Contacts of the strand formed by residues 13 - 32 (chain A) 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 ARG 13 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR* 1.3 85.5 - - - +
14A PHE* 1.3 61.7 + - - +
54A VAL* 4.2 20.5 - - + +
55A LEU 3.1 12.1 - - - +
56A ASN* 4.8 11.2 - - + +
111A TRP* 3.8 9.2 - - - +
113A LEU* 4.1 26.5 + - + +
114A GLY* 4.3 21.8 - - - +
118A SO4 2.7 37.9 + - - +
45B THR 4.8 1.8 + - - -
46B ASN* 3.4 24.5 + - - +
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Residues in contact with PHE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.5 26.7 - - + -
12A THR 3.8 7.9 - - - -
13A ARG* 1.3 76.1 - - - +
15A GLY* 1.3 63.9 + - - +
16A VAL* 4.2 12.1 - - + -
30A VAL* 4.5 1.3 - - + -
32A VAL* 4.1 3.8 - - + -
53A GLN 3.9 0.3 - - - +
54A VAL* 3.4 3.1 - - - -
55A LEU* 2.8 74.6 + - + -
56A ASN 3.7 2.7 - - - -
57A SER* 3.6 23.3 - - - -
63A VAL* 3.8 33.4 - - + -
109A ILE* 3.6 22.9 - - + -
110A ASN 3.5 11.9 - - - +
111A TRP* 4.0 3.6 - - + -
113A LEU* 3.6 8.3 - - - -
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 1.3 78.8 - - - +
16A VAL* 1.3 60.2 + - - +
53A GLN 3.5 6.7 - - - -
54A VAL* 4.5 0.7 - - - -
108A VAL 4.3 0.2 - - - -
109A ILE* 3.1 6.1 - - - -
110A ASN* 2.9 39.1 + - - -
113A LEU* 3.6 7.4 - - - +
47B ASN* 3.7 24.0 - - - -
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Residues in contact with VAL 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 4.2 6.7 - - + -
15A GLY* 1.3 74.6 - - - +
17A THR* 1.3 65.2 + - - +
30A VAL* 3.9 20.9 - - + -
40A PHE* 3.7 23.4 - - + -
52A THR* 3.2 3.1 - - - -
53A GLN* 2.9 42.6 + - + +
55A LEU* 4.0 25.6 - - + -
107A VAL* 3.7 24.7 - - + -
108A VAL 3.4 2.9 - - - -
109A ILE* 3.9 15.5 - - + -
47B ASN* 5.0 0.2 - - - +
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Residues in contact with THR 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY 5.0 0.3 - - - -
16A VAL* 1.3 76.8 + - - +
18A ALA* 1.3 63.8 + - - +
19A PHE* 3.9 27.5 - - + -
40A PHE* 4.8 0.2 - - - -
49A VAL* 4.0 13.2 - - + -
51A GLY 3.3 10.8 - - - +
52A THR* 2.8 25.1 + - - +
106A VAL 3.8 0.5 - - - +
107A VAL* 3.3 5.2 - - - +
108A VAL* 2.8 38.2 + - - +
110A ASN* 5.2 0.5 + - - -
19B PHE* 3.4 28.1 - - + -
47B ASN* 4.7 2.4 + - - -
49B VAL* 4.6 2.7 - - + -
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Residues in contact with ALA 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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17A THR* 1.3 76.1 - - - +
19A PHE* 1.3 59.1 + - - +
28A VAL* 4.1 18.8 - - + -
40A PHE* 3.9 18.4 - - + -
49A VAL* 3.3 8.1 - - - +
50A ILE* 2.8 48.6 + - + -
51A GLY 2.9 7.9 + - - +
105A ALA* 5.9 0.2 - - + -
106A VAL 3.2 7.2 - - - +
107A VAL* 4.2 6.7 - - + -
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Residues in contact with PHE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.9 23.1 - - + -
18A ALA* 1.3 75.1 - - - +
20A ALA* 1.3 59.7 - - - +
21A ASN* 4.3 0.8 + - - -
47A ASN* 3.4 44.2 - - - +
48A ALA 3.3 5.6 - - - -
49A VAL* 3.6 24.5 - - + -
50A ILE* 4.7 3.0 - - - +
103A ASN 4.5 0.3 - - - +
105A ALA* 3.3 6.1 - - - +
106A VAL* 2.8 54.8 + - + +
108A VAL* 4.0 22.9 - - + -
17B THR* 3.4 35.7 - - + -
19B PHE* 4.5 4.7 - + - -
52B THR* 4.5 0.9 - - - -
108B VAL* 5.5 6.1 - - + -
110B ASN* 5.2 5.4 - - - -
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 1.3 75.1 - - - +
21A ASN* 1.3 62.2 + - - +
26A GLN* 4.1 15.9 - - + -
43A GLN* 4.4 2.0 - - - -
44A SER* 3.1 28.9 - - - +
47A ASN* 3.0 25.7 + - - -
48A ALA 3.1 7.7 + - - -
50A ILE* 3.7 23.8 - - + -
104A ASP 3.4 8.5 - - - +
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Residues in contact with ASN 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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20A ALA* 1.3 77.0 + - - +
22A SER* 1.3 59.4 + - - +
44A SER 3.2 2.9 - - - -
45A THR* 4.0 3.6 - - - +
46A ASN 3.9 0.2 - - - -
47A ASN* 2.9 45.6 + - - +
103A ASN* 3.2 33.9 + - - +
104A ASP* 3.0 12.0 + - - +
106A VAL* 4.4 5.9 - - - +
115A FUL 3.1 0.4 + - - -
117A CA 2.4 31.2 - - - -
110B ASN* 4.4 0.2 - - - +
113B LEU* 3.6 8.4 - - - +
114B GLY* 3.0 38.6 + - - +
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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
----------------------------------------------------------
21A ASN* 1.3 78.0 - - - +
23A SER* 1.3 61.2 + - - +
24A GLY 3.0 11.6 + - - +
26A GLN* 3.5 12.8 - - - -
43A GLN* 2.9 21.1 + - - +
44A SER 2.8 11.5 + - - +
45A THR* 3.4 7.6 - - - +
96A ASP* 2.6 28.9 + - - -
104A ASP* 3.7 11.0 - - - -
115A FUL 2.7 26.9 + - - -
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Residues in contact with SER 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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22A SER* 1.3 76.3 + - - +
24A GLY* 1.3 62.2 + - - +
25A THR 4.0 0.5 + - - -
43A GLN* 3.9 17.0 + - - +
45A THR* 4.2 4.5 - - - -
115A FUL 2.9 32.2 + - - +
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Residues in contact with GLY 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* 3.0 17.0 + - - +
23A SER* 1.3 84.4 + - - +
25A THR* 1.3 62.8 + - - -
26A GLN* 3.1 24.3 + - - +
42A GLY 4.4 0.5 - - - +
43A GLN* 4.1 4.9 - - - +
44A SER 5.3 0.2 + - - -
69A VAL* 4.1 15.9 - - - -
96A ASP* 4.7 0.9 - - - -
115A FUL 4.1 1.1 + - - -
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Residues in contact with THR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A SER 4.0 1.0 + - - -
24A GLY* 1.3 70.5 - - - -
26A GLN* 1.3 63.9 + - - +
27A THR* 4.7 3.2 + - - +
41A SER* 3.7 22.0 - - - +
42A GLY* 3.5 17.9 - - - +
43A GLN* 3.9 15.2 - - + +
69A VAL* 3.5 26.2 - - - +
70A ASN* 4.2 12.7 + - - -
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 4.1 13.7 - - + -
22A SER* 3.5 4.3 - - - -
24A GLY 3.1 17.9 - - - +
25A THR* 1.3 71.9 - - - +
27A THR* 1.3 60.6 + - - +
28A VAL* 4.0 1.3 - - + -
40A PHE 3.6 0.5 - - - +
41A SER* 3.1 26.2 + - - -
42A GLY 2.8 15.8 + - - +
50A ILE* 3.9 15.4 - - + +
67A VAL* 3.6 12.9 - - + +
68A SER 3.9 1.3 - - - -
69A VAL* 3.5 13.3 - - - +
74A SER* 4.6 1.6 + - - -
94A SER* 4.3 0.8 + - - -
96A ASP* 2.9 22.7 - - - +
104A ASP* 3.3 28.8 + - - +
105A ALA* 3.2 27.6 - - + +
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Residues in contact with THR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 4.7 4.3 + - - +
26A GLN* 1.3 73.1 + - - +
28A VAL* 1.3 62.9 + - - +
29A ASN* 4.0 12.3 + - - +
39A THR* 3.9 24.0 - - + -
40A PHE 3.3 3.8 - - - +
41A SER* 4.1 10.6 + - - +
66A GLN 3.7 0.5 - - - +
67A VAL* 3.3 5.1 - - - +
68A SER* 2.9 49.9 + - - +
70A ASN 5.2 4.4 + - - -
71A GLY 5.9 0.2 + - - -
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Residues in contact with VAL 28 (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 ALA* 4.1 18.2 - - + -
27A THR* 1.3 76.0 - - - +
29A ASN* 1.3 65.7 + - - +
30A VAL* 4.5 11.8 - - + +
38A ALA 3.8 0.7 - - - +
39A THR* 3.2 5.0 - - - -
40A PHE* 2.8 52.9 + - + +
50A ILE* 4.2 13.9 - - + -
65A VAL* 4.1 15.3 - - + -
66A GLN 3.5 3.4 - - - +
67A VAL* 4.2 12.6 - - + -
105A ALA* 4.3 12.3 - - + -
107A VAL* 3.9 22.7 - - + -
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Residues in contact with ASN 29 (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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27A THR* 4.1 12.7 - - - +
28A VAL* 1.3 73.6 - - - +
30A VAL* 1.3 63.7 + - - +
31A LEU* 3.9 14.0 - - + +
36A THR* 4.2 10.9 - - + +
38A ALA 3.6 0.9 + - - +
39A THR* 2.7 42.2 + - - +
64A GLN 3.6 1.0 - - - +
65A VAL* 3.4 5.5 - - - +
66A GLN* 2.8 47.2 + - + +
68A SER* 4.9 4.3 + - - -
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Residues in contact with VAL 30 (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 PHE* 4.5 4.9 - - + -
16A VAL* 3.9 28.7 - - + -
28A VAL* 4.5 13.2 - - + +
29A ASN* 1.3 77.8 - - - +
31A LEU* 1.3 58.5 + - - +
32A VAL* 4.6 0.7 - - + -
36A THR* 3.7 0.9 - - - -
37A ALA* 2.7 32.4 + - - +
38A ALA* 2.8 23.0 + - + +
40A PHE* 4.9 3.6 - - + -
55A LEU* 3.7 26.9 - - + -
63A VAL* 4.0 24.9 - - + -
64A GLN 3.4 4.0 - - - +
65A VAL* 4.8 7.2 - - + -
109A ILE* 5.4 0.2 - - + -
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Residues in contact with LEU 31 (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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29A ASN* 3.9 19.5 - - + +
30A VAL* 1.3 78.5 - - - +
32A VAL* 1.3 62.8 + - - +
33A ASN 4.2 0.2 - - - -
34A ASN* 4.7 15.5 - - - -
35A GLU 3.2 11.7 - - - +
36A THR* 4.3 17.9 - - - +
62A LYS 3.8 0.7 - - - +
63A VAL* 3.3 6.9 - - - +
64A GLN* 2.8 64.2 + - + +
66A GLN* 3.8 29.4 - - + +
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 4.1 22.4 - - + -
30A VAL* 4.1 2.0 + - + -
31A LEU* 1.3 78.1 - - - +
33A ASN* 1.3 72.7 + - + +
34A ASN 3.1 0.2 - - - -
35A GLU* 2.8 23.7 + - - +
37A ALA* 3.7 23.6 - - + -
55A LEU* 4.5 4.3 - - + -
56A ASN 3.1 27.8 - - - +
57A SER 3.2 24.0 - - - +
58A GLY* 3.6 7.2 - - - +
62A LYS 3.6 3.4 - - - +
63A VAL* 4.5 2.7 - - + -
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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