Contacts of the strand formed by residues 35 - 56 (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 GLU 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.2 4.6 - - - +
32A VAL 2.8 32.7 + - - +
33A ASN 4.3 3.4 - - - +
34A ASN* 1.3 79.9 - - - +
36A THR* 1.3 67.3 + - - +
37A ALA* 3.1 1.6 + - - +
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Residues in contact with THR 36 (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* 4.2 12.4 + - + +
30A VAL 3.8 5.2 - - - +
31A LEU* 4.2 15.3 - - - +
35A GLU* 1.3 73.1 - - - +
37A ALA* 1.3 61.3 + - - +
38A ALA 4.0 9.6 - - - +
39A THR* 3.6 23.8 - - - +
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Residues in contact with ALA 37 (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 VAL 2.7 14.9 + - - +
32A VAL* 3.7 32.5 - - + -
35A GLU 3.1 1.7 + - - +
36A THR* 1.3 75.2 - - - +
38A ALA* 1.3 59.5 + - - +
53A GLN* 4.4 3.8 + - - -
55A LEU* 4.2 19.5 - - + +
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Residues in contact with ALA 38 (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 VAL 4.4 0.9 - - - -
29A ASN* 3.6 0.5 - - - -
30A VAL* 2.8 38.1 + - + +
36A THR* 3.8 3.6 - - - +
37A ALA* 1.3 80.7 - - - +
39A THR* 1.3 67.4 + - - +
40A PHE* 4.6 9.9 - - + -
53A GLN* 3.9 22.4 - - - +
55A LEU* 3.8 21.8 - - + -
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Residues in contact with THR 39 (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* 3.9 18.6 - - + -
28A VAL 3.2 6.7 - - - +
29A ASN* 2.7 30.4 + - - +
36A THR* 3.6 10.4 - - - +
38A ALA* 1.3 76.5 + - - +
40A PHE* 1.3 73.2 + - - +
41A SER* 4.3 3.0 + - - -
53A GLN* 5.5 0.4 + - - -
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Residues in contact with PHE 40 (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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16A VAL* 3.7 41.7 - - + -
18A ALA* 3.9 16.4 - - + -
26A GLN 3.6 0.8 - - - +
27A THR* 3.3 4.0 - - - -
28A VAL* 2.8 48.3 + - + +
30A VAL* 4.9 4.9 - - + -
38A ALA* 4.6 7.0 - - + -
39A THR* 1.3 84.8 - - - +
41A SER* 1.3 61.9 + - - +
50A ILE* 3.8 18.6 - - + +
51A GLY* 3.6 21.8 - - - -
52A THR 3.6 20.2 - - - -
53A GLN* 3.8 32.3 - - + -
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Residues in contact with SER 41 (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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25A THR* 3.7 14.2 - - - +
26A GLN 3.1 10.8 + - - -
27A THR* 4.1 11.6 + - - -
39A THR* 4.3 3.1 + - - -
40A PHE* 1.3 77.0 - - - +
42A GLY* 1.3 59.5 + - - +
50A ILE* 3.8 14.3 + - - +
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Residues in contact with GLY 42 (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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25A THR* 3.5 6.6 - - - -
26A GLN* 2.8 37.5 + - - +
41A SER* 1.3 78.7 + - - +
43A GLN* 1.3 60.6 + - - -
50A ILE* 3.7 21.6 - - - +
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Residues in contact with GLN 43 (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* 4.4 2.5 - - - -
22A SER 2.9 24.3 + - - +
23A SER* 3.9 20.5 + - - +
24A GLY 4.1 7.0 - - - +
25A THR* 3.9 17.5 - - + +
42A GLY* 1.3 75.0 - - - +
44A SER* 1.3 79.4 + - - +
45A THR* 3.8 10.1 + - - +
48A ALA* 5.5 0.5 - - - +
50A ILE* 4.0 3.3 - - - +
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Residues in contact with SER 44 (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* 3.1 28.3 - - - +
22A SER 2.8 23.6 + - - +
43A GLN* 1.3 88.5 - - - +
45A THR* 1.3 58.5 + - - +
46A ASN* 2.9 20.4 + - - +
48A ALA* 3.2 35.3 + - - +
50A ILE* 5.1 0.9 - - - -
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Residues in contact with THR 45 (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 ASN* 4.0 4.9 - - - +
22A SER* 3.4 35.4 - - - +
23A SER* 3.9 5.4 - - - +
43A GLN* 3.8 9.0 + - - +
44A SER* 1.3 71.8 + - - +
46A ASN* 1.3 62.1 + - - +
47A ASN 3.7 2.0 - - - -
115A FUL 4.4 11.9 - - + -
13B ARG* 5.3 2.6 + - - -
113B LEU* 5.3 0.3 - - - +
114B GLY* 3.3 25.4 + - - +
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Residues in contact with ASN 46 (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 ASN* 3.9 0.9 - - - -
44A SER* 2.9 5.8 + - - +
45A THR* 1.3 84.5 - - - +
47A ASN* 1.3 71.4 + - - +
48A ALA* 3.2 4.6 + - + +
13B ARG* 2.5 34.9 + - - +
54B VAL* 3.6 25.2 - - - +
113B LEU* 4.9 2.7 - - - +
114B GLY 5.3 0.2 - - - +
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Residues in contact with ASN 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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19A PHE* 3.4 28.1 - - - +
20A ALA 3.0 17.6 + - - -
21A ASN* 2.9 30.5 + - - +
46A ASN* 1.3 79.1 - - - +
48A ALA* 1.3 65.7 + - - +
49A VAL* 3.6 0.3 + - - +
15B GLY* 3.8 15.8 - - - -
17B THR* 4.8 2.4 + - - -
52B THR* 4.9 7.8 + - - +
54B VAL* 4.6 3.8 - - + +
110B ASN* 2.9 34.7 + - - +
113B LEU* 3.6 19.5 - - + -
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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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19A PHE* 3.3 0.7 - - - -
20A ALA* 3.1 23.4 + - - +
43A GLN 5.5 0.2 - - - +
44A SER* 3.2 25.0 + - - +
46A ASN* 3.2 3.4 - - + +
47A ASN* 1.3 76.8 - - - +
49A VAL* 1.3 70.0 - - - +
50A ILE* 3.4 4.5 + - + +
52B THR* 6.1 3.1 - - - -
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Residues in contact with VAL 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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17A THR* 4.0 11.4 - - + -
18A ALA 3.3 7.6 - - - +
19A PHE* 3.6 27.8 - - + -
47A ASN 3.6 0.4 + - - +
48A ALA* 1.3 77.3 - - - +
50A ILE* 1.3 63.0 + - - +
51A GLY* 3.5 27.8 - - - +
52A THR* 4.4 9.2 - - + -
49B VAL* 4.6 16.4 - - + -
52B THR* 5.0 14.2 - - + +
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Residues in contact with ILE 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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18A ALA* 2.8 36.0 + - + +
19A PHE 4.5 2.5 - - - +
20A ALA* 3.7 25.6 - - + -
26A GLN* 3.9 31.2 - - + +
28A VAL* 4.2 8.7 - - + -
40A PHE* 3.8 13.8 - - + +
41A SER 3.8 11.7 + - - +
42A GLY* 3.7 35.2 - - - +
43A GLN* 4.0 4.9 - - - +
44A SER* 5.1 0.7 - - - -
48A ALA* 3.8 5.4 - - + +
49A VAL* 1.3 76.3 - - - +
51A GLY* 1.3 57.6 + - - +
105A ALA* 5.5 0.2 - - + -
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Residues in contact with GLY 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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17A THR* 3.3 0.5 - - - -
18A ALA 2.9 25.5 + - - -
40A PHE* 3.6 24.9 - - - -
49A VAL* 3.4 10.2 - - - +
50A ILE* 1.3 83.9 - - - +
52A THR* 1.3 63.9 + - - -
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Residues in contact with THR 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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16A VAL 3.2 7.5 + - - -
17A THR* 2.8 27.2 + - - -
40A PHE* 3.6 4.7 - - - -
49A VAL* 4.4 6.7 - - + -
51A GLY* 1.3 75.0 - - - -
53A GLN* 1.3 68.1 + - - +
19B PHE* 4.8 0.2 - - - -
47B ASN* 4.8 6.6 + - - -
49B VAL* 3.6 23.3 - - + +
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Residues in contact with GLN 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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15A GLY* 3.5 2.6 - - - -
16A VAL* 2.9 37.5 + - + +
37A ALA 4.4 4.2 + - - -
38A ALA* 3.9 12.6 - - - +
39A THR 5.5 0.2 + - - -
40A PHE* 3.8 23.1 - - + -
52A THR* 1.3 78.6 + - - +
54A VAL* 1.3 77.3 + - - +
55A LEU* 3.1 28.2 - - + +
47B ASN* 5.5 0.3 + - - -
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Residues in contact with VAL 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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13A ARG* 4.2 23.6 - - + +
14A PHE 3.4 3.6 - - - +
15A GLY* 4.9 0.4 - - - -
53A GLN* 1.3 85.7 + - - +
55A LEU* 1.3 74.3 + - - +
113A LEU* 3.6 31.6 - - + -
46B ASN* 3.6 30.7 - - + +
47B ASN* 4.5 3.8 - - + -
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Residues in contact with LEU 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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13A ARG* 3.1 8.4 - - - +
14A PHE* 2.8 51.3 + - + -
16A VAL* 4.0 15.0 - - + -
30A VAL* 3.7 29.8 - - + -
32A VAL* 4.5 1.6 - - + -
37A ALA* 4.2 20.0 - - + +
38A ALA* 3.8 18.4 - - + -
53A GLN* 3.1 32.3 - - - +
54A VAL* 1.3 78.8 - - - +
56A ASN* 1.3 62.6 + - - +
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Residues in contact with ASN 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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11A ASN* 2.7 44.6 + - - +
12A THR 3.5 7.2 - - - +
13A ARG* 4.3 10.7 - - + +
14A PHE* 3.7 2.5 - - - -
32A VAL* 3.1 24.8 - - - +
55A LEU* 1.3 75.0 - - - +
57A SER* 1.3 58.5 + - - +
58A GLY* 2.8 29.8 + - - -
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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