 - - + +
2G G 3.0 42.1 + - - -
3G A 5.0 3.0 + - - -
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Residues in contact with THR 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D THR* 2.9 28.6 + - - +
38D ASP* 3.4 12.9 + - - +
39D GLU 3.2 0.2 - - - -
40D ARG* 1.3 80.7 + - - +
42D ARG* 1.3 56.7 + - - +
44D LYS* 3.3 11.4 + - - +
45D VAL* 2.9 41.4 + - + +
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Residues in contact with ARG 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C SAM 3.6 11.8 + - - -
38D ASP 3.0 13.6 + - - +
39D GLU* 3.0 44.5 + - - +
40D ARG 3.2 0.4 - - - -
41D THR* 1.3 78.2 - - - +
43D ARG* 1.3 67.7 + - - +
45D VAL* 3.1 7.9 + - + +
46D ASN* 3.0 44.1 + - - +
48D LEU* 4.5 8.2 - - - +
73D ASP* 2.9 42.4 + - - -
76D LEU* 5.4 0.4 - - - +
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Residues in contact with ARG 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200C SAM 3.0 24.7 + - - -
39D GLU* 3.1 27.9 + - - +
40D ARG 3.6 6.1 - - - +
42D ARG* 1.3 77.8 - - - +
44D LYS* 1.3 61.8 + - - +
46D ASN 3.4 0.7 + - - -
47D ASN 3.1 3.5 + - - -
48D LEU* 2.8 46.1 + - + +
49D ARG 4.1 1.8 - - - -
50D HIS* 2.9 33.1 + - - +
51D ALA* 3.8 13.5 - - + +
56D LEU* 3.4 27.6 - - - +
59D GLU* 2.8 41.6 + - - -
71D PRO* 4.0 3.2 - - - +
76D LEU* 3.2 32.8 - - + +
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Residues in contact with LYS 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ARG* 3.0 43.3 + - - +
41D THR* 3.5 11.2 - - - +
43D ARG* 1.3 76.5 - - - +
45D VAL* 1.3 57.3 + - + +
47D ASN* 2.8 30.5 + - - +
48D LEU 4.9 0.4 - - - +
51D ALA* 3.4 37.0 + - + +
52D THR* 5.4 1.8 - - - +
2G G 5.3 1.2 + - - -
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Residues in contact with VAL 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D THR* 2.9 32.7 + - + +
42D ARG* 3.5 7.2 - - + +
44D LYS* 1.3 77.2 - - + +
46D ASN* 1.3 73.5 + - - +
47D ASN* 3.3 10.9 + - - -
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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