Contacts of the helix formed by residues 52 - 63 (chain A) in PDB entry 1M9H
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A VAL* 3.0 35.8 + - - +
23A LYS 5.2 0.2 - - - +
24A VAL 3.0 17.2 + - - -
26A PRO* 3.8 12.6 - - + -
29A THR* 3.2 23.4 + - - +
46A THR* 2.9 21.0 + - - -
47A ALA 4.6 0.4 + - - -
50A TYR* 3.4 17.5 + - - +
51A GLY* 1.3 79.7 - - - +
53A GLU* 1.3 65.7 + - - +
54A GLU* 3.2 4.1 + - - +
55A GLY 3.3 5.1 + - - +
56A VAL* 3.3 18.9 + - - +
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Residues in contact with GLU 53 (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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46A THR* 3.8 25.6 - - + +
47A ALA 3.9 3.4 - - - +
48A ALA* 3.4 24.2 + - - +
51A GLY* 3.8 1.9 - - - -
52A ASN* 1.3 78.1 + - - +
54A GLU* 1.3 57.6 + - - +
56A VAL* 3.2 2.8 + - - -
57A GLY* 2.9 25.6 + - - -
74A THR* 2.5 25.0 + - - -
93A SER* 2.9 29.6 + - - -
96A LYS* 3.4 38.4 + - + +
97A LEU* 3.3 21.6 - - + +
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Residues in contact with GLU 54 (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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51A GLY 6.1 0.2 - - - +
52A ASN* 3.2 1.3 - - - -
53A GLU* 1.3 77.9 - - - +
55A GLY* 1.3 52.8 + - - +
57A GLY* 3.2 1.7 + - - -
58A ALA* 2.7 37.4 + - - +
96A LYS* 3.3 45.9 - - + +
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Residues in contact with GLY 55 (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 PRO 4.9 5.5 + - - -
29A THR* 4.2 5.4 - - - -
30A GLN* 3.5 31.4 - - - +
52A ASN* 3.3 8.9 + - - +
53A GLU 3.3 0.4 - - - -
54A GLU* 1.3 78.8 - - - +
56A VAL* 1.3 52.8 + - - +
58A ALA* 3.2 3.0 + - - -
59A ALA* 2.8 35.5 + - - +
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Residues in contact with VAL 56 (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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21A VAL* 4.1 18.6 - - + -
29A THR* 3.8 13.9 - - + +
33A VAL* 4.1 14.5 - - + +
44A ILE* 3.8 23.1 - - + -
46A THR* 4.1 13.0 - - + -
52A ASN 3.3 14.1 + - - +
53A GLU 3.2 8.2 + - - +
55A GLY* 1.3 74.3 - - - +
57A GLY* 1.3 60.0 + - - +
59A ALA* 3.1 2.8 + - - +
60A ILE* 2.8 51.2 + - + +
72A ILE* 4.9 2.7 - - + -
97A LEU* 3.9 12.8 - - + -
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Residues in contact with GLY 57 (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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53A GLU 2.9 13.2 + - - -
54A GLU 3.6 3.1 - - - -
56A VAL* 1.3 77.0 - - - +
58A ALA* 1.3 62.8 + - - +
60A ILE* 3.3 9.6 + - - +
61A ALA* 3.0 25.3 + - - +
96A LYS 4.5 0.7 - - - -
97A LEU* 3.2 31.4 - - - +
98A ALA* 5.5 2.8 - - - +
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Residues in contact with ALA 58 (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 GLN* 3.5 27.4 - - - +
54A GLU 2.7 21.0 + - - +
55A GLY* 3.6 5.4 - - - +
57A GLY* 1.3 74.1 - - - +
59A ALA* 1.3 56.0 + - - +
61A ALA* 3.5 5.4 + - - +
62A ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 59 (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 GLN* 3.5 23.0 - - - +
33A VAL* 3.4 37.5 - - + -
34A GLU* 3.7 12.1 - - + +
37A LEU* 3.9 3.8 - - - +
55A GLY 2.8 20.4 + - - +
56A VAL 3.1 0.9 + - - +
58A ALA* 1.3 68.9 - - - +
60A ILE* 1.3 60.2 + - - +
62A ALA* 3.2 2.8 + - - +
63A SER* 2.9 28.8 + - - -
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Residues in contact with ILE 60 (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 VAL* 5.2 2.7 - - + -
37A LEU* 4.2 9.0 - - + -
44A ILE* 5.5 2.0 - - + -
56A VAL* 2.8 32.5 + - + +
57A GLY* 3.4 10.3 - - - +
59A ALA* 1.3 75.9 - - - +
61A ALA* 1.3 60.1 + - - +
63A SER* 2.5 35.9 + - - +
65A ILE 4.9 4.6 - - - +
67A ARG* 5.6 2.2 - - - -
70A LEU* 3.7 26.5 - - + -
72A ILE* 3.7 29.2 - - + -
97A LEU* 5.2 0.2 - - + -
99A LEU* 4.1 31.9 - - + -
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLY 3.0 13.3 + - - +
58A ALA* 3.8 6.7 - - - +
60A ILE* 1.3 81.1 - - - +
62A ALA* 1.3 63.8 + - - +
63A SER 3.0 7.8 - - - +
64A GLY* 5.0 0.2 - - - -
98A ALA* 6.3 2.9 - - + -
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Residues in contact with ALA 62 (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 GLN* 4.0 4.0 - - - +
34A GLU* 2.9 30.5 - - - +
58A ALA 2.9 16.3 + - - +
59A ALA 3.5 2.9 - - - +
60A ILE 3.1 0.2 - - - -
61A ALA* 1.3 76.8 - - - +
63A SER* 1.3 63.1 + - - +
64A GLY* 3.6 1.4 + - - -
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Residues in contact with SER 63 (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 GLU* 5.4 2.4 - - - +
37A LEU* 3.5 28.7 - - - +
59A ALA 2.9 7.0 + - - -
60A ILE* 2.5 30.1 + - - +
61A ALA 3.0 9.8 - - - +
62A ALA* 1.3 75.7 - - - +
64A GLY* 1.3 63.6 + - - +
65A ILE* 3.4 30.3 + - - +
70A LEU* 4.9 0.2 - - - +
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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