Contacts of the strand formed by residues 13 - 32 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12C THR* 1.3 86.6 - - - +
14C PHE* 1.3 57.5 - - - +
54C VAL* 2.9 38.3 - - + +
55C LEU 3.2 9.4 - - - +
56C ASN* 4.2 12.2 - - - +
111C TRP* 3.9 4.7 - - - +
113C LEU* 3.6 29.6 + - + +
46D ASN* 3.2 30.1 + - - +
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Residues in contact with PHE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 3.5 24.9 - - + -
12C THR 3.7 7.6 - - - -
13C ARG* 1.3 75.5 - - - +
15C GLY* 1.3 65.0 + - - +
16C VAL* 4.3 11.7 - - + -
30C VAL* 4.7 0.4 - - + -
32C VAL* 4.3 4.7 - - + -
54C VAL* 3.4 3.6 - - - +
55C LEU* 2.8 74.5 + - + +
56C ASN 3.7 2.7 - - - -
57C SER* 3.6 23.1 - - - -
63C VAL* 3.9 32.3 - - + -
109C ILE* 3.6 22.2 - - + -
110C ASN 3.5 12.3 - - - +
111C TRP* 3.9 5.2 - - + -
113C LEU* 3.7 7.4 - - - -
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Residues in contact with GLY 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PHE* 1.3 79.0 - - - +
16C VAL* 1.3 61.8 + - - +
17C THR* 5.1 0.2 - - - -
53C GLN 3.5 7.2 - - - -
54C VAL* 4.5 1.1 - - - -
109C ILE* 3.1 6.1 - - - -
110C ASN* 2.9 38.9 + - - -
113C LEU* 3.8 6.4 - - - +
47D ASN* 3.7 22.4 - - - -
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Residues in contact with VAL 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PHE* 4.3 6.5 - - + -
15C GLY* 1.3 73.7 - - - +
17C THR* 1.3 65.6 + - - +
30C VAL* 3.9 20.2 - - + -
40C PHE* 3.9 23.4 - - + -
52C THR* 3.2 2.4 - - - -
53C GLN* 2.9 42.9 + - + +
55C LEU* 3.9 25.8 - - + -
107C VAL* 3.8 24.0 - - + -
108C VAL 3.4 3.1 - - - -
109C ILE* 3.8 15.5 - - + -
47D ASN* 5.0 0.2 - - - +
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Residues in contact with THR 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLY 5.1 0.3 - - - -
16C VAL* 1.3 77.1 + - - +
18C ALA* 1.3 63.9 + - - +
19C PHE* 3.8 28.6 - - + -
49C VAL* 4.0 16.2 - - + -
51C GLY 3.3 11.7 - - - +
52C THR* 2.8 22.8 + - - +
106C VAL 3.8 0.3 - - - +
107C VAL* 3.3 4.5 - - - +
108C VAL* 2.8 37.7 + - - +
110C ASN* 5.3 0.5 + - - -
17D THR* 5.3 0.2 - - + -
19D PHE* 3.3 28.1 - - + -
47D ASN* 5.0 1.4 + - - -
49D VAL* 5.0 2.2 - - + -
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Residues in contact with ALA 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 1.3 74.8 - - - +
19C PHE* 1.3 58.9 + - - +
28C VAL* 4.2 9.4 - - + -
40C PHE* 3.8 21.0 - - + -
49C VAL* 3.3 6.9 - - - +
50C ILE* 2.8 47.3 + - + -
51C GLY 2.8 9.0 + - - +
106C VAL 3.2 7.2 - - - +
107C VAL* 4.1 15.3 - - + -
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Residues in contact with PHE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 3.8 24.0 - - + -
18C ALA* 1.3 75.2 - - - +
20C ALA* 1.3 61.2 + - - +
21C ASN* 4.6 0.9 - - - +
47C ASN* 3.4 48.7 - - - +
48C ALA 3.3 6.1 - - - -
49C VAL* 3.7 21.8 - - + -
50C ILE* 4.7 3.4 - - - +
103C ASN 4.6 0.2 - - - +
105C ALA* 3.3 6.1 - - - +
106C VAL* 2.8 54.2 + - + +
108C VAL* 4.0 23.8 - - + -
17D THR* 3.3 34.5 - - + -
19D PHE* 5.2 2.0 - + - -
52D THR* 4.1 1.3 - - - -
108D VAL* 5.7 4.7 - - + -
110D ASN* 4.9 7.2 - - - -
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Residues in contact with ALA 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE* 1.3 75.3 - - - +
21C ASN* 1.3 63.0 + - - +
22C SER 5.1 0.4 - - - +
26C GLN* 4.1 15.9 - - + -
42C GLY 4.4 0.9 - - - +
43C GLN 4.4 1.1 - - - -
44C SER* 3.2 33.1 - - - +
47C ASN* 3.0 25.3 + - - -
48C ALA 3.1 6.7 + - - -
50C ILE* 3.8 20.9 - - + -
104C ASP 3.4 8.5 - - - +
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Residues in contact with ASN 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE* 4.6 0.2 - - - +
20C ALA* 1.3 76.3 - - - +
22C SER* 1.3 57.8 + - - +
44C SER 3.2 3.1 - - - -
45C THR* 4.0 4.4 - - - +
46C ASN 3.9 0.2 - - - -
47C ASN* 3.0 44.3 + - - -
103C ASN* 3.2 32.1 + - - +
104C ASP* 2.9 14.7 + - - +
106C VAL* 4.4 5.3 - - - +
115C FUC 3.8 0.4 - - - -
117C CA 2.4 30.7 - - - -
110D ASN* 4.6 0.2 - - - +
113D LEU* 3.6 9.6 - - - +
114D GLY* 3.0 36.4 + - - +
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Residues in contact with SER 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ASN* 1.3 77.1 - - - +
23C SER* 1.3 64.3 + - - +
24C GLY 3.1 11.4 + - - +
26C GLN* 3.4 15.0 - - - -
43C GLN* 3.0 18.5 - - - +
44C SER 2.8 11.3 + - - +
45C THR* 3.4 8.0 - - - +
96C ASP* 2.7 29.0 + - - -
104C ASP* 3.8 9.4 - - - -
115C FUC 2.9 21.8 + - - -
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Residues in contact with SER 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C SER* 1.3 76.4 + - - +
24C GLY* 1.3 62.2 + - - +
25C THR 3.9 0.5 + - - -
43C GLN* 3.5 18.3 - - - +
45C THR* 4.3 4.9 - - - -
115C FUC 2.9 31.8 + - - +
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Residues in contact with GLY 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C SER* 3.1 15.7 + - - +
23C SER* 1.3 85.0 + - - +
25C THR* 1.3 62.9 + - - -
26C GLN* 3.1 22.5 + - - +
42C GLY 4.4 0.2 - - - +
43C GLN* 3.9 5.7 - - - +
69C VAL* 4.1 14.6 - - - -
96C ASP* 4.8 0.7 - - - -
115C FUC 4.3 1.7 + - - -
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Residues in contact with THR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C SER 3.9 0.8 + - - -
24C GLY* 1.3 69.7 - - - -
26C GLN* 1.3 64.8 + - - +
27C THR* 3.9 4.1 + - - +
41C SER* 3.9 20.9 - - - +
42C GLY* 3.6 17.7 - - - +
43C GLN* 3.8 14.2 - - + +
68C SER 3.9 0.3 - - - +
69C VAL* 3.6 24.3 - - - +
70C ASN 4.5 2.3 + - - -
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Residues in contact with GLN 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ALA* 4.1 10.1 - - + -
22C SER* 3.4 8.3 - - - -
24C GLY 3.1 21.2 + - - +
25C THR* 1.3 73.1 - - - +
27C THR* 1.3 62.2 + - - +
28C VAL* 4.0 1.8 - - + -
40C PHE 3.4 1.4 - - - +
41C SER* 3.2 6.6 + - - -
42C GLY 2.8 38.7 + - - +
50C ILE* 4.1 13.5 - - + +
67C VAL* 3.6 7.3 - - + +
68C SER 3.9 1.3 - - - -
69C VAL* 3.4 19.5 - - - +
74C SER* 4.6 0.9 + - - -
94C SER* 4.3 0.2 + - - -
96C ASP* 3.0 25.3 + - - -
104C ASP* 3.3 26.3 - - - +
105C ALA* 3.2 24.1 - - + +
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Residues in contact with THR 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C THR* 4.8 4.5 + - - +
26C GLN* 1.3 74.1 + - - +
28C VAL* 1.3 62.1 + - - +
29C ASN* 3.9 12.8 + - - -
39C THR* 4.0 23.1 - - + -
40C PHE 3.4 3.4 - - - -
41C SER* 4.4 10.9 + - - +
66C GLN 3.8 0.7 - - - +
67C VAL* 3.3 4.4 - - - -
68C SER* 2.9 49.5 + - - +
69C VAL* 5.8 0.2 - - - -
70C ASN 5.9 1.0 + - - -
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Residues in contact with VAL 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ALA* 4.2 8.7 - - + -
26C GLN* 4.8 0.7 - - + -
27C THR* 1.3 74.6 - - - +
29C ASN* 1.3 62.2 + - - +
30C VAL* 4.1 9.8 + - + -
38C ALA 3.9 0.3 - - - +
39C THR* 3.2 6.3 - - - +
40C PHE* 2.8 56.8 + - + +
50C ILE* 4.1 22.2 - - + -
65C VAL* 4.1 9.9 - - + -
66C GLN 3.4 8.7 - - - +
67C VAL* 4.2 14.1 - - + -
105C ALA* 4.2 13.7 - - + -
107C VAL* 3.8 22.2 - - + -
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Residues in contact with ASN 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C THR* 4.3 18.4 - - - -
28C VAL* 1.3 76.7 - - - +
30C VAL* 1.3 62.4 + - - +
31C LEU* 4.0 6.0 - - + +
36C THR* 5.0 12.3 - - + +
38C ALA 3.6 5.2 - - - +
39C THR* 4.4 10.5 - - - +
64C GLN 3.6 1.2 - - - +
65C VAL* 3.5 4.2 - - - +
66C GLN* 2.8 50.6 + - + +
68C SER* 5.7 2.5 - - - -
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PHE* 4.7 5.4 - - + -
16C VAL* 3.9 26.5 - - + -
28C VAL* 4.4 14.1 - - + -
29C ASN* 1.3 75.3 - - - +
31C LEU* 1.3 59.1 + - - +
32C VAL* 4.8 0.9 - - + -
36C THR* 3.7 0.9 - - - +
37C ALA* 2.7 33.3 + - - +
38C ALA* 2.8 22.9 + - + +
40C PHE* 4.5 9.9 - - + -
55C LEU* 3.8 26.0 - - + -
63C VAL* 4.1 22.7 - - + -
64C GLN 3.5 3.8 - - - +
65C VAL* 4.9 8.1 - - + -
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASN* 5.0 7.9 - - + +
30C VAL* 1.3 75.4 - - - +
32C VAL* 1.3 62.4 + - - +
34C ASN* 4.4 15.3 - - - +
35C GLU* 3.2 11.0 - - - +
36C THR* 3.3 39.7 - - + +
62C LYS 3.7 0.5 - - - +
63C VAL* 3.3 7.6 - - - +
64C GLN* 2.7 63.5 + - + +
66C GLN* 3.0 33.9 - - - +
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Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C PHE* 4.3 19.5 - - + -
30C VAL* 4.8 1.6 - - + -
31C LEU* 1.3 78.3 - - - +
33C ASN* 1.3 75.3 + - + +
35C GLU* 2.8 24.3 + - - +
37C ALA* 3.5 26.2 - - + -
55C LEU* 4.7 3.4 - - + -
56C ASN 3.5 20.9 - - - +
57C SER* 3.3 28.7 - - - +
58C GLY* 4.3 2.9 - - - +
62C LYS 3.4 4.9 - - - +
63C VAL* 4.7 2.5 - - + -
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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
------------------------------------------------------------
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