Contacts of the strand formed by residues 46 - 56 (chain A) in PDB entry 2OG9
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 GLU 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TYR* 3.4 26.2 - - + +
25A LEU 3.1 18.4 - - - +
26A PRO* 4.2 4.5 - - + +
27A LEU* 3.9 4.1 - - - +
44A MSE 3.4 21.3 - - - +
45A THR* 1.3 92.0 + - - +
47A ILE* 1.3 67.2 + - - +
48A ALA 4.3 0.2 - - - -
70A ARG 4.9 4.5 + - - -
376A ARG* 3.0 31.4 + - - -
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Residues in contact with ILE 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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24A TYR* 4.6 2.5 - - - -
25A LEU* 2.8 47.2 + - + +
27A LEU* 4.1 9.9 - - + -
44A MSE 4.0 13.9 - - + -
46A GLU* 1.3 80.7 - - - +
48A ALA* 1.3 65.7 + - - +
49A ILE* 3.5 22.1 + - + -
67A TYR* 4.2 14.4 - - + -
68A SER 3.6 14.1 - - - +
69A LYS* 4.3 12.8 - - + -
316A PHE* 4.7 12.3 - - + -
339A TRP* 3.6 34.8 - - + -
340A LEU* 4.9 0.7 - - + -
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Residues in contact with ALA 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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22A SER* 5.1 2.2 - - - +
23A CYS 3.7 4.7 - - - -
24A TYR* 3.6 31.9 - - + -
47A ILE* 1.3 71.4 - - - +
49A ILE* 1.3 60.8 + - - +
67A TYR* 3.2 6.1 - - - +
68A SER* 3.0 38.5 + - - +
70A ARG 5.5 1.6 - - - +
73A GLY* 3.6 29.2 - - - +
76A GLN* 5.1 1.0 - - - +
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Residues in contact with ILE 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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21A SER 3.4 1.7 - - - +
22A SER* 3.5 3.2 - - - -
23A CYS* 2.7 47.9 + - + +
25A LEU* 4.4 6.1 - - + -
47A ILE* 3.7 29.4 - - + +
48A ALA* 1.3 73.5 - - - +
50A LEU* 1.3 61.0 + - - +
51A PHE* 3.7 36.7 + - + -
65A PHE* 4.1 14.6 - - + -
66A SER 3.7 8.7 - - - +
67A TYR* 3.8 13.2 - - + -
316A PHE* 5.2 1.1 - - + -
340A LEU* 4.3 15.5 - - + -
343A LEU* 3.7 24.5 - - + -
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Residues in contact with LEU 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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20A ILE* 4.3 9.6 - - + -
21A SER 3.4 14.8 - - - +
22A SER* 4.7 2.2 - - - +
48A ALA 4.1 0.8 + - - -
49A ILE* 1.3 71.6 - - - +
51A PHE* 1.3 66.2 + - - +
65A PHE* 3.0 26.4 - - - -
66A SER* 2.9 33.5 + - - +
67A TYR* 4.6 0.2 - - - +
73A GLY 5.9 0.4 - - - +
76A GLN* 3.9 23.7 + - + +
77A PHE* 4.1 30.7 - - + -
80A ALA* 3.8 21.5 - - + -
118A ALA* 4.0 9.4 - - - -
121A ALA* 3.9 16.3 - - + +
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Residues in contact with PHE 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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19A ARG 3.7 1.0 - - - +
20A ILE* 3.1 7.6 - - - +
21A SER* 2.8 48.3 + - - +
23A CYS* 3.8 29.8 - - + -
49A ILE* 3.7 25.8 - - + -
50A LEU* 1.3 74.6 - - - +
52A ALA* 1.3 60.1 + - - +
53A GLU* 4.3 2.2 - - - +
63A LEU* 4.1 11.4 - - + -
64A GLY 3.5 5.6 - - - +
65A PHE* 3.8 17.3 - + + -
343A LEU* 3.8 21.3 - - + -
344A PHE* 3.7 19.3 - + - -
367A LEU* 3.4 36.1 - - + -
371A VAL* 4.1 14.1 - - + -
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Residues in contact with ALA 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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19A ARG 3.4 4.3 - - - -
20A ILE* 4.4 2.5 - - + -
50A LEU 4.0 0.2 + - - -
51A PHE* 1.3 75.6 - - - +
53A GLU* 1.3 61.4 - - - +
54A ILE* 5.3 0.2 - - + -
63A LEU* 3.4 7.3 - - - +
64A GLY 3.0 30.4 + - - +
121A ALA* 3.6 35.7 - - + +
122A PHE* 3.8 27.1 - - + -
125A ALA* 3.8 4.4 - - + +
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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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17A TRP* 4.0 22.4 - - + -
18A VAL* 3.2 7.3 - - - +
19A ARG* 2.6 75.3 + - + +
21A SER* 4.2 2.1 + - - -
51A PHE* 5.5 2.2 - - + +
52A ALA* 1.3 78.4 - - - +
54A ILE* 1.3 63.2 + - - +
61A GLN* 4.4 15.6 + - - +
62A GLY 3.4 6.3 - - - +
63A LEU* 3.9 16.2 - - + -
367A LEU* 4.2 16.7 - - + +
384A ARG* 4.9 4.3 + - - -
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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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15A ILE* 3.9 33.7 - - + -
17A TRP* 3.6 3.6 - - - -
18A VAL* 4.4 12.3 - - + -
53A GLU* 1.3 80.1 - - - +
55A GLU* 1.3 68.9 + - - +
61A GLN* 3.2 4.9 - - - +
62A GLY* 2.8 35.9 + - - +
87A LEU* 4.1 19.1 - - + -
122A PHE* 3.7 29.4 - - + +
125A ALA* 3.8 13.0 - - + -
126A LEU* 3.9 18.8 - - + -
129A LEU* 4.1 14.5 - - + +
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Residues in contact with GLU 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* 3.8 2.4 - - - +
16A THR* 3.0 20.9 + - - -
17A TRP* 3.1 31.9 + - + +
54A ILE* 1.3 79.2 - - - +
56A THR* 1.3 65.6 + - - +
59A GLY 6.2 0.2 - - - -
60A HIS 3.2 6.1 - - - +
61A GLN* 2.7 40.9 + - + +
384A ARG* 3.1 46.7 + - - +
385A PRO* 3.3 22.2 - - + +
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Residues in contact with THR 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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13A ASP* 2.6 29.8 + - - +
14A ARG 3.1 14.8 - - - +
15A ILE* 4.2 7.2 - - + -
16A THR* 3.5 7.0 - - - -
54A ILE* 5.0 0.2 - - + -
55A GLU* 1.3 78.1 - - - +
57A ALA* 1.3 59.2 + - - +
58A GLY 3.3 1.6 + - - -
59A GLY* 2.9 19.8 + - - -
60A HIS* 3.0 22.7 + - + +
92A PRO* 3.8 23.3 - - + -
129A LEU* 3.8 19.3 - - + -
385A PRO* 3.6 12.1 - - - +
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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