Contacts of the strand formed by residues 30 - 35 (chain C) in PDB entry 3BSQ
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 GLN 30 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C HIS* 3.0 24.4 + - + +
28C PRO 4.5 3.1 - - - +
29C TRP* 1.3 85.3 - - + +
31C VAL* 1.3 74.4 + - - +
42C GLY* 4.5 2.1 - - - -
43C GLY 3.7 8.5 + - - +
44C VAL* 4.8 0.2 - - - -
66C LEU* 4.3 5.9 - - - +
67C GLY* 5.1 0.3 - - - -
68C SER* 3.9 14.7 + - - +
133C SER* 2.7 40.9 + - - +
134C GLY* 4.2 3.8 - - - -
135C TRP* 3.7 24.7 - - + -
149C LEU* 3.8 17.4 - - + +
193C GLY* 4.4 1.6 - - - -
194C PRO* 3.2 25.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C PRO 5.9 0.4 - - - +
29C TRP 3.9 8.5 - - - +
30C GLN* 1.3 83.1 - - - +
32C ALA* 1.3 63.9 + - - +
33C LEU* 4.8 2.2 - - + -
42C GLY* 3.7 1.7 - - - -
43C GLY* 3.0 42.6 + - - +
44C VAL 3.9 0.4 - - - +
45C LEU* 4.2 9.9 - - + -
51C VAL* 3.7 25.1 - - + -
64C VAL* 4.2 10.8 - - + -
65C HIS 3.2 9.4 - - - +
66C LEU* 3.4 34.1 - - + -
135C TRP* 3.3 16.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C VAL* 1.3 75.0 - - - +
33C LEU* 1.3 64.6 + - - +
34C LEU* 3.9 4.5 - - + -
39C LEU* 4.2 12.1 - - + -
41C CYS 3.7 4.0 - - - -
63C THR 3.4 1.4 - - - +
64C VAL* 3.4 5.5 - - - +
65C HIS* 2.7 55.8 + - + +
71C LEU* 4.0 8.5 - - + -
135C TRP* 3.6 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C VAL* 4.8 1.6 - - + -
32C ALA* 1.3 75.7 - - - +
34C LEU* 1.3 61.8 + - - +
39C LEU* 4.0 0.7 - - - -
40C HIS* 2.9 28.6 + - + +
41C CYS* 2.8 29.6 + - + +
42C GLY 4.4 7.2 - - - +
51C VAL* 4.6 13.9 - - + -
53C THR* 3.6 34.8 - - + +
57C CYS* 4.8 2.9 - - + +
59C MET* 6.5 0.2 - - - -
62C TYR* 3.9 35.7 - - + -
63C THR 3.5 2.7 - - - +
64C VAL* 3.6 33.4 - - + -
100C MET* 4.9 0.2 - - + -
102C VAL* 4.6 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ALA* 4.5 6.3 - - + +
33C LEU* 1.3 77.4 - - - +
35C SER* 1.3 61.1 + - - +
36C GLY 4.7 1.3 - - - +
37C ASN* 4.3 23.6 - - - +
38C GLN 3.3 9.6 - - - +
39C LEU* 3.6 34.3 - - + +
40C HIS* 4.6 1.8 - - - -
59C MET* 5.2 1.4 - - - +
62C TYR* 3.9 6.2 + - - -
63C THR* 2.8 55.2 + - + +
65C HIS* 3.9 25.1 - - + -
71C LEU* 4.7 14.1 - - + -
78C ARG* 6.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU* 1.3 73.6 - - - +
36C GLY* 1.3 63.1 + - - +
38C GLN* 2.8 34.1 + - - +
40C HIS* 4.3 6.9 - - - +
59C MET* 3.3 37.0 - - - +
60C ASN* 5.2 2.8 + - - -
61C GLU 4.8 3.9 + - - -
62C TYR 5.6 0.9 - - - +
63C THR* 5.6 0.4 - - - -
----------------------------------------------------------
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