Contacts of the strand formed by residues 63 - 76 (chain A) in PDB entry 3EO1
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 PHE 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A GLN* 4.7 0.9 - - - -
46A ARG* 3.9 22.2 - - - -
48A LEU* 4.3 17.5 - - + -
49A ILE* 4.2 15.9 - - + +
55A ARG* 3.3 26.2 + - - +
59A ILE* 3.5 28.0 - - + -
60A PRO* 3.5 19.9 + - + +
61A ASP 2.8 4.4 + - - +
62A ARG* 1.3 85.0 - - + +
64A SER* 1.3 60.3 + - - +
65A GLY 4.3 0.2 - - - -
74A LEU* 5.4 4.9 - - + -
75A THR 4.0 0.9 - - - -
76A ILE* 3.4 47.8 - - + -
83A ASP* 3.0 28.7 - - - -
87A TYR* 4.1 9.4 - - - -
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Residues in contact with SER 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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53A SER* 5.6 0.4 - - - +
55A ARG* 5.2 5.8 - - - +
61A ASP 4.9 4.0 + - - -
62A ARG 4.0 3.6 + - - -
63A PHE* 1.3 75.1 - - - +
65A GLY* 1.3 64.8 + - - +
73A THR 4.0 0.7 - - - +
74A LEU* 3.7 4.9 - - - +
75A THR* 2.8 59.3 + - - +
77A SER* 5.4 2.3 + - - -
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Residues in contact with GLY 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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36A TRP* 5.2 2.7 - - - -
49A ILE* 4.2 16.3 - - - +
53A SER* 2.8 41.6 + - - +
64A SER* 1.3 77.8 - - - +
66A SER* 1.3 62.5 + - - -
73A THR 3.5 9.0 - - - -
74A LEU* 4.4 5.4 - - - -
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Residues in contact with SER 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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36A TRP* 5.5 1.3 + - - +
52A ALA* 4.5 5.3 - - - +
53A SER* 3.1 15.8 + - - +
65A GLY* 1.3 75.5 - - - -
67A GLY* 1.3 62.8 + - - +
72A PHE* 3.4 6.8 - - - +
73A THR* 2.9 48.4 + - - -
75A THR* 5.7 1.2 - - - +
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Residues in contact with GLY 67 (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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31A SER* 4.5 4.3 - - - +
52A ALA* 4.0 14.6 - - - +
53A SER* 4.5 0.6 + - - -
66A SER* 1.3 80.2 - - - +
68A SER* 1.3 64.6 + - - -
71A ASP 3.5 13.2 - - - -
72A PHE* 3.8 8.1 - - - -
73A THR* 4.9 0.4 - - - -
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Residues in contact with SER 68 (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 GLY 4.2 3.1 - - - -
31A SER* 3.9 21.1 - - - -
67A GLY* 1.3 75.8 - - - -
69A GLY* 1.3 62.6 + - - +
70A THR 2.9 9.9 + - - -
71A ASP* 3.5 14.0 + - - +
72A PHE* 3.7 13.2 - - - -
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Residues in contact with GLY 69 (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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28A SER* 3.4 11.2 - - - -
29A LEU* 2.5 48.1 + - - +
30A GLY 3.8 1.2 + - - -
68A SER* 1.3 73.3 - - - +
70A THR* 1.3 62.0 + - - -
72A PHE* 3.4 8.6 - - - -
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Residues in contact with THR 70 (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 CYS 3.2 2.8 - - - +
24A ARG* 3.2 11.1 - - - +
25A ALA* 2.9 48.2 + - - +
26A SER 5.1 0.9 - - - +
27A GLN* 3.7 14.1 - - - +
28A SER* 3.9 9.4 - - - -
68A SER 2.9 1.6 + - - -
69A GLY* 1.3 77.7 - - - -
71A ASP* 1.3 76.1 + - - +
72A PHE* 3.6 7.7 - - - -
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Residues in contact with ASP 71 (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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22A SER* 5.6 4.0 - - - +
23A CYS 3.6 3.1 - - - -
24A ARG* 2.9 46.6 + - - +
67A GLY* 3.5 13.3 - - - -
68A SER 3.5 11.9 + - - +
70A THR* 1.3 86.8 + - - +
72A PHE* 1.3 62.5 + - - +
73A THR* 5.2 4.2 - - + +
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Residues in contact with PHE 72 (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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22A SER* 3.5 0.5 + - - -
23A CYS* 3.0 37.8 + - + +
25A ALA* 4.9 0.4 - - + -
29A LEU* 3.4 42.0 - - + -
30A GLY 3.9 8.7 - - - -
31A SER 5.1 1.6 - - - -
34A LEU* 3.7 44.4 - - + -
36A TRP* 4.0 6.7 - - + +
52A ALA* 4.3 11.2 - - + -
66A SER 3.4 8.1 - - - +
67A GLY 3.8 14.6 - - - -
68A SER* 3.7 20.6 - - - -
69A GLY 3.4 18.4 - - - -
70A THR 3.6 15.7 - - - -
71A ASP* 1.3 75.5 - - - +
73A THR* 1.3 68.6 + - - +
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Residues in contact with THR 73 (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 THR* 4.8 8.3 - - + -
21A LEU 3.1 13.5 - - - +
22A SER* 4.2 12.6 - - - +
36A TRP* 4.1 5.6 - - - -
64A SER 4.0 0.7 - - - +
65A GLY* 3.5 2.8 - - - -
66A SER* 2.9 46.0 + - - -
67A GLY* 5.6 0.3 - - - -
71A ASP* 5.2 4.0 - - + +
72A PHE* 1.3 82.3 - - - +
74A LEU* 1.3 60.0 + - - +
75A THR* 4.1 13.4 + - - +
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Residues in contact with LEU 74 (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 ALA 3.7 0.5 - - - +
20A THR* 3.6 0.5 - - - -
21A LEU* 2.8 58.8 + - + +
36A TRP* 3.4 53.0 - - + -
48A LEU* 4.6 6.1 - - + -
49A ILE* 3.4 30.5 - - + -
63A PHE* 5.4 2.5 - - + -
64A SER 3.7 7.4 - - - +
65A GLY* 4.4 1.3 - - - -
73A THR* 1.3 72.1 - - - +
75A THR* 1.3 65.1 + - - +
76A ILE* 4.3 9.8 + - + -
87A TYR* 3.8 20.4 - - + -
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Residues in contact with THR 75 (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 ARG* 5.3 8.1 - - - -
19A ALA 3.1 6.3 - - - -
20A THR* 3.5 27.4 - - + -
62A ARG 3.1 7.1 - - - +
63A PHE* 4.9 0.2 - - - -
64A SER* 2.8 48.7 + - - +
66A SER* 5.7 1.1 - - - +
73A THR* 4.6 9.4 - - - +
74A LEU* 1.3 82.4 - - - +
76A ILE* 1.3 63.3 - - - +
77A SER* 3.6 1.4 + - - -
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Residues in contact with ILE 76 (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 GLU 3.7 1.9 - - - +
18A ARG* 3.2 1.1 - - - -
19A ALA* 2.7 48.8 + - + +
21A LEU* 5.4 2.5 - - + -
62A ARG* 3.4 14.1 - - - +
63A PHE* 3.4 40.2 - - + -
74A LEU* 4.8 9.9 - - + +
75A THR* 1.3 72.5 - - - +
77A SER* 1.3 64.3 + - - +
78A ARG 4.6 0.2 - - - +
79A LEU* 3.7 24.9 - - + -
83A ASP* 3.6 17.5 - - + +
87A TYR* 3.8 23.6 - - + +
105A LEU* 3.9 13.2 - - + -
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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