Contacts of the strand formed by residues 49 - 55 (chain A) in PDB entry 1MQ8
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 ARG 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A THR* 4.8 20.0 + - - +
21A CYS 3.6 6.7 - - - -
22A SER* 4.0 21.1 + - - +
31A LEU* 4.1 1.5 - - - +
45A PRO 5.0 3.1 - - - +
46A GLY* 4.7 8.0 - - - -
47A ASN 3.3 13.7 + - - +
48A ASN* 1.3 80.0 - - - +
50A LYS* 1.3 65.6 + - - +
51A VAL* 5.1 6.7 - - + -
16C SER* 3.7 14.3 + - - -
18C LEU* 6.1 0.2 - - - +
53C GLU* 3.1 26.3 + - - -
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Residues in contact with LYS 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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19A VAL 3.4 0.9 - - - +
20A THR* 3.1 1.7 - - - -
21A CYS* 2.7 45.0 + - - +
31A LEU* 3.2 46.6 + - + +
41A GLU* 4.8 15.5 + - + +
43A LEU 6.0 2.7 - - - +
47A ASN 5.0 6.3 + - - -
49A ARG* 1.3 78.9 + - - +
51A VAL* 1.3 67.2 + - - +
52A TYR* 3.0 37.8 - - + +
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Residues in contact with VAL 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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18A LEU* 4.3 0.7 - - + -
19A VAL 3.1 9.9 - - - +
20A THR* 3.4 23.3 - - + -
41A GLU* 3.7 4.7 - - - +
42A LEU* 2.9 55.6 + - + +
43A LEU 5.7 2.6 + - - -
49A ARG* 5.1 8.1 - - + -
50A LYS* 1.3 78.8 - - - +
52A TYR* 1.3 73.7 + - - +
18C LEU* 3.5 26.5 - - + -
42C LEU* 5.2 7.6 - - + -
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Residues in contact with TYR 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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18A LEU* 3.2 22.7 - - - +
19A VAL 3.0 19.5 + - - +
21A CYS* 4.0 16.4 - - - -
31A LEU 4.1 0.2 + - - -
32A GLY* 3.1 22.7 - - - -
33A ILE* 3.1 42.3 + - + -
39A LYS* 4.1 28.3 - - + -
40A LYS 3.4 10.8 - - - +
41A GLU* 4.2 16.2 - - + +
42A LEU* 4.3 3.0 - - - +
50A LYS* 3.0 41.7 - - + +
51A VAL* 1.3 85.7 - - - +
53A GLU* 1.3 66.7 + - - +
54A LEU* 5.0 3.6 - - + +
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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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16A SER* 3.5 20.2 + - - -
17A VAL 3.0 13.7 - - - +
18A LEU* 3.5 17.9 - - + +
38A PRO 3.2 12.6 - - - +
40A LYS* 3.0 40.4 + - + +
42A LEU* 5.5 5.4 - - + -
52A TYR* 1.3 80.9 - - - +
54A LEU* 1.3 62.1 + - - +
55A SER* 3.4 12.7 + - - -
49C ARG* 3.1 29.8 + - - -
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Residues in contact with LEU 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 GLY 4.1 0.5 - - - +
16A SER* 3.1 3.2 - - - -
17A VAL* 2.8 43.4 + - + +
19A VAL* 3.5 27.6 - - + -
33A ILE* 4.3 9.0 - - + -
35A THR* 3.6 28.0 - - + +
37A LEU* 3.6 24.1 - - + +
38A PRO 3.6 6.7 - - - +
39A LYS* 4.8 8.7 - - + -
52A TYR* 5.3 2.2 - - + -
53A GLU* 1.3 71.6 - - - +
55A SER* 1.3 61.3 + - - +
57A VAL* 5.0 0.7 - - - +
63A PRO* 3.2 34.8 - - + -
80A LEU* 4.0 9.2 - - + -
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Residues in contact with SER 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 GLY 3.8 0.2 - - - -
16A SER* 3.9 15.0 - - - -
37A LEU* 4.5 1.0 - - - +
38A PRO* 3.0 46.0 + - - +
40A LYS* 5.4 2.6 - - - +
53A GLU* 3.8 14.7 + - - -
54A LEU* 1.3 76.2 - - - +
56A ASN* 1.3 79.1 + - - +
57A VAL* 3.3 4.2 + - - -
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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