Contacts of the strand formed by residues 50 - 56 (chain C) in PDB entry 3OP5
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 CYS 50 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLN 5.4 1.6 - - - -
42C PRO* 4.6 6.1 - - - -
44C GLY 3.3 17.5 - - - +
45C GLN* 4.7 8.5 - - + -
49C GLY* 1.4 75.8 - - - +
51C ILE* 1.3 62.6 + - - +
52C TYR* 3.6 38.4 - - + +
70C VAL 3.5 1.0 - - - +
71C LYS 3.7 0.2 - - - -
72C VAL* 2.7 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C PRO* 3.5 4.2 - - - +
43C ILE* 2.8 42.1 + - + -
44C GLY* 2.8 23.5 + - - +
49C GLY 5.8 1.8 - - - +
50C CYS* 1.3 76.6 - - - +
52C TYR* 1.3 58.8 + - - +
69C VAL* 3.9 28.0 - - + -
70C VAL 3.2 4.3 - - - +
71C LYS* 3.8 21.5 - - + -
365C REB 3.6 69.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLN* 2.9 29.0 + - - +
23C PHE* 3.1 35.4 + + + +
39C VAL* 3.7 17.5 - - + -
40C GLY 4.1 6.7 - - - +
41C LEU 3.4 6.5 - - - +
42C PRO* 3.5 41.1 - - + -
43C ILE* 4.2 5.8 - - - +
50C CYS* 3.6 22.0 - - - +
51C ILE* 1.3 73.3 - - - +
53C LEU* 1.3 59.7 + - - +
69C VAL* 3.2 6.6 - - - +
70C VAL* 2.8 44.7 + - + -
72C VAL* 3.7 34.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL* 3.7 0.7 - - - -
40C GLY* 2.7 30.4 + - - -
41C LEU* 2.9 37.6 + - + +
43C ILE* 3.8 34.5 - - + +
52C TYR* 1.3 76.5 - - - +
54C ALA* 1.3 57.1 + - - +
64C SER* 3.8 27.8 - - - -
66C ALA* 4.0 15.0 - - + -
68C CYS 3.8 2.5 - - - +
133C ARG* 3.7 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C TRP* 5.2 6.3 - - + -
38C LYS 3.4 13.0 - - - +
39C VAL* 5.0 0.7 - - + -
40C GLY* 4.6 0.4 - - - +
53C LEU* 1.3 78.1 - - - +
55C ASP* 1.3 64.0 + - - +
66C ALA* 3.5 9.2 - - - +
68C CYS* 2.9 37.4 + - + +
69C VAL 4.0 21.8 - - - +
70C VAL* 4.1 12.8 - - + +
130C ILE* 5.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C TRP* 3.5 17.3 - - - +
38C LYS* 2.8 35.8 + - + +
54C ALA* 1.3 76.0 - - - +
56C MET* 1.3 84.2 + - - +
66C ALA* 5.1 4.4 - - + -
67C PRO* 3.5 31.2 - - + +
68C CYS* 4.7 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ALA 4.0 8.7 - - - +
37C TRP* 3.8 21.2 - - + -
38C LYS* 4.5 3.5 - - - +
55C ASP* 1.3 93.4 + - - +
57C ASN* 1.3 67.2 + - - +
58C SER* 3.4 7.7 + - - -
114C TRP* 6.4 1.3 - - + -
----------------------------------------------------------
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