Contacts of the strand formed by residues 44 - 54 (chain B) in PDB entry 2BME
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 GLY 44 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A VAL* 3.4 15.5 - - - -
46A GLU* 4.6 0.4 - - - -
64A TRP* 4.7 11.9 - - - -
42B THR* 3.5 5.9 + - - -
43B ILE* 1.3 75.4 - - - +
45B VAL* 1.3 63.1 + - - +
66B THR* 4.7 0.2 - - - -
67B ALA* 3.5 25.4 + - - +
72B PHE* 4.2 9.9 - - - -
75B VAL* 4.8 10.4 - - - +
76B THR* 5.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY* 3.5 1.9 - - - -
45A VAL* 3.0 43.3 + - + +
75A VAL* 5.9 0.9 - - + -
42B THR* 4.3 2.5 - - - +
44B GLY* 1.3 74.0 - - - +
46B GLU* 1.3 75.4 + - - +
64B TRP* 3.9 30.7 - - + -
65B ASP 3.6 18.6 - - - +
66B THR* 4.3 8.7 - - + -
75B VAL* 5.7 0.4 - - + -
79B TYR* 3.2 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.2 30.6 - - + +
44A GLY* 4.9 0.2 - - - -
45A VAL 5.6 0.4 - - - +
46A GLU* 4.2 17.1 - - + +
24B SER* 4.8 4.3 + - - -
27B LEU* 5.7 1.3 - - + -
36B LYS* 5.5 6.9 - - - -
42B THR* 4.1 22.7 + - + +
43B ILE 5.6 0.5 + - - -
45B VAL* 1.3 82.3 - - - +
47B PHE* 1.3 59.3 + - - +
64B TRP* 3.6 6.1 - - - -
65B ASP* 2.8 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 2.8 35.3 + - - +
71A ARG* 4.1 21.4 + - - -
72A PHE* 3.7 31.2 - + + -
27B LEU* 4.4 5.5 - - - +
46B GLU* 1.3 75.8 - - - +
48B GLY* 1.4 73.2 + - - +
49B SER* 3.9 10.8 - - - -
62B GLN* 3.7 45.5 - - + -
63B ILE 3.3 14.1 - - - -
64B TRP* 3.5 42.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 5.6 2.0 - - - -
27B LEU* 4.0 5.9 - - - +
31B ILE* 3.5 23.3 - - - -
47B PHE* 1.4 82.1 - - - +
49B SER* 1.3 62.0 + - - -
62B GLN 3.9 0.2 - - - -
63B ILE* 2.9 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 4.8 10.2 + - - +
31B ILE* 3.7 18.5 - - - +
47B PHE* 3.9 19.8 - - - -
48B GLY* 1.3 75.0 - - - -
50B LYS* 1.3 62.9 + - - +
60B LYS* 4.0 23.6 + - - -
61B LEU 3.1 14.4 - - - -
62B GLN* 4.5 0.4 - - - -
63B ILE* 5.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 3.6 55.9 - - + +
31B ILE* 4.3 13.5 + - + +
33B LYS* 3.1 25.6 - - - +
49B SER* 1.3 79.1 - - - +
51B ILE* 1.3 76.0 + - - +
52B ILE* 4.3 7.2 - - - -
59B VAL 3.7 0.9 - - - +
60B LYS* 4.5 1.3 - - - -
61B LEU* 2.9 33.8 + - - +
63B ILE* 5.2 0.4 - - + +
161B GLU* 3.8 19.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLU 4.0 26.5 - - - +
6B THR 3.8 18.2 - - - +
7B TYR* 4.2 7.2 - - + -
50B LYS* 1.3 84.4 + - - +
52B ILE* 1.3 64.5 + - - +
58B TYR* 4.0 33.8 - - + -
59B VAL 3.3 10.8 - - - +
60B LYS* 3.9 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 3.8 29.8 - - + -
50B LYS* 4.3 10.3 - - + -
51B ILE* 1.3 79.7 - - - +
53B ASN* 1.3 60.2 + - - +
54B VAL* 3.7 20.3 + - + -
57B LYS 3.6 1.2 - - - +
58B TYR* 3.4 3.9 - - - -
59B VAL* 2.8 48.1 + - + +
61B LEU* 4.0 17.0 - - + -
161B GLU* 5.0 5.8 - - - +
164B PHE 4.7 0.2 - - - -
165B VAL* 3.9 28.3 - - + +
168B ALA* 3.8 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 1.3 73.7 - - - +
54B VAL* 1.3 61.0 + - - +
55B GLY 3.9 1.7 + - - -
56B GLY* 2.8 36.1 + - - +
57B LYS 3.6 2.5 - - - -
58B TYR* 3.5 39.8 + - + -
165B VAL* 5.8 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 3.7 32.3 - - + -
53B ASN* 1.3 73.4 - - - +
55B GLY* 1.3 62.3 + - - +
57B LYS* 2.7 42.0 + - + +
59B VAL* 4.2 11.9 - - + -
165B VAL* 4.5 9.9 - - + -
168B ALA* 4.4 8.3 - - + -
169B ARG* 3.7 30.7 - - + +
172B LEU* 3.8 21.8 - - + -
----------------------------------------------------------
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