Contacts of the strand formed by residues 35 - 56 (chain D) in PDB entry 1OXC
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 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31D LEU* 4.0 2.9 - - - -
32D VAL 2.9 33.9 + - - +
33D ASN* 4.3 6.7 - - + +
34D ASN* 1.3 90.9 - - + +
36D THR* 1.3 68.8 + - - +
37D ALA* 3.2 2.1 + - - +
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Residues in contact with THR 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ASN* 2.8 39.6 + - - +
30D VAL 3.6 4.7 - - - -
31D LEU* 4.3 4.7 - - - +
35D GLU* 1.3 76.0 + - - +
37D ALA* 1.3 60.7 + - - +
38D ALA* 3.7 7.9 - - - +
39D THR* 3.5 14.6 - - - +
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Residues in contact with ALA 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D VAL 2.8 12.5 + - - +
32D VAL* 3.7 28.3 - - + -
35D GLU 3.2 2.9 + - - +
36D THR* 1.3 74.2 - - - +
38D ALA* 1.3 64.3 + - - +
53D GLN* 4.3 3.8 + - - -
55D LEU* 3.9 24.1 - - + +
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Residues in contact with ALA 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D VAL 4.4 0.2 - - - -
29D ASN* 3.3 2.8 - - - +
30D VAL* 2.9 32.1 + - + -
36D THR* 3.7 2.3 - - - +
37D ALA* 1.3 82.6 - - - +
39D THR* 1.3 68.2 + - - +
40D PHE* 4.1 13.9 - - + -
53D GLN* 3.7 29.4 - - + +
55D LEU* 4.2 13.9 - - + -
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Residues in contact with THR 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D THR* 4.1 21.8 - - + -
28D VAL 3.2 11.4 - - - +
29D ASN* 3.0 22.5 + - + +
36D THR* 3.5 8.1 - - - +
38D ALA* 1.3 74.9 + - - +
40D PHE* 1.3 72.9 + - - +
41D SER* 4.4 6.5 + - - +
53D GLN* 5.0 2.2 + - - +
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Residues in contact with PHE 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D VAL* 4.3 21.3 - - + -
18D ALA* 3.6 29.6 - - + -
26D GLN 3.4 1.5 - - - +
27D THR* 3.4 0.7 - - - -
28D VAL* 2.8 43.6 + - + +
30D VAL* 4.3 15.3 - - + -
38D ALA* 4.1 17.5 - - + -
39D THR* 1.3 80.2 - - - +
41D SER* 1.3 65.1 + - - +
42D GLY 4.3 0.2 - - - -
50D ILE* 3.3 26.7 - - + +
51D GLY* 3.6 31.0 - - - -
52D THR 4.0 2.2 - - - -
53D GLN* 3.4 28.7 - - + -
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Residues in contact with SER 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D THR* 4.5 10.5 - - - -
26D GLN 3.1 7.9 - - - -
27D THR* 4.0 17.5 + - - +
39D THR* 4.4 6.2 - - - +
40D PHE* 1.3 77.4 + - - +
42D GLY* 1.3 56.9 + - - +
50D ILE* 4.6 6.5 + - - +
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Residues in contact with GLY 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ALA* 4.2 1.4 - - - +
25D THR* 4.0 7.6 - - - +
26D GLN* 2.8 38.3 + - - +
41D SER* 1.3 74.6 - - - +
43D GLN* 1.3 60.0 + - - -
50D ILE* 3.9 22.7 - - - +
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Residues in contact with GLN 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ALA* 4.5 1.6 - - - -
22D SER 2.8 26.3 + - - +
23D SER* 3.5 25.0 + - - +
24D GLY 3.9 8.7 - - - +
25D THR* 4.0 15.9 - - - +
42D GLY* 1.3 74.4 - - - +
44D SER* 1.3 77.2 + - - +
45D THR* 3.9 7.9 - - - +
48D ALA* 5.3 0.7 - - - +
50D ILE* 4.6 2.0 - - - +
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Residues in contact with SER 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ALA* 3.1 16.1 - - - +
21D ASN* 3.1 7.8 + - - -
22D SER 2.8 22.1 + - - -
43D GLN* 1.3 92.3 - - - +
45D THR* 1.3 58.2 + - - +
46D ASN* 3.0 21.8 + - - +
48D ALA* 3.4 34.7 + - - +
50D ILE* 5.4 0.2 - - - -
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Residues in contact with THR 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 4.5 0.7 - - - +
114C GLY* 3.1 31.4 + - - +
21D ASN* 3.8 4.9 - - - +
22D SER* 3.7 30.7 - - - +
23D SER* 4.3 3.4 - - - +
43D GLN* 3.9 8.7 - - - +
44D SER* 1.3 72.3 + - - +
46D ASN* 1.3 79.6 + - - +
47D ASN 3.7 2.2 - - - -
115D FUL 4.5 12.3 - - + -
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Residues in contact with ASN 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ARG* 3.2 27.8 + - - +
54C VAL* 3.3 22.2 - - + +
113C LEU* 4.7 5.2 - - - -
21D ASN* 3.9 0.7 - - - -
44D SER* 3.0 6.8 + - - +
45D THR* 1.3 99.1 + - - +
47D ASN* 1.3 70.1 + - - +
48D ALA* 3.3 3.5 + - - -
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Residues in contact with ASN 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLY* 3.7 16.0 - - - -
16C VAL 5.0 0.2 - - - +
17C THR* 5.0 1.0 + - - -
52C THR* 4.9 4.2 + - - -
53C GLN 5.5 0.2 + - - -
54C VAL* 4.5 4.0 - - + +
110C ASN* 2.9 32.6 + - - -
113C LEU* 3.5 22.9 - - + -
19D PHE* 3.3 28.4 - - - +
20D ALA 3.0 11.7 + - - +
21D ASN* 2.9 31.1 + - - -
46D ASN* 1.3 79.0 - - - +
48D ALA* 1.3 67.2 + - - +
49D VAL* 3.5 3.3 + - - +
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Residues in contact with ALA 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE* 3.2 2.9 - - - -
20D ALA 3.2 21.2 + - - -
43D GLN 5.3 0.9 - - - +
44D SER* 3.4 26.0 + - - +
46D ASN 3.3 5.1 - - - -
47D ASN* 1.3 78.9 - - - +
49D VAL* 1.3 63.0 + - - +
50D ILE* 3.2 11.8 + - + +
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Residues in contact with VAL 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C THR* 4.7 2.7 - - + +
49C VAL* 5.3 4.7 - - + -
52C THR* 3.6 36.9 - - + +
17D THR* 3.8 12.6 - - + -
18D ALA 3.3 7.0 - - - +
19D PHE* 3.6 20.6 - - + -
47D ASN 4.5 0.9 - - - +
48D ALA* 1.3 70.1 - - - +
50D ILE* 1.3 61.1 + - - +
51D GLY* 3.2 25.4 + - - +
52D THR* 4.2 11.7 - - + -
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Residues in contact with ILE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ALA* 2.9 27.4 + - + +
19D PHE 4.4 3.1 - - - +
20D ALA* 3.9 25.1 - - + -
26D GLN* 4.1 21.3 - - + +
28D VAL* 4.1 24.9 - - + -
40D PHE* 3.3 20.9 - - + +
41D SER 4.6 3.1 + - - +
42D GLY* 3.9 32.3 - - - +
43D GLN 4.6 1.8 - - - +
48D ALA* 3.2 12.1 + - + +
49D VAL* 1.3 72.1 - - - +
51D GLY* 1.3 55.5 + - - +
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Residues in contact with GLY 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D THR* 3.3 0.5 - - - -
18D ALA 2.8 27.4 + - - -
40D PHE* 3.6 25.8 - - - -
49D VAL* 3.1 9.8 + - - +
50D ILE* 1.3 81.7 - - - +
52D THR* 1.3 64.7 + - - -
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Residues in contact with THR 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C PHE* 4.1 8.5 - - - -
47C ASN* 5.0 5.5 + - - -
49C VAL* 4.1 20.3 - - + +
16D VAL 3.1 6.7 + - - -
17D THR* 2.8 28.8 + - - +
40D PHE* 4.0 3.4 - - - -
49D VAL* 4.2 7.4 - - + -
51D GLY* 1.3 76.0 - - - -
53D GLN* 1.3 70.7 + - - +
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Residues in contact with GLN 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ASN* 5.4 0.4 + - - -
15D GLY* 3.4 3.6 - - - -
16D VAL* 2.9 42.1 + - + +
37D ALA 4.3 3.6 + - - -
38D ALA* 3.7 20.7 - - - +
39D THR 5.0 1.9 + - - +
40D PHE* 3.4 25.7 - - + -
52D THR* 1.3 81.7 + - - +
54D VAL* 1.3 68.3 + - - +
55D LEU* 4.1 13.0 - - + +
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Residues in contact with VAL 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ASN* 3.3 41.5 - - - +
47C ASN* 4.2 5.8 - - + +
13D ARG* 3.5 33.4 - - + +
14D PHE 3.3 4.0 - - - +
15D GLY* 4.9 0.7 - - - -
53D GLN* 1.3 79.9 + - - +
55D LEU* 1.3 75.6 + - - +
113D LEU* 3.6 29.2 - - + -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ARG* 3.2 6.3 - - - +
14D PHE* 2.8 53.0 + - + -
16D VAL* 4.0 17.0 - - + -
30D VAL* 3.8 28.5 - - + -
32D VAL* 4.3 3.1 - - + -
37D ALA* 3.9 37.7 - - + +
38D ALA* 4.2 6.5 - - + -
53D GLN* 4.0 15.9 - - + +
54D VAL* 1.3 85.1 - - - +
56D ASN* 1.3 63.0 + - - +
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Residues in contact with ASN 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ASN* 3.3 29.5 + - - +
12D THR 3.7 3.1 - - - -
13D ARG* 4.3 20.7 - - + +
14D PHE* 3.8 3.3 - - - -
32D VAL* 3.3 16.5 - - - +
55D LEU* 1.3 74.4 - - - +
57D SER* 1.3 63.9 + - - +
58D GLY* 2.8 31.0 + - - -
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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