Contacts of the strand formed by residues 47 - 54 (chain B) in PDB entry 4PBY
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 ALA 47 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B THR* 1.3 78.7 + - - +
48B GLN* 1.3 63.9 + - - +
66B LEU* 4.9 0.4 - - + -
67B VAL 3.4 8.7 - - - -
68B LEU* 4.0 10.3 - - + -
131B ARG* 3.4 7.4 + - - -
379B ASP* 2.9 21.8 + - + +
380B PHE* 4.2 12.7 - - - +
381B SER* 3.9 9.6 - - - +
391B CYS* 4.5 11.7 - - - -
393B VAL* 4.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 1.3 77.5 - - - +
49B TRP* 1.3 72.0 + - - +
66B LEU* 3.8 4.8 - - - +
67B VAL* 2.7 43.4 + - + +
130B ALA 3.6 3.7 - - - +
131B ARG* 3.0 54.8 - - - +
132B TYR* 3.1 35.2 + - + +
381B SER* 3.7 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLN* 1.3 86.3 - - - +
50B LEU* 1.3 64.7 + - - +
64B HIS* 3.5 26.9 - - + -
65B ARG 3.4 15.9 - - - -
66B LEU* 3.4 20.9 - - + -
84B VAL* 3.8 35.9 - - + -
86B LEU* 4.6 3.4 - - + -
132B TYR* 3.5 8.7 + - - -
381B SER* 3.2 48.6 + - - +
382B TRP 3.6 0.4 - - - -
383B ASN* 3.5 44.6 - - + +
384B PRO* 3.6 20.8 - - + +
389B VAL* 4.2 13.2 - - + -
391B CYS* 3.5 22.8 - - + +
401B VAL* 4.5 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLN 3.6 0.4 + - - -
49B TRP* 1.3 84.3 - - - +
51B PRO* 1.3 77.4 - - + +
52B ASP* 3.2 11.1 + - - +
64B HIS* 5.9 0.7 - - - +
65B ARG* 2.7 65.8 + - + +
66B LEU 4.4 0.4 - - - -
67B VAL* 3.8 29.2 - - + -
81B ILE* 4.1 19.5 - - + -
132B TYR* 4.4 8.3 - - + -
137B PRO* 3.5 28.0 - - + +
140B ILE* 5.3 0.9 - - + -
154B TYR* 4.9 6.5 - - + +
384B PRO* 3.9 5.8 - - - +
385B ASN* 4.6 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 1.3 88.2 - - + +
52B ASP* 1.3 73.5 + - - +
53B VAL* 4.9 0.5 - - - +
132B TYR* 3.7 33.2 - - + +
134B PRO 5.8 0.9 - - - +
137B PRO* 4.0 23.3 - - + -
384B PRO* 4.3 13.8 - - + +
385B ASN* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.2 9.7 - - - +
51B PRO* 1.3 98.7 - - - +
53B VAL* 1.3 63.1 + - - +
54B THR* 5.4 5.8 - - + -
63B ILE 4.2 4.2 - - - +
64B HIS* 4.3 10.7 + - - +
65B ARG* 4.5 24.4 + - - +
137B PRO* 4.0 14.2 - - - +
385B ASN* 4.3 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B PRO 4.9 0.4 - - - +
52B ASP* 1.3 76.3 - - - +
54B THR* 1.3 67.2 + - - +
55B ARG* 3.8 30.1 + - - +
62B SER* 3.9 15.3 - - - -
63B ILE 3.4 10.5 - - - +
64B HIS* 3.5 30.7 - - + +
385B ASN* 3.4 32.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP* 5.4 4.3 - - + -
53B VAL* 1.3 78.2 - - - +
55B ARG* 1.3 61.6 + - - +
56B PRO* 3.2 9.3 - - - +
62B SER* 3.8 0.3 - - - -
63B ILE* 3.0 52.8 + - + +
65B ARG* 6.3 3.8 - - - -
----------------------------------------------------------
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