Contacts of the strand formed by residues 43 - 51 (chain A) in PDB entry 1MDU
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 ALA 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ARG* 3.6 2.3 - - - +
22A VAL* 2.9 29.5 + - + +
42A ASP* 1.3 76.2 - - - +
44A TYR* 1.3 67.8 + - - +
64A TRP 3.3 9.9 - - - +
65A LEU* 3.9 16.6 - - + -
69A CYS* 4.3 2.7 - - + +
73A GLU* 3.6 39.5 + - + +
74A SER* 4.2 0.7 - - - +
77A ALA* 4.0 3.8 - - + -
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Residues in contact with TYR 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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19A ILE* 4.3 2.7 - - + -
20A TRP 3.2 11.9 - - - +
21A ARG* 3.4 37.2 - - + +
22A VAL 4.5 0.7 - - - +
30A VAL* 4.3 13.2 - - + -
37A ASP 4.1 6.5 + - - -
38A PHE* 3.5 29.3 - + + -
39A PHE* 2.7 49.1 + - - +
42A ASP* 3.9 8.5 - - + -
43A ALA* 1.3 77.8 - - - +
45A VAL* 1.3 65.1 + - - +
46A ILE* 3.9 15.3 - - + -
63A TYR* 3.1 8.1 - - - +
64A TRP* 2.8 64.3 + + + +
77A ALA* 4.4 1.9 - - - +
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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
----------------------------------------------------------
19A ILE* 3.6 1.4 - - - -
20A TRP* 2.9 42.4 + - + +
22A VAL* 4.8 0.7 - - + -
27A LEU* 4.0 26.5 - - + -
44A TYR* 1.3 77.9 - - - +
46A ILE* 1.3 64.0 + - - +
61A LEU* 4.2 9.9 - - + -
62A HIS 3.4 4.7 - - - +
63A TYR* 4.3 0.2 - - - +
77A ALA* 3.8 31.6 - - + +
80A PHE* 4.1 5.8 - - + -
81A THR* 4.1 15.0 - - - +
84A LEU* 3.9 27.4 - - + -
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Residues in contact with ILE 46 (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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17A LEU* 3.5 28.9 - - + -
18A GLN 3.4 6.5 - - - +
19A ILE* 4.0 25.4 - - + -
38A PHE* 4.3 3.4 - - + -
44A TYR* 3.9 23.1 - - + +
45A VAL* 1.3 81.6 - - - +
47A LEU* 1.3 63.5 + - - +
48A LYS 4.8 0.4 - - - +
60A ASP 3.7 1.2 - - - +
61A LEU* 3.4 6.3 - - - +
62A HIS* 2.6 54.7 + - + +
64A TRP* 4.0 16.6 - - + -
106A PHE* 4.0 25.1 - - + -
109A TYR* 4.7 4.9 - - + -
110A PHE* 5.1 1.1 - - + -
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Residues in contact with LEU 47 (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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11A ALA* 4.1 5.4 - - + -
12A GLY* 3.4 21.5 - - - +
16A GLY 3.7 1.2 - - - +
17A LEU* 3.5 3.8 - - - +
18A GLN* 2.8 57.6 + - + +
20A TRP* 3.6 25.7 - - + -
46A ILE* 1.3 75.4 - - - +
48A LYS* 1.3 63.1 + - - +
49A THR* 3.9 7.2 + - - +
59A TYR* 3.8 32.3 - - + -
60A ASP 3.7 4.9 - - - +
61A LEU* 3.8 22.4 - - + -
84A LEU* 5.2 2.0 - - + -
88A LEU* 4.3 10.8 - - + -
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Residues in contact with LYS 48 (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 GLY* 3.6 17.0 + - - +
17A LEU* 4.1 15.3 - - + +
46A ILE 4.1 0.8 + - - -
47A LEU* 1.3 72.8 - - - +
49A THR* 1.3 63.3 + - - +
50A VAL* 3.9 26.6 + - + +
58A GLN 3.7 1.4 - - - +
59A TYR* 3.5 4.9 - - - -
60A ASP* 2.9 39.5 + - + +
109A TYR* 3.6 63.2 + - + +
111A LYS* 5.7 4.0 - - - +
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Residues in contact with THR 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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12A GLY* 3.7 10.5 - - - +
14A GLU 3.2 32.4 + - - +
15A PRO* 3.3 4.7 - - + +
16A GLY* 2.9 34.5 + - - +
18A GLN* 4.3 2.6 + - - +
47A LEU* 3.9 7.3 + - - +
48A LYS* 1.3 77.6 - - - +
50A VAL* 1.3 67.2 + - - +
57A LEU* 3.8 21.1 - - + -
58A GLN 3.5 2.9 - - - -
59A TYR* 3.5 35.2 - - + -
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Residues in contact with VAL 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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15A PRO* 4.9 0.4 - - - -
48A LYS* 3.9 26.9 - - + +
49A THR* 1.3 79.0 - - - +
51A GLN* 1.3 62.6 + - - +
52A LEU* 4.4 4.3 - - + -
56A ASN 3.8 0.3 - - - +
57A LEU* 3.3 7.3 - - - -
58A GLN* 2.9 70.6 + - + +
60A ASP* 5.7 5.4 - - - +
313E ASP* 6.3 0.2 - - - -
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Residues in contact with GLN 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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15A PRO* 3.5 12.7 - - + +
50A VAL* 1.3 73.4 - - - +
52A LEU* 1.3 75.2 + - - +
55A GLY* 4.1 11.0 - - - +
56A ASN 3.5 3.4 - - - -
57A LEU* 4.0 15.0 - - + +
312E ALA* 3.3 34.3 + - + +
313E ASP* 3.2 29.0 + - - +
316E GLN* 3.0 27.3 - - - +
329E ILE 5.2 0.2 - - - +
330E LYS* 5.0 0.7 - - - -
331E ILE* 3.9 24.2 + - - +
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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