Contacts of the helix formed by residues 53 - 66 (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 ASN 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ILE* 5.1 8.0 - - + +
26A VAL* 5.7 0.9 - - + -
33B LEU* 4.0 8.5 - - - +
36B LEU* 3.4 38.7 - - + +
37B THR* 3.4 21.5 + - - -
40B ARG* 3.2 43.4 + - - +
52B THR* 1.3 71.7 - - - +
54B SER* 1.3 63.2 + - - +
56B LEU* 3.3 2.6 + - - +
57B LEU* 3.0 30.8 + - + +
2F G 3.0 16.4 + - - +
3F A 5.0 5.5 + - - -
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Residues in contact with SER 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR 4.2 1.2 + - - -
26A VAL* 3.5 17.8 - - - +
27A SER* 2.9 46.5 + - - -
52B THR* 4.0 4.3 - - - -
53B ASN* 1.3 77.2 - - - +
55B GLU* 1.3 58.9 + - - +
57B LEU* 3.3 3.3 + - - +
58B CYS* 3.0 33.9 + - - -
1F A 4.1 3.8 - - - -
2F G 2.6 22.5 + - - -
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Residues in contact with GLU 55 (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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10B PRO 5.7 0.7 - - - +
11B TYR* 3.8 25.9 - - + +
17B LYS* 4.9 12.9 + - - +
50B HIS* 2.9 53.3 + - + +
52B THR* 2.6 37.9 + - - +
54B SER* 1.3 76.5 - - - +
56B LEU* 1.3 60.1 + - - +
58B CYS* 3.9 6.0 - - + +
59B GLU* 2.9 37.7 + - - +
1F A 5.9 2.2 - - - -
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE* 4.7 2.5 - - + -
36B LEU* 3.7 26.2 - - + +
39B GLU* 3.8 17.3 - - + -
40B ARG* 3.6 36.3 - - + +
43B ARG* 3.3 42.2 - - - +
52B THR 3.1 18.6 + - - +
53B ASN 3.6 4.9 - - - +
55B GLU* 1.3 76.4 - - - +
57B LEU* 1.3 58.5 + - - +
59B GLU* 4.0 0.7 - - - -
60B ALA* 3.0 17.3 + - - +
200B SAM 2.9 40.0 + - + +
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 4.2 7.0 - - + -
26A VAL* 3.7 34.3 - - + -
57A LEU* 4.1 37.3 - - + +
58A CYS* 5.7 0.7 - - - -
61A PHE* 3.9 26.9 - - + -
26B VAL* 5.0 2.7 - - + -
28B ILE* 5.5 5.4 - - + -
36B LEU* 4.0 28.0 - - + -
53B ASN 3.0 19.5 + - - +
54B SER* 3.7 4.3 - - - +
56B LEU* 1.3 76.3 - - - +
58B CYS* 1.3 60.3 + - - +
60B ALA* 3.8 2.8 - - - +
61B PHE* 2.9 30.7 + - - +
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Residues in contact with CYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 5.2 2.9 - - - -
27A SER 3.7 18.4 - - - -
28A ILE* 3.8 26.7 - - - -
29A PRO* 3.8 10.3 - - - -
32A VAL* 4.7 7.0 - - + +
57A LEU* 5.7 1.3 - - - -
10B PRO* 3.5 23.3 - - + +
54B SER 3.0 21.8 + - - +
55B GLU* 3.4 6.7 + - - +
57B LEU* 1.3 72.9 - - - +
59B GLU* 1.3 65.8 + - - +
61B PHE* 3.4 4.8 + - - +
62B LEU* 3.2 29.3 + - - +
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Residues in contact with GLU 59 (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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10B PRO* 3.7 22.4 - - + -
11B TYR* 2.5 38.6 + - + +
43B ARG* 2.8 43.1 + - - -
50B HIS* 3.7 2.6 - - - +
55B GLU 2.9 23.4 + - - +
56B LEU* 4.0 0.2 - - - -
58B CYS* 1.3 77.6 - - - +
60B ALA* 1.3 61.8 + - - +
62B LEU* 3.5 2.1 + - - +
63B HIS* 3.0 24.1 + - - +
68B GLN* 5.4 0.9 - - - +
70B LEU* 3.9 7.9 - - + +
71B PRO* 3.9 11.7 - - + +
200B SAM 2.9 16.9 + - - +
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Residues in contact with ALA 60 (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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57A LEU 5.6 0.2 - - - +
60A ALA* 3.8 4.1 - - - +
61A PHE* 3.8 22.9 - - + +
64A ALA* 3.6 28.7 - - + -
56B LEU 3.0 20.1 + - - +
57B LEU* 3.8 4.7 - - - +
58B CYS 3.3 0.2 - - - -
59B GLU* 1.3 75.8 - - - +
61B PHE* 1.3 59.7 + - - +
63B HIS* 3.3 3.1 + - - +
64B ALA* 2.8 30.7 + - - +
70B LEU* 4.2 3.6 - - - -
200B SAM 3.7 4.5 + - - +
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Residues in contact with PHE 61 (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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32A VAL* 4.2 17.9 - - + -
35A ILE* 3.8 25.6 - - + -
36A LEU* 3.4 57.0 - - + -
39A GLU* 4.7 2.2 - - + -
56A LEU* 4.6 8.3 - - + -
57A LEU* 3.9 16.8 - - + -
60A ALA* 3.7 11.8 - - + +
199A SAM 3.5 28.9 - + - -
57B LEU 2.9 18.6 + - - +
58B CYS* 3.9 4.5 - - - +
59B GLU 3.3 0.2 - - - -
60B ALA* 1.3 77.1 - - - +
62B LEU* 1.3 59.3 + - + +
64B ALA* 3.1 3.5 + - - +
65B PHE* 2.7 47.3 + + + +
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Residues in contact with LEU 62 (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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32A VAL* 4.0 14.8 - - + -
35A ILE* 4.1 19.3 - - + -
8B ILE* 3.3 50.3 - - + +
9B SER 3.8 0.9 - - - +
10B PRO* 3.5 29.2 - - + -
58B CYS 3.2 10.5 + - - +
59B GLU* 4.0 3.1 - - - +
61B PHE* 1.3 88.3 - - + +
63B HIS* 1.3 59.1 + - - +
65B PHE* 4.3 2.5 - - + +
66B THR* 2.7 44.8 + - + -
68B GLN* 3.6 13.5 - - - +
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Residues in contact with HIS 63 (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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63A HIS* 3.5 15.6 + + - -
64A ALA* 4.0 8.1 - - + -
199A SAM 2.9 21.2 + - - -
59B GLU 3.0 18.9 + - - +
60B ALA 3.5 2.2 - - - +
62B LEU* 1.3 76.2 - - - +
64B ALA* 1.3 60.6 + - - +
67B GLY* 2.7 31.3 + - - -
68B GLN* 2.8 34.5 + - + +
69B PRO* 5.1 2.2 - - + -
70B LEU* 3.5 31.4 + - + +
200B SAM 2.8 52.5 + - - -
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Residues in contact with ALA 64 (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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60A ALA* 3.7 15.3 - - + -
63A HIS* 4.0 9.2 - - + -
70A LEU* 3.6 18.1 - - + +
199A SAM 3.2 54.7 + - + +
60B ALA 2.8 17.2 + - - +
61B PHE 3.4 3.8 - - - +
63B HIS* 1.3 79.2 - - - +
65B PHE* 1.3 60.8 + - - +
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Residues in contact with PHE 65 (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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35A ILE* 3.7 28.0 - - + -
39A GLU* 3.6 34.8 - - + -
199A SAM 3.4 59.6 + + + +
61B PHE* 2.7 34.9 + + + +
62B LEU* 4.1 3.8 - - + +
64B ALA* 1.3 74.3 - - - +
66B THR* 1.3 71.6 + - + +
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Residues in contact with THR 66 (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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199A SAM 4.5 2.6 - - - +
2B GLU 5.2 0.5 - - - +
3B TRP* 3.2 30.7 - - - +
4B SER 4.6 0.9 + - - -
6B GLU 5.7 1.1 - - - +
8B ILE* 4.3 23.6 - - + -
62B LEU* 2.7 31.9 + - + +
65B PHE* 1.3 90.8 - - + +
67B GLY* 1.3 57.7 + - - +
68B GLN* 3.1 27.0 + - - +
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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
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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