Contacts of the strand formed by residues 35 - 56 (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 GLU 35 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 3.2 4.6 - - - +
32C VAL 2.8 37.8 + - - +
33C ASN* 4.2 4.3 - - + +
34C ASN* 1.3 79.5 - - - +
36C THR* 1.3 68.1 + - - +
37C ALA* 3.2 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ASN* 5.0 9.3 - - + +
30C VAL 3.7 1.6 - - - +
31C LEU* 3.3 22.5 - - + +
35C GLU* 1.3 73.3 - - - +
37C ALA* 1.3 62.5 + - - +
38C ALA* 3.9 10.8 - - - +
39C THR* 3.8 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL 2.7 8.9 + - - +
32C VAL* 3.5 35.4 - - + -
35C GLU 3.2 0.8 + - - +
36C THR* 1.3 75.0 - - - +
38C ALA* 1.3 63.2 + - - +
53C GLN* 4.4 3.5 + - - -
55C LEU* 3.9 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C VAL 3.9 0.4 - - - +
29C ASN* 3.6 0.7 - - - -
30C VAL* 2.8 35.4 + - + +
36C THR* 3.7 4.3 - - - +
37C ALA* 1.3 84.4 - - - +
39C THR* 1.3 66.7 + - - +
40C PHE* 4.5 13.0 - - + -
53C GLN* 4.1 21.3 - - - +
55C LEU* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C THR* 4.0 23.1 - - + -
28C VAL 3.2 10.6 + - - +
29C ASN* 4.4 8.2 - - - -
36C THR* 3.8 15.1 - - - +
38C ALA* 1.3 76.9 + - - +
40C PHE* 1.3 76.1 + - - +
41C SER* 4.3 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C VAL* 3.9 42.4 - - + -
18C ALA* 3.8 19.7 - - + -
26C GLN 3.4 2.6 - - - +
27C THR* 3.4 0.9 - - - -
28C VAL* 2.8 50.7 + - + +
30C VAL* 4.5 6.3 - - + -
38C ALA* 4.5 9.6 - - + -
39C THR* 1.3 84.0 - - - +
41C SER* 1.3 60.5 + - - +
50C ILE* 3.7 26.1 - - + +
51C GLY* 3.5 33.4 - - - -
52C THR 3.9 5.4 - - - -
53C GLN* 4.1 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C THR* 3.9 14.7 - - - +
26C GLN 3.2 6.4 + - - -
27C THR* 4.4 10.2 + - - -
39C THR* 4.2 8.2 + - - -
40C PHE* 1.3 74.1 - - - +
42C GLY* 1.3 60.5 + - - +
50C ILE* 4.4 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA* 4.4 0.2 - - - +
25C THR* 4.0 6.0 - - - +
26C GLN* 2.8 37.7 + - - +
41C SER* 1.3 78.2 + - - +
43C GLN* 1.3 61.2 - - - -
50C ILE* 3.7 22.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA* 4.4 1.8 - - - -
22C SER 3.0 20.3 - - - +
23C SER* 3.5 24.9 - - - +
24C GLY 3.9 8.3 - - - +
25C THR* 3.8 16.4 - - - +
42C GLY* 1.3 74.6 - - - +
44C SER* 1.3 75.7 + - - +
45C THR* 3.8 8.0 + - - +
48C ALA* 5.4 0.7 - - - +
50C ILE* 4.2 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA* 3.2 26.2 - - - +
21C ASN* 3.2 1.4 + - - -
22C SER 2.8 22.0 + - - +
24C GLY 5.2 0.2 + - - -
43C GLN* 1.3 91.2 - - - +
45C THR* 1.3 59.5 + - - +
46C ASN* 3.0 20.2 + - - +
48C ALA* 3.2 35.4 + - - +
50C ILE* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ASN* 4.0 5.6 - - - +
22C SER* 3.4 35.0 - - - +
23C SER* 4.0 5.4 - - - +
43C GLN* 3.8 8.4 + - - +
44C SER* 1.3 72.5 + - - +
46C ASN* 1.3 61.3 + - - +
47C ASN 3.7 2.2 - - - -
115C FUC 4.4 7.2 - - + -
113D LEU* 5.1 0.5 - - - +
114D GLY* 3.3 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ASN* 3.9 1.1 - - - -
44C SER* 3.0 6.0 + - - +
45C THR* 1.3 83.7 - - - +
47C ASN* 1.3 71.8 + - - +
48C ALA* 3.2 5.8 + - + +
13D ARG* 2.9 32.3 + - - +
54D VAL* 3.3 25.3 - - - +
113D LEU* 4.9 3.8 - - - +
114D GLY 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE* 3.4 30.0 - - - +
20C ALA 3.0 12.0 + - - -
21C ASN* 3.0 33.9 + - - +
46C ASN* 1.3 79.0 - - - +
48C ALA* 1.3 66.6 + - - +
49C VAL* 3.5 1.0 + - - +
15D GLY* 3.7 15.2 - - - -
17D THR* 5.0 1.2 + - - -
52D THR* 5.0 5.1 + - - -
53D GLN 5.4 0.4 + - - -
54D VAL* 4.2 4.6 - - + +
110D ASN* 3.0 32.0 + - - -
113D LEU* 3.5 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE* 3.3 1.6 - - - -
20C ALA 3.1 23.1 + - - -
43C GLN 5.4 0.4 - - - +
44C SER* 3.2 24.6 + - - +
46C ASN* 3.2 4.8 + - + +
47C ASN* 1.3 77.0 - - - +
49C VAL* 1.3 66.9 + - - +
50C ILE* 3.2 7.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 4.0 11.2 - - + -
18C ALA 3.3 6.7 - - - +
19C PHE* 3.7 27.4 - - + +
47C ASN 3.5 0.4 + - - +
48C ALA* 1.3 74.2 - - - +
50C ILE* 1.3 58.8 + - - +
51C GLY 3.4 30.7 - - - +
52C THR* 4.2 10.8 - - + -
17D THR* 5.2 2.5 - - + -
49D VAL* 5.3 5.4 - - + -
52D THR* 4.1 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ALA* 2.8 28.7 + - + +
19C PHE 4.5 2.7 - - - +
20C ALA* 3.8 24.0 - - + -
26C GLN* 4.1 24.5 - - + +
28C VAL* 4.1 13.7 - - + -
40C PHE* 3.7 23.9 - - + +
41C SER 4.4 6.3 + - - +
42C GLY* 3.7 40.2 - - - +
43C GLN* 4.2 4.0 - - - +
44C SER* 5.2 1.3 - - - -
48C ALA* 3.2 8.0 + - + +
49C VAL* 1.3 72.2 - - - +
51C GLY* 1.3 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C THR* 3.3 1.2 - - - -
18C ALA 2.8 27.3 + - - -
40C PHE* 3.5 25.8 - - - -
49C VAL* 3.2 10.5 - - - +
50C ILE* 1.3 83.7 - - - +
52C THR* 1.3 60.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C VAL 3.2 6.5 + - - -
17C THR* 2.8 26.3 + - - -
40C PHE* 3.9 3.1 - - - -
49C VAL* 4.2 7.4 - - + -
51C GLY* 1.3 76.3 - - - -
53C GLN* 1.3 66.1 + - - +
19D PHE* 4.4 1.4 - - - -
47D ASN* 4.9 5.0 + - - -
49D VAL* 3.6 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLY* 3.5 3.6 - - - -
16C VAL* 2.9 37.1 + - + +
37C ALA 4.4 3.6 + - - -
38C ALA* 4.1 12.0 - - - +
40C PHE* 4.1 22.7 - - + -
52C THR* 1.3 80.4 + - - +
54C VAL* 1.3 79.7 + - - +
55C LEU* 3.2 27.4 - - - +
47D ASN* 5.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ARG* 2.9 51.1 - - + +
14C PHE 3.4 2.7 - - - +
15C GLY* 5.0 0.4 - - - -
53C GLN* 1.3 85.3 + - - +
55C LEU* 1.3 68.4 + - - +
113C LEU* 3.7 12.8 - - + -
46D ASN* 3.3 30.5 - - + +
47D ASN* 4.5 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ARG* 3.2 7.5 - - - +
14C PHE* 2.8 52.9 + - + -
16C VAL* 3.9 18.2 - - + -
30C VAL* 3.8 29.2 - - + -
32C VAL* 5.1 1.8 - - + -
37C ALA* 3.9 27.6 - - + +
38C ALA* 4.0 10.8 - - + -
53C GLN* 3.2 30.5 + - - +
54C VAL* 1.3 75.5 - - - +
56C ASN* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASN* 3.4 26.4 + - - +
12C THR 3.6 9.6 - - - -
13C ARG* 4.2 9.0 - - + +
14C PHE* 3.7 4.0 - - - -
32C VAL* 3.5 17.0 - - - +
55C LEU* 1.3 75.8 - - - +
57C SER* 1.3 62.8 + - - +
58C GLY* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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