Contacts of the strand formed by residues 18 - 24 (chain F) in PDB entry 1BHC
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 ILE 18 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F ALA* 3.2 35.2 - - + -
17F ARG* 1.3 79.9 - - - +
19F ILE* 1.3 75.7 + - - +
20F ARG* 4.0 22.7 - - + +
34F VAL* 3.4 2.7 - - - -
35F TYR* 2.7 44.7 + - + +
37F GLY* 4.9 0.2 - - - -
17J ARG 4.6 6.3 - - - +
19J ILE* 3.4 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F ARG 4.2 0.4 + - - -
18F ILE* 1.3 81.1 - - - +
20F ARG* 1.3 83.2 + - - +
21F TYR* 4.6 13.5 - - + +
32F THR* 4.0 18.8 - - + -
33F PHE 3.4 4.9 - - - +
34F VAL* 5.0 1.8 - - + -
46F LYS 5.2 1.7 - - - +
18G ILE* 3.5 48.7 - - + +
20G ARG* 4.1 10.1 - - - +
35G TYR* 4.0 14.8 - - + -
37G GLY* 3.9 24.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 2.4 47.2 + - - -
53B ARG* 3.7 7.3 - - - +
18F ILE* 4.0 17.0 - - + +
19F ILE* 1.3 84.1 - - - +
21F TYR* 1.3 67.7 + - - +
32F THR* 3.1 6.8 - - - -
33F PHE* 2.9 49.8 + - + -
35F TYR* 3.4 39.6 - - + -
44F ASN* 3.0 19.4 + - - +
45F PHE 3.7 9.0 - - - +
46F LYS* 3.8 27.2 - - - +
19J ILE* 4.2 9.9 - - - +
21J TYR* 5.1 1.0 + - - -
32J THR* 4.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 21 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 2.9 32.0 + - + -
52A MET* 5.7 1.3 - - + -
60A SCN 3.7 15.3 - - - -
19F ILE* 4.6 10.1 - - + +
20F ARG* 1.3 79.8 - - - +
22F PHE* 1.3 63.4 + - - +
30F CYS* 4.6 5.6 - - + -
31F GLN* 3.1 17.9 - - - +
32F THR* 3.6 24.3 - - + +
33F PHE* 3.6 2.2 - - - -
44F ASN* 3.5 5.2 - - - -
45F PHE* 2.9 44.7 + - - +
46F LYS 3.7 14.8 - - - -
48F ALA* 3.6 39.7 - - + -
51F CYS* 4.1 20.6 - - + -
20G ARG* 4.6 0.7 + - - -
46G LYS* 4.2 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 22 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F GLU 4.8 0.4 - - - -
8F PRO* 5.4 0.2 - - + -
9F PRO* 3.4 36.8 - - + -
21F TYR* 1.3 75.5 - - - +
23F TYR* 1.3 74.9 + - - +
24F ASN* 3.5 17.2 + - + -
30F CYS* 3.0 1.9 - - - -
31F GLN* 2.8 62.9 + - + -
32F THR 3.3 20.2 - - - -
33F PHE* 3.6 25.4 - + + -
43F ASN* 3.5 26.7 - - - +
45F PHE* 4.6 0.2 - - - -
51F CYS* 3.7 6.7 - - - -
59F SCN 4.2 5.6 - - - -
39G ARG* 5.1 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 23 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F ARG* 3.2 38.2 + - - -
5F CYS* 3.4 35.4 - - + +
6F LEU 5.6 0.2 - - - -
7F GLU 4.3 1.9 - - - +
22F PHE* 1.3 76.6 - - - +
24F ASN* 1.3 56.6 + - - +
25F ALA* 3.5 23.8 + - + -
28F GLY* 3.4 24.6 + - - -
29F LEU* 3.8 21.8 - - - -
30F CYS* 3.9 11.7 - - - -
43F ASN* 3.0 24.0 + - - +
51F CYS* 3.7 6.0 - - - -
55F CYS* 3.5 38.6 - - + -
56F GLY* 4.0 10.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F PHE* 3.5 18.5 + - + -
23F TYR* 1.3 74.2 - - - +
25F ALA* 1.3 51.0 + - - +
26F LYS* 3.1 21.8 + - - +
27F ALA* 3.3 14.8 + - + +
28F GLY 2.8 30.0 + - - -
29F LEU 2.7 21.7 + - - +
31F GLN* 2.6 33.9 + - + +
----------------------------------------------------------
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