Contacts of the strand formed by residues 19 - 24 (chain K) in PDB entry 2BX5
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 VAL 19 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J PRO* 5.4 5.8 - - + -
11K LEU* 3.4 35.4 - - + -
13K ALA* 4.4 12.6 - - + -
17K ASP 3.8 0.4 + - - -
18K ARG* 1.3 77.0 - - - +
20K THR* 1.3 59.7 + - - +
21K ILE* 3.7 14.8 - - + -
73K LEU 3.8 0.9 - - - +
74K THR* 3.5 3.0 - - - +
75K ILE* 2.7 62.7 + - + +
78K LEU* 3.7 31.2 - - + -
104K VAL* 3.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 20 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J PRO* 6.2 1.2 - - - +
20J THR* 3.5 41.6 - - + +
22J THR* 3.8 25.0 + - - +
7K SER 4.6 2.3 - - - +
8K PRO* 4.8 6.2 - - - +
11K LEU* 5.1 2.8 - - - +
18K ARG* 4.1 2.5 + - - -
19K VAL* 1.3 74.1 + - - +
21K ILE* 1.3 68.1 + - - +
22K THR* 4.3 3.4 + - - +
72K THR* 5.0 11.7 - - + -
73K LEU 3.9 3.8 - - - +
74K THR* 4.2 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 21 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K GLN* 3.6 17.9 - - + +
7K SER 3.3 17.9 - - - +
8K PRO* 4.3 2.0 - - + -
11K LEU* 4.3 4.5 - - + -
19K VAL* 3.7 15.5 - - + -
20K THR* 1.3 76.9 - - - +
22K THR* 1.3 59.9 + - - +
35K TRP* 4.2 2.5 - - + -
72K THR* 3.2 6.6 - - - -
73K LEU* 2.8 56.9 + - + +
75K ILE* 4.7 1.8 - - + -
86K TYR* 4.0 22.7 - - + -
102K THR* 3.4 25.1 - - + +
104K VAL* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 22 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J ARG* 3.5 42.9 - - + +
19J VAL 5.6 0.2 - - - -
20J THR* 4.0 12.5 + - - -
5K THR 3.5 1.2 - - - +
6K GLN* 3.4 3.2 - - - +
7K SER* 2.7 56.4 + - - +
20K THR* 4.9 2.4 + - - +
21K ILE* 1.3 75.4 - - - +
23K CYS* 1.3 70.1 + - - +
24K ARG* 3.9 8.5 - - + -
35K TRP* 4.7 1.6 - - - -
70K ASP* 4.3 5.2 - - - +
71K PHE 3.6 5.8 - - - +
72K THR* 4.3 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 23 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K MET* 3.6 20.9 - - - -
5K THR 3.2 9.2 - - - -
6K GLN* 4.4 0.4 - - - +
21K ILE 4.2 0.6 + - - -
22K THR* 1.3 73.5 - - - +
24K ARG* 1.3 78.8 + - - +
33K LEU* 4.2 3.8 - - - -
35K TRP* 3.6 15.9 - - + -
71K PHE* 2.5 40.8 + - + +
88K CYS* 2.0 55.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J ARG* 3.7 18.7 - - + +
4K MET* 3.5 3.2 - - - +
5K THR* 2.9 48.9 + - - +
22K THR* 3.9 13.0 - - + -
23K CYS* 1.3 88.1 - - - +
25K ALA* 1.3 64.3 + - - +
69K THR* 2.8 46.1 + - - +
70K ASP* 3.6 24.0 + - - +
71K PHE* 4.6 1.8 - - - +
----------------------------------------------------------
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