Contacts of the strand formed by residues 25 - 32 (chain B) in PDB entry 1BWN
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 PHE 25 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.6 29.8 - - + +
12B LYS 3.1 4.7 - - - -
13B ARG* 3.8 40.2 - - + -
23B LEU* 5.0 7.0 - - + -
24B ASN* 1.3 83.5 - - + +
26B LYS* 1.3 70.9 - - - +
70B GLU* 5.2 3.1 - - - -
76B GLU* 3.7 7.4 - - - +
77B ARG* 3.5 47.3 - - - -
114B PHE* 4.1 14.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLU* 4.8 8.3 + - - +
1B 4IP 3.9 41.8 + - - +
11B LEU* 3.4 6.4 - - - -
12B LYS* 2.9 36.2 + - + +
24B ASN* 4.2 16.6 - - - +
25B PHE* 1.3 83.2 - - - +
27B LYS* 1.3 63.2 + - - +
28B ARG* 3.5 41.1 - - + +
172B 4IP 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 4.6 1.4 + - - -
44A PHE* 2.5 56.9 + - + +
45A GLU* 3.6 25.6 + - - +
46A ARG 4.0 0.4 - - - -
47A GLY* 2.9 26.7 - - - +
9B ILE* 4.5 2.7 - - + -
10B PHE 3.2 6.5 - - - +
11B LEU* 3.9 10.4 - - + +
26B LYS* 1.3 72.7 - - - +
28B ARG* 1.3 80.6 + - - +
40B TYR 4.6 0.2 - - - +
42B TYR 5.0 1.4 + - - -
76B GLU* 5.6 2.9 - - - +
95B ILE 3.1 25.7 + - - -
96B GLU* 4.3 4.8 - - - +
98B PHE* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLU* 3.8 16.0 + - - -
1B 4IP 2.7 37.6 + - - -
9B ILE* 3.3 6.1 - - - -
10B PHE 2.6 35.6 + - - +
12B LYS* 3.9 17.0 - - + -
26B LYS* 3.5 36.6 - - - +
27B LYS* 1.3 90.4 + - - +
29B LEU* 1.3 61.4 + - - +
30B PHE* 3.6 19.5 - - + -
39B TYR* 4.2 11.0 - - + -
40B TYR 3.3 20.0 - - - +
41B LYS* 3.8 19.7 - - - +
42B TYR* 5.2 2.9 - - - +
53B LYS* 3.6 22.2 - - - +
172B 4IP 4.4 7.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ILE* 3.8 17.0 - - + -
7B GLU* 3.8 34.3 - - + +
8B SER 3.3 16.8 - - - +
9B ILE* 4.0 9.0 - - + +
28B ARG* 1.3 72.1 - - - +
30B PHE* 1.3 59.1 + - - +
31B LEU* 4.6 5.2 - - + -
39B TYR* 3.3 2.6 - - - -
40B TYR* 2.9 42.4 + - + +
42B TYR* 4.3 25.2 - - + +
49B ARG* 3.4 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLU* 3.2 6.2 - - - +
8B SER 2.7 33.5 + - - +
10B PHE* 3.6 37.5 - + + -
12B LYS* 3.9 29.2 - - + -
28B ARG* 3.6 25.8 - - + -
29B LEU* 1.3 73.8 - - - +
31B LEU* 1.3 63.5 + - - +
37B LEU* 4.2 17.0 - - + -
38B SER 3.4 7.9 - - - -
39B TYR* 3.7 28.7 - + + -
102B PHE* 6.3 0.4 - + - -
111B LEU* 4.1 15.3 - - + -
113B VAL* 4.2 15.3 - - + -
124B TRP* 3.5 18.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 3.8 19.7 - - + -
6B LEU 3.5 4.3 - - - +
7B GLU* 2.7 52.9 - - + +
29B LEU* 4.6 4.3 - - + -
30B PHE* 1.3 75.0 - - - +
32B LEU* 1.3 60.3 + - - +
33B THR* 4.1 4.6 - - + +
36B LYS 3.7 1.4 - - - +
37B LEU* 3.5 4.7 - - - +
38B SER* 3.0 35.1 + - - +
40B TYR* 3.8 30.7 - - + +
49B ARG* 3.8 25.6 - - + +
124B TRP* 4.1 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 3.5 1.9 - - - -
5B ILE* 2.5 55.1 + - + +
6B LEU* 3.1 14.8 + - + +
31B LEU* 1.3 72.5 - - - +
33B THR* 1.3 85.6 + - - +
36B LYS 3.4 11.2 - - - +
37B LEU* 4.4 7.6 - - + -
58B VAL* 4.4 6.5 - - + -
124B TRP* 3.6 24.2 - - + -
127B GLN* 4.3 20.6 - - + +
128B LEU* 3.7 29.6 - - + -
131B VAL* 4.5 5.2 - - + -
----------------------------------------------------------
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