Contacts of the helix formed by residues 30 - 45 (chain A) in PDB entry 1MJP
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PRO* 1.3 67.2 - - - +
31A LYS* 1.3 52.8 - - - +
33A LEU* 2.7 17.5 + - + +
34A LYS* 2.6 35.7 + - - +
19B GLU 4.5 6.3 - - - +
20B GLN* 2.9 27.5 + - - +
21B VAL 4.1 2.2 - - - +
22B LYS* 3.6 37.5 - - + +
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PRO* 4.6 4.0 - - + +
30A LEU* 1.3 77.1 - - - +
32A VAL* 1.3 63.3 + - + +
34A LYS* 3.6 8.0 - - - +
35A ILE* 3.3 29.8 + - + +
8B ILE* 4.4 24.5 - - + +
9B SER 5.5 3.4 - - - +
104B TYR* 4.3 25.1 + - - +
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 4.0 13.9 - - + -
29A PRO* 2.7 39.8 + - + +
31A LYS* 1.3 70.6 - - + +
33A LEU* 1.3 67.9 + - - +
35A ILE* 3.1 8.4 + - - +
36A LEU* 2.7 21.1 + - + +
8B ILE* 4.8 4.5 - - + -
9B SER 3.9 15.9 - - - +
10B PRO* 4.3 3.1 - - + -
58B CYS* 4.7 10.8 - - - +
61B PHE* 3.6 28.5 - - + -
62B LEU* 4.1 20.6 - - + -
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 3.2 27.5 - - + +
29A PRO 2.9 6.1 + - - +
30A LEU* 2.7 18.1 + - + +
32A VAL* 1.3 75.5 - - - +
34A LYS* 1.3 57.8 + - - +
36A LEU* 2.7 16.5 + - + -
37A THR* 2.6 57.5 + - - +
53A ASN* 4.5 4.9 - - - +
22B LYS* 4.8 29.6 - - + -
24B ILE* 4.6 17.0 - - + -
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU 2.6 18.8 + - - +
31A LYS* 3.6 10.1 - - - +
33A LEU* 1.3 72.5 - - - +
35A ILE* 1.3 63.0 + - + +
37A THR* 3.3 5.1 + - - -
38A ASP* 2.6 66.5 + - - +
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Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LYS* 3.3 16.1 + - + +
32A VAL* 3.1 8.8 + - - +
34A LYS* 1.3 83.7 - - + +
36A LEU* 1.3 67.2 + - - +
38A ASP* 3.4 8.2 + - - +
39A GLU* 3.4 15.2 + - - +
8B ILE* 3.5 33.4 - - + -
61B PHE* 3.8 21.4 - - + -
62B LEU* 4.8 2.2 - - + -
65B PHE* 3.9 29.5 - - + -
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 4.9 7.6 - - + -
32A VAL 2.7 12.5 + - - +
33A LEU* 2.7 25.5 + - + +
35A ILE* 1.3 70.0 - - - +
37A THR* 1.3 54.2 + - - +
38A ASP 2.7 12.8 + - - -
39A GLU* 2.7 19.9 + - - +
40A ARG 3.3 6.2 + - - -
53A ASN* 3.6 33.4 - - + +
56A LEU* 3.8 20.5 - - + +
57A LEU* 3.7 30.1 - - + -
24B ILE* 5.3 2.7 - - + -
61B PHE* 3.3 41.9 - - + -
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Residues in contact with THR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 2.6 33.9 + - - +
34A LYS* 3.8 4.9 - - - +
36A LEU* 1.3 74.4 - - - +
38A ASP* 1.3 58.5 + - - +
39A GLU 3.3 0.2 - - - -
40A ARG* 3.3 24.9 + - - +
41A THR* 3.0 29.2 + - - +
53A ASN* 3.1 29.9 + - - -
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LYS* 2.6 53.3 + - - +
35A ILE* 3.5 8.9 - - - +
36A LEU 2.7 5.1 + - - -
37A THR* 1.3 73.8 - - - +
39A GLU* 1.3 58.9 + - - +
41A THR* 3.4 13.5 + - - -
42A ARG* 3.0 21.5 + - - +
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Residues in contact with GLU 39 (chain A).
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 3.4 6.8 + - - +
36A LEU* 2.7 14.3 + - - +
38A ASP* 1.3 72.7 - - - +
40A ARG* 1.3 60.7 + - - +
41A THR 3.2 0.2 - - - -
42A ARG* 2.7 51.3 + - - +
43A ARG* 2.8 44.6 + - + +
56A LEU* 3.3 24.9 - - + +
61B PHE* 5.5 2.0 - - + -
65B PHE* 3.7 31.7 - - + -
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Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU 3.3 2.4 + - - -
37A THR* 3.3 28.4 + - - +
39A GLU* 1.3 77.4 - - - +
41A THR* 1.3 66.5 + - - +
43A ARG* 3.2 6.8 + - - +
44A LYS* 2.9 43.3 + - + +
51A ALA* 3.1 28.0 - - - +
52A THR* 3.7 1.6 - - - +
53A ASN* 2.9 49.8 + - - +
56A LEU* 3.8 12.3 - - + +
2D G 2.8 33.1 + - - -
3D A 5.4 4.2 + - - -
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Residues in contact with THR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A THR* 3.0 19.9 + - - +
38A ASP* 3.4 18.7 + - - +
40A ARG* 1.3 76.8 + - - +
42A ARG* 1.3 57.6 + - - +
44A LYS* 3.1 10.0 + - + +
45A VAL* 2.7 49.7 + - + +
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP 3.0 14.3 + - - +
39A GLU* 2.7 52.7 + - - +
41A THR* 1.3 78.1 - - - +
43A ARG* 1.3 66.4 + - - +
44A LYS 3.3 0.5 + - - -
45A VAL* 3.9 5.8 - - + -
46A ASN* 3.3 39.8 + - - +
48A LEU* 4.7 5.9 - - - +
73A ASP* 3.5 30.7 + - - -
76A LEU* 5.9 1.2 - - - +
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Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLU* 2.8 38.9 + - - +
40A ARG 3.2 1.1 + - - +
42A ARG* 1.3 77.4 - - - +
44A LYS* 1.3 59.1 + - - +
46A ASN 4.0 0.2 - - - -
47A ASN 3.7 1.7 + - - -
48A LEU* 2.9 49.1 + - + +
49A ARG 4.2 0.7 - - - -
50A HIS* 2.6 46.2 + - - +
51A ALA* 3.3 18.4 - - + +
56A LEU* 3.0 33.5 - - - +
59A GLU* 2.6 39.0 + - - -
71A PRO* 4.5 7.5 + - - +
76A LEU* 3.3 29.3 - - + +
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Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG* 2.9 33.8 + - + +
41A THR* 3.3 9.0 - - - +
43A ARG* 1.3 75.9 - - - +
45A VAL* 1.3 59.9 + - + +
46A ASN 3.1 8.6 + - - -
47A ASN* 3.6 11.6 + - - -
48A LEU 5.5 0.2 - - - -
51A ALA* 3.9 28.8 + - + +
52A THR* 5.6 3.6 - - - +
78A LYS* 5.8 1.2 + - - -
2D G 5.9 0.2 + - - -
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A THR* 2.7 43.2 + - + +
42A ARG* 3.7 9.2 - - + +
44A LYS* 1.3 74.7 - - + +
46A ASN* 1.3 71.0 + - - +
47A ASN 3.7 0.9 - - - -
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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