Contacts of the helix formed by residues 48 - 59 (chain A) in PDB entry 2M8L
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 THR 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A PRO* 4.3 2.7 - - + -
2A ILE* 3.8 23.3 - - + -
12A HIS* 2.6 43.5 + - + +
46A GLY 3.5 0.4 + - - -
47A ALA* 1.3 75.5 - - - +
49A PRO* 1.3 76.3 - - - +
50A GLN* 3.4 4.5 + - - -
51A ASP* 3.0 16.5 + - - +
52A LEU* 3.0 20.6 + - - +
114A GLN* 3.5 11.3 + - + -
115A ILE* 4.5 6.3 - - + +
118A MET* 3.8 9.4 - - + -
127A GLY* 4.5 1.1 - - - -
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Residues in contact with PRO 49 (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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48A THR* 1.3 83.5 - - - +
50A GLN* 1.3 62.0 + - - +
52A LEU* 3.2 4.6 + - + +
53A ASN* 3.0 24.5 + - - +
103A ASP 4.6 0.7 - - - +
104A ILE 3.3 28.7 - - - +
105A ALA 5.0 0.3 - - - +
106A GLY* 4.1 10.1 - - - +
114A GLN* 3.3 28.0 - - + +
118A MET* 4.9 0.4 - - + -
126A VAL* 3.7 37.9 - - + +
127A GLY* 3.9 7.2 - - - -
130A TYR* 4.0 15.9 - - + -
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Residues in contact with GLN 50 (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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12A HIS* 3.0 19.9 + - - -
14A ALA* 5.5 5.1 - - - +
48A THR 3.2 0.2 - - - -
49A PRO* 1.3 76.0 - - - +
51A ASP* 1.3 79.7 + - - +
53A ASN* 2.3 44.5 - - - +
54A THR* 2.7 34.3 + - - +
106A GLY* 5.9 0.2 - - - -
111A LEU* 3.4 25.1 - - + +
114A GLN* 3.0 16.1 + - - +
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Residues in contact with ASP 51 (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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1A PRO* 2.6 37.2 - - - +
12A HIS* 3.4 12.3 - - - -
14A ALA* 4.3 1.2 - - - -
15A ILE* 3.2 37.8 + - + +
47A ALA* 3.7 10.4 - - + -
48A THR* 3.0 13.1 + - - +
50A GLN* 1.3 99.5 + - - +
52A LEU* 1.3 64.5 + - - +
54A THR* 3.1 6.2 + - - -
55A MET* 3.0 26.9 + - - +
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Residues in contact with LEU 52 (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 PHE* 4.0 16.4 - - + -
44A SER* 3.7 33.9 - - - +
47A ALA* 3.8 11.4 - - + +
48A THR 3.0 17.1 + - - +
49A PRO* 3.6 6.5 - - + +
51A ASP* 1.3 76.4 - - - +
53A ASN* 1.3 62.5 + - - +
55A MET* 3.2 5.7 + - + +
56A LEU* 3.1 28.7 + - - +
127A GLY* 3.5 26.2 - - - +
130A TYR* 3.4 31.0 - - + -
131A LYS* 3.6 17.3 - - + +
134A ILE* 3.8 7.6 - - + -
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Residues in contact with ASN 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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49A PRO 3.0 10.5 + - - +
50A GLN* 2.3 37.4 + - - +
52A LEU* 1.3 76.3 - - - +
54A THR* 1.3 87.3 + - - +
56A LEU* 3.2 9.3 + - - +
57A ASN* 2.9 30.5 + - - +
105A ALA 5.2 6.8 + - - +
106A GLY* 5.3 7.1 + - - -
130A TYR* 4.5 12.2 - - + +
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Residues in contact with THR 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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15A ILE* 5.3 10.5 - - + +
20A LEU* 4.5 19.7 - - + -
50A GLN* 2.7 33.0 + - - +
51A ASP* 3.2 11.4 - - - -
53A ASN* 1.3 88.7 + - - +
55A MET* 1.3 62.7 + - - +
56A LEU 3.4 0.5 + - - -
57A ASN* 3.5 7.4 + - - +
58A THR* 3.0 24.1 + - - +
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Residues in contact with MET 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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15A ILE* 4.1 22.7 - - + -
19A THR* 4.3 19.5 - - + +
20A LEU* 3.4 23.6 - - - -
23A TRP* 3.1 64.5 + - + +
40A PHE* 4.4 5.4 - - + -
43A LEU* 4.4 11.7 - - + +
44A SER* 4.5 16.6 - - - +
51A ASP* 3.0 20.5 + - + +
52A LEU* 3.2 10.7 + - + +
54A THR* 1.3 75.7 - - - +
56A LEU* 1.3 66.3 + - + +
58A THR* 3.3 13.5 - - - -
59A VAL 3.6 2.6 + - - -
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Residues in contact with LEU 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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23A TRP* 5.1 5.6 - - + +
40A PHE* 4.1 28.5 - - + -
52A LEU 3.1 15.1 + - - +
53A ASN* 3.2 9.6 + - - +
55A MET* 1.3 76.3 - - - +
57A ASN* 1.3 64.1 + - - +
58A THR 3.1 2.0 - - - -
59A VAL* 3.1 12.7 + - + +
60A GLY* 3.0 21.3 + - - -
69A LEU* 4.2 28.3 - - + -
73A ILE* 4.9 6.3 - - + -
130A TYR* 4.5 10.8 - - - +
134A ILE* 4.0 27.1 - - + -
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Residues in contact with ASN 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 ASN 2.9 17.2 + - - +
54A THR* 3.9 7.2 - - - +
55A MET 3.4 0.2 - - - -
56A LEU* 1.3 76.4 - - - +
58A THR* 1.3 62.8 + - - +
60A GLY* 3.4 12.5 + - - +
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Residues in contact with THR 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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20A LEU* 3.1 36.2 - - + +
23A TRP* 4.8 1.3 - - + -
24A VAL* 3.6 37.2 - - + +
54A THR* 3.0 13.6 + - - +
55A MET 3.3 13.0 + - - -
56A LEU 3.1 0.2 - - - -
57A ASN* 1.3 82.3 + - - +
59A VAL* 1.3 59.6 + - + +
60A GLY 3.5 0.4 + - - -
61A GLY 5.4 0.2 + - - -
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Residues in contact with VAL 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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23A TRP* 3.6 37.0 - - + +
24A VAL* 4.2 13.5 - - + -
27A VAL* 3.7 35.7 - - + -
55A MET 3.6 6.0 + - - +
56A LEU* 3.1 15.2 + - + +
58A THR* 1.3 82.1 - - - +
60A GLY* 1.3 61.9 + - - +
61A GLY 3.2 4.5 + - - -
62A HIS* 3.4 24.6 + - + +
66A MET* 5.8 0.5 - - - +
69A LEU* 6.2 3.1 - - + -
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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