Contacts of the strand formed by residues 52 - 66 (chain A) in PDB entry 1MUI
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 GLY 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ILE 4.1 0.3 - - - +
48A GLY* 4.9 0.7 - - - -
49A GLY 2.9 26.9 + - - -
50A ILE 3.5 2.8 + - - -
51A GLY* 1.3 81.2 - - - +
53A PHE* 1.3 62.6 + - - -
50B ILE* 4.1 0.5 - - - +
51B GLY* 3.0 17.2 - - - -
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Residues in contact with PHE 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 MET* 3.7 36.3 - - + -
47A ILE 3.5 15.3 - - - +
48A GLY* 4.8 3.1 - - - -
52A GLY* 1.3 77.4 - - - -
54A ILE* 1.3 64.0 + - - +
55A LYS* 5.5 3.4 - - + -
51B GLY* 4.7 1.6 + - - +
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Residues in contact with ILE 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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32A VAL* 4.8 0.7 - - + -
46A MET* 3.3 6.5 - - - +
47A ILE* 3.3 47.6 + - + +
52A GLY 4.3 0.2 + - - -
53A PHE* 1.3 79.5 - - - +
55A LYS* 1.3 61.9 + - - +
56A VAL* 3.6 22.8 + - + -
79A PRO* 3.5 38.8 - - + +
80A THR* 4.5 5.2 - - - +
50B ILE* 3.4 43.3 - - + +
51B GLY* 4.3 3.4 - - - +
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Residues in contact with LYS 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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42A TRP* 5.9 1.2 - - - -
44A PRO* 3.9 27.9 - - - +
45A LYS 3.6 7.3 - - - +
46A MET* 3.3 32.1 - - + +
53A PHE* 5.5 3.1 - - + -
54A ILE* 1.3 72.8 - - - +
56A VAL* 1.3 64.1 + - - +
57A ARG* 4.0 7.8 + - - -
79A PRO* 3.5 17.2 - - - +
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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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32A VAL* 4.3 8.5 - - + -
42A TRP* 5.6 0.4 - - - -
44A PRO* 3.8 2.9 - - - +
45A LYS* 2.6 51.5 + - + +
47A ILE* 4.4 10.1 - - + -
54A ILE* 3.6 30.3 - - + +
55A LYS* 1.3 80.6 + - - +
57A ARG* 1.3 64.2 + - - +
76A LEU* 3.8 34.1 - - + -
77A VAL 3.2 20.6 - - - +
78A GLY* 3.7 7.9 - - - +
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Residues in contact with ARG 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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35A GLU* 2.8 41.9 + - - -
42A TRP* 3.4 54.7 - - + -
43A LYS 4.0 0.2 - - - -
55A LYS 4.0 8.7 + - - -
56A VAL* 1.3 74.1 - - - +
58A GLN* 1.3 60.8 + - - +
59A TYR* 3.8 14.0 - - + +
75A VAL 3.8 0.7 - - - +
76A LEU* 3.3 8.0 - - - -
77A VAL* 2.9 44.6 + - + +
78A GLY* 3.1 10.5 - - - -
79A PRO* 4.4 2.6 - - - +
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Residues in contact with GLN 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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41A ARG 3.7 0.2 - - - +
42A TRP* 2.9 30.3 - - - +
43A LYS* 3.2 33.5 + - + +
45A LYS* 3.2 31.0 + - + +
57A ARG* 1.3 71.4 - - - +
59A TYR* 1.3 66.6 + - - +
60A ASP* 2.9 28.6 + - - -
74A THR* 3.3 21.6 - - + +
76A LEU* 3.5 15.3 - - + -
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Residues in contact with TYR 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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36A MET 5.7 0.9 + - - -
38A LEU* 3.8 42.7 + - + +
40A GLY* 3.1 29.7 + - - -
41A ARG 3.2 17.9 - - - -
42A TRP* 3.6 30.9 - + + -
57A ARG* 3.8 21.4 - - + +
58A GLN* 1.3 88.5 - - - +
60A ASP* 1.3 65.1 + - - +
62A ILE* 3.5 27.6 - - + -
73A GLY 3.8 0.7 - - - +
74A THR* 2.9 7.4 - - - +
75A VAL* 2.9 38.7 + - + +
77A VAL* 4.5 9.6 - - + -
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Residues in contact with ASP 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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41A ARG 5.3 0.8 + - - -
43A LYS* 5.7 5.7 - - - +
58A GLN* 2.9 29.0 + - - -
59A TYR* 1.3 72.6 - - - +
61A GLN* 1.3 78.6 + - + +
62A ILE* 3.3 13.0 + - - +
73A GLY 4.1 2.0 - - - -
74A THR* 3.4 15.9 + - - +
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Residues in contact with GLN 61 (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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60A ASP* 1.3 79.6 - - + +
62A ILE* 1.3 61.7 + - - +
63A LEU 3.8 2.3 + - - -
72A ILE* 3.1 38.1 - - - +
73A GLY* 3.7 6.7 + - - -
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Residues in contact with ILE 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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15A ILE* 4.5 7.6 - - + -
16A GLY 5.8 1.3 - - - +
38A LEU* 5.0 18.2 - - + -
39A PRO* 6.2 2.2 - - + -
40A GLY* 5.5 7.4 - - - +
59A TYR* 3.5 41.3 - - + +
60A ASP 3.4 13.7 - - - +
61A GLN* 1.3 75.0 - - - +
63A LEU* 1.3 74.0 + - - +
64A ILE* 3.2 14.0 + - + +
72A ILE* 3.6 3.0 - - - +
73A GLY 3.1 29.1 + - - +
75A VAL* 3.9 21.1 - - + -
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Residues in contact with LEU 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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14A LYS 4.2 2.4 - - - +
15A ILE* 3.4 15.2 - - - +
16A GLY 4.7 2.4 + - - -
61A GLN 3.8 3.4 + - - -
62A ILE* 1.3 75.0 - - - +
64A ILE* 1.3 71.3 + - - +
65A GLU* 4.7 15.5 - - + +
70A LYS* 4.2 29.2 - - + -
71A ALA 3.7 8.3 - - - +
72A ILE* 3.4 24.9 - - + +
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Residues in contact with ILE 64 (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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13A ILE* 4.6 14.6 - - + -
14A LYS 3.7 4.5 - - - +
15A ILE* 3.4 22.4 - - + -
31A THR* 5.2 1.6 - - + -
33A LEU* 5.8 1.6 - - + -
62A ILE 3.2 12.3 - - - +
63A LEU* 1.3 81.6 - - - +
65A GLU* 1.3 61.8 + - - +
66A ILE* 3.4 25.2 + - + +
71A ALA* 2.7 43.3 + - - +
73A GLY 4.8 0.9 - - - +
75A VAL* 3.3 28.5 - - + -
85A ILE* 5.2 2.7 - - + -
89A LEU* 3.3 35.4 - - + -
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Residues in contact with GLU 65 (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 THR 4.1 0.9 - - - +
13A ILE* 3.8 0.7 - - - -
14A LYS* 3.2 64.1 + - + +
63A LEU* 4.7 16.1 - - + +
64A ILE* 1.3 72.1 - - - +
66A ILE* 1.3 60.0 + - - +
67A CYS 3.3 7.4 + - - -
68A GLY* 4.4 6.7 + - - +
69A HIS 3.2 12.3 - - - +
70A LYS* 3.5 41.1 + - + +
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Residues in contact with ILE 66 (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 VAL* 3.9 28.3 - - + -
13A ILE* 4.1 11.7 - - + -
24A LEU* 4.9 2.5 - - + -
64A ILE* 3.7 21.8 - - + +
65A GLU* 1.3 67.0 - - - +
67A CYS* 1.3 71.4 + - + +
68A GLY 3.5 0.2 - - - -
69A HIS* 2.6 29.6 + - - +
71A ALA* 4.6 6.5 - - + -
85A ILE* 4.0 20.6 - - + -
89A LEU* 3.9 32.5 - - + -
93A ILE* 4.4 32.4 - - + +
99B PHE* 5.1 2.4 - - + -
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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