Contacts of the helix formed by residues 25 - 37 (chain A) in PDB entry 1MG8
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 ILE 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A THR 4.4 1.8 - - - +
24A SER* 1.3 92.9 - - - +
26A LEU* 1.3 60.4 + - - +
27A GLN 3.2 0.4 - - - -
28A LEU* 2.9 16.2 - - + +
29A LYS* 2.8 54.2 + - - +
45A VAL* 4.1 8.7 - - + +
52A LEU* 4.0 30.5 - - + +
53A PRO 3.5 21.8 - - - +
54A ASN* 3.9 1.7 + - - +
56A LEU* 3.7 12.0 + - + +
57A THR 4.5 2.2 - - - +
58A VAL* 4.7 1.6 - - + -
63A LEU* 3.7 31.6 - - + -
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Residues in contact with LEU 26 (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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25A ILE* 1.3 74.8 - - - +
27A GLN* 1.3 63.4 + - + +
28A LEU 2.9 1.1 - - - -
29A LYS* 2.6 31.0 + - + -
30A GLU* 2.6 34.1 + - + +
40A ALA* 3.1 32.1 - - + +
41A ASP* 4.9 1.6 - - - +
54A ASN* 3.3 39.2 + - + +
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Residues in contact with GLN 27 (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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23A THR* 4.2 18.2 - - + +
24A SER* 3.5 35.1 + - - +
25A ILE 3.9 0.2 - - - +
26A LEU* 1.3 89.8 - - + +
28A LEU* 1.3 60.8 + - - +
30A GLU* 3.1 18.3 + - + +
31A VAL* 3.2 21.0 + - - +
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Residues in contact with LEU 28 (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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5A VAL* 5.2 4.3 - - + -
7A VAL* 4.5 2.7 - - + -
17A VAL* 4.9 6.5 - - + -
19A VAL* 4.0 29.4 - - + -
23A THR* 4.6 13.0 - - + -
24A SER 3.7 5.3 + - - +
25A ILE* 2.9 33.0 - - + +
27A GLN* 1.3 82.4 - - - +
29A LYS* 1.3 58.2 + - - +
31A VAL* 3.6 2.9 + - + +
32A VAL* 3.1 32.9 + - + +
45A VAL* 2.9 36.1 - - + -
58A VAL* 5.0 3.4 - - + -
63A LEU* 6.3 1.6 - - + -
69A VAL* 5.7 3.4 - - + -
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Residues in contact with LYS 29 (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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25A ILE* 2.8 33.7 + - - +
26A LEU* 2.6 26.5 + - + +
28A LEU* 1.3 73.5 - - - +
30A GLU* 1.3 47.2 + - - -
33A ALA* 2.6 38.6 + - - +
40A ALA* 3.1 20.5 - - + +
43A LEU* 3.3 21.1 - - - +
44A ARG* 3.4 28.2 - - + +
45A VAL* 3.1 41.2 + - + +
46A ILE* 5.6 1.6 - - - +
52A LEU 4.1 6.1 + - - -
54A ASN* 3.1 25.3 + - - +
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Residues in contact with GLU 30 (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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26A LEU* 2.6 34.6 + - + +
27A GLN* 3.3 15.9 - - + +
28A LEU 3.1 0.4 - - - -
29A LYS* 1.3 73.3 - - - +
31A VAL* 1.3 55.1 + - + +
33A ALA* 3.0 2.5 + - - +
34A LYS* 2.7 54.5 + - + +
39A PRO* 5.5 0.7 - - - +
40A ALA* 3.5 20.9 + - + +
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Residues in contact with VAL 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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15A PHE* 4.1 5.6 - - + -
17A VAL* 3.1 35.7 - - + -
18A GLU 6.0 1.1 - - - +
19A VAL* 6.0 0.9 - - + -
23A THR* 6.0 4.9 - - + -
27A GLN* 3.2 18.4 + - - +
28A LEU* 4.2 5.2 - - + +
30A GLU* 1.3 78.8 - - + +
32A VAL* 1.3 65.9 + - + +
34A LYS* 2.9 28.4 + - + +
35A ARG* 3.3 18.6 + - - +
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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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7A VAL* 3.2 42.2 - - + -
9A PHE* 2.7 60.2 - - + -
15A PHE* 3.5 13.0 - - + -
17A VAL* 5.1 0.4 - - + -
28A LEU* 3.1 29.7 + - + +
29A LYS* 4.5 0.7 - - - -
31A VAL* 1.3 78.2 - - + +
33A ALA* 1.3 63.3 + - - +
36A GLN* 3.0 2.6 + - - +
43A LEU* 3.1 15.3 - - + -
45A VAL* 4.2 1.6 - - + -
71A ILE* 3.7 8.5 - - + -
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Residues in contact with ALA 33 (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 LYS 2.6 20.7 + - - +
30A GLU* 3.1 10.8 - - - +
31A VAL 3.0 0.2 - - - -
32A VAL* 1.3 80.0 - - - +
34A LYS* 1.3 62.7 + - + +
37A GLY* 3.1 2.4 + - - -
38A VAL 2.5 44.9 + - - +
39A PRO* 3.5 1.6 - - + -
40A ALA* 3.1 21.1 - - - +
43A LEU* 2.8 15.8 - - + +
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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 GLU* 2.7 42.0 + - + +
31A VAL* 2.9 20.2 + - + +
33A ALA* 1.3 79.6 - - + +
35A ARG* 1.3 76.0 + - - +
37A GLY* 3.2 12.6 + - - -
38A VAL 5.5 0.4 - - - +
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Residues in contact with ARG 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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9A PHE* 3.2 27.9 - - + -
13A TYR* 5.7 2.8 + - - -
15A PHE* 3.2 34.3 - - + -
16A PRO 4.8 4.2 + - - -
17A VAL* 5.5 3.6 - - - +
18A GLU 5.6 1.8 - - - +
31A VAL* 3.3 24.1 + - - +
32A VAL 3.4 0.2 + - - -
34A LYS* 1.3 92.4 - - - +
36A GLN* 1.3 60.2 + - - +
37A GLY 3.5 0.2 + - - -
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Residues in contact with GLN 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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9A PHE* 2.8 43.2 - - + +
10A ASN* 4.5 19.6 - - - +
32A VAL 3.0 9.7 + - - +
33A ALA 3.8 2.5 - - - +
34A LYS 3.1 0.4 - - - -
35A ARG* 1.3 78.8 - - - +
37A GLY* 1.3 59.1 + - - +
38A VAL* 2.9 37.1 - - + +
43A LEU* 3.3 23.9 - - + +
71A ILE* 4.3 3.7 - - - +
73A GLN* 3.7 12.2 + - - +
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Residues in contact with GLY 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 ALA 3.1 3.6 + - - -
34A LYS 3.2 7.9 + - - -
35A ARG 3.2 4.8 - - - -
36A GLN* 1.3 74.6 - - - +
38A VAL* 1.3 66.1 + - - +
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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