Contacts of the strand formed by residues 15 - 26 (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 ILE 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ARG* 1.3 71.6 - - - +
16A THR* 1.3 64.3 + - - +
17A TRP 4.1 1.8 - - - +
18A VAL* 3.9 27.6 - - + -
54A ILE* 3.9 18.2 - - + -
55A GLU 3.8 5.2 - - - +
56A THR* 4.2 2.0 - - + -
87A LEU* 3.3 37.5 - - + +
88A ILE* 3.6 3.1 - - + +
89A GLY* 2.6 29.3 + - - -
90A GLU 2.8 19.0 + - - +
92A PRO* 3.9 16.4 - - + -
98A LEU* 4.1 17.5 - - + -
126A LEU* 4.1 23.1 - - + -
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Residues in contact with THR 16 (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 ARG* 3.1 34.7 + - - +
15A ILE* 1.3 78.4 - - - +
17A TRP* 1.3 61.1 + - - +
55A GLU 3.0 5.1 + - - -
56A THR 3.5 16.3 + - - -
57A ALA* 3.6 21.6 - - + +
88A ILE* 3.6 12.4 - - + +
382A GLY* 3.2 8.3 - - - -
383A THR* 3.0 37.1 + - - -
385A PRO* 3.9 9.0 - - - +
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Residues in contact with TRP 17 (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 1.7 - - - +
16A THR* 1.3 79.9 - - - +
18A VAL* 1.3 72.2 + - - +
19A ARG* 3.4 42.0 - - + -
53A GLU* 4.0 25.6 - - + -
54A ILE* 3.6 0.5 - - - -
55A GLU* 3.1 67.5 + - + +
88A ILE* 3.9 0.6 - - - +
380A GLN* 3.1 27.9 + - - +
381A VAL 3.4 16.8 - - - -
382A GLY 3.8 8.7 - - - -
383A THR 3.8 0.2 - - - +
384A ARG* 3.6 67.1 - - + +
385A PRO* 4.3 5.8 - - + -
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Residues in contact with VAL 18 (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 19.7 - - + -
17A TRP* 1.3 83.8 - - - +
19A ARG* 1.3 67.4 + - - +
20A ILE* 4.7 0.4 - - + -
53A GLU 3.2 11.2 - - - +
54A ILE* 4.4 5.4 - - + -
84A ALA* 4.4 11.4 - - + +
87A LEU* 4.3 16.8 - - + -
88A ILE* 4.0 10.1 - - + -
122A PHE* 3.6 33.7 - - + -
380A GLN* 3.1 5.0 - - - +
381A VAL* 3.0 44.0 + - + +
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Residues in contact with ARG 19 (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* 3.4 35.2 - - + -
18A VAL* 1.3 76.4 - - - +
20A ILE* 1.3 66.6 + - - +
21A SER* 2.7 28.1 + - - -
51A PHE 3.7 0.3 - - - +
52A ALA* 3.4 3.3 - - - -
53A GLU* 2.6 75.4 + - + +
367A LEU* 5.1 4.8 - - - +
372A LYS* 4.2 8.9 - - - +
375A THR* 4.9 3.6 + - - +
378A GLU* 2.8 42.9 + - - +
379A ALA 3.4 11.2 - - - +
380A GLN* 4.1 12.6 - - + +
384A ARG* 5.9 0.9 - - - +
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Residues in contact with ILE 20 (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 VAL* 4.7 2.7 - - + +
19A ARG* 1.3 77.1 - - - +
21A SER* 1.3 63.5 + - - +
50A LEU* 4.3 6.3 - - + -
51A PHE 3.1 10.1 - - - +
52A ALA* 4.4 3.4 - - + -
77A PHE* 3.5 23.6 - - + +
80A ALA* 3.7 7.4 - - + +
81A ARG* 3.2 46.9 - - + +
84A ALA* 5.2 4.3 - - + -
121A ALA* 6.3 0.2 - - + -
122A PHE* 3.6 36.1 - - + -
378A GLU* 3.1 5.9 - - - +
379A ALA* 2.9 42.1 + - + +
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Residues in contact with SER 21 (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* 2.7 39.0 + - - -
20A ILE* 1.3 74.7 - - - +
22A SER* 1.3 61.1 + - - +
23A CYS* 3.7 0.7 - - - -
49A ILE 3.4 1.2 - - - +
50A LEU* 3.4 8.6 - - - +
51A PHE* 2.8 48.8 + - - +
53A GLU* 4.2 1.7 + - - -
77A PHE* 4.4 0.4 - - - -
367A LEU* 6.2 0.9 - - - -
371A VAL* 5.6 2.5 - - - -
375A THR* 4.1 19.5 - - - -
377A GLU 3.5 5.2 - - - -
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Residues in contact with SER 22 (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* 1.3 70.3 - - - +
23A CYS* 1.3 59.6 + - - +
24A TYR* 3.5 24.8 + - - -
48A ALA* 5.1 2.3 - - - +
49A ILE 3.5 6.3 + - - -
50A LEU* 4.7 2.8 - - - +
73A GLY* 4.3 8.1 + - - -
77A PHE* 3.9 21.9 - - - +
375A THR* 3.5 2.8 - - - -
376A ARG* 3.0 26.5 + - - -
377A GLU* 2.8 33.7 + - - -
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Residues in contact with CYS 23 (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* 3.7 0.9 + - - -
22A SER* 1.3 73.7 - - - +
24A TYR* 1.3 64.2 + - - +
25A LEU 3.5 1.9 + - - -
49A ILE* 2.7 45.9 + - + +
51A PHE* 3.8 18.4 - - + -
343A LEU* 3.7 29.8 - - - -
371A VAL* 4.0 22.2 - - + -
374A TRP* 3.6 25.8 - - - -
375A THR* 4.1 4.3 - - - +
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Residues in contact with TYR 24 (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 21.8 + - - -
23A CYS* 1.3 73.4 - - - +
25A LEU* 1.3 60.2 + - - +
26A PRO* 3.3 13.5 - - - +
46A GLU* 3.4 27.5 - - + +
47A ILE 3.7 1.6 - - - -
48A ALA* 3.6 26.5 - - + -
73A GLY 4.1 0.3 - - - -
74A PRO* 3.3 36.7 - - + +
374A TRP* 2.9 27.7 + - - +
376A ARG* 3.3 63.6 + - + +
377A GLU* 5.3 3.0 + - + -
82B GLU* 5.0 4.0 + - - -
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Residues in contact with LEU 25 (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* 3.5 2.4 + - - -
24A TYR* 1.3 69.7 - - - +
26A PRO* 1.3 76.7 - - + +
27A LEU* 3.6 12.8 + - + +
46A GLU* 3.1 5.6 - - - -
47A ILE* 2.8 48.8 + - + +
49A ILE* 4.4 9.2 - - + -
339A TRP 3.3 28.7 - - - +
340A LEU* 3.5 28.0 - - + -
342A PRO* 4.4 7.6 - - + -
343A LEU* 4.1 15.9 - - + -
374A TRP* 3.6 30.3 - - + -
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Residues in contact with PRO 26 (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 3.3 11.4 - - - +
25A LEU* 1.3 94.9 - - + +
27A LEU* 1.3 64.2 + - - +
28A ALA 3.8 1.7 + - - -
45A THR 3.8 7.0 - - - +
46A GLU* 4.2 6.1 - - + +
374A TRP* 3.4 45.0 - - + +
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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