Contacts of the strand formed by residues 84 - 89 (chain e) in PDB entry 4PJO
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 84 (chain e).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33e VAL* 4.1 7.6 - - + -
34e TRP 3.8 4.0 - - - -
36e TYR* 4.4 4.2 - - - +
54e MET* 3.1 50.0 - - + +
56e LEU* 3.9 19.7 - - + -
79e LEU* 3.9 20.9 - - + -
80e LYS 4.5 0.9 - - - +
81e GLY* 3.1 14.1 + - - +
82e ASP 4.0 2.9 - - - +
83e ASN* 1.3 76.2 - - - +
85e THR* 1.3 65.0 + - - +
86e LEU* 3.7 13.9 - - - +
87e LEU* 4.1 22.4 - - + -
61g VAL* 5.7 0.7 - - + +
63g ARG* 3.2 27.0 - - + +
66g SER* 4.7 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 85 (chain e).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34e TRP* 2.9 13.6 + - + -
35e LEU 3.6 11.9 - - - -
36e TYR* 3.4 19.9 - - - +
83e ASN 3.3 0.6 + - - -
84e ILE* 1.3 74.7 - - - +
86e LEU* 1.3 70.1 + - + +
21g LEU* 4.3 18.2 - - + -
22g ASN* 4.1 2.0 - - - +
25g ARG* 3.4 23.8 + - - +
62g ILE* 3.5 5.9 - - - +
63g ARG 3.1 21.0 + - - -
66g SER* 3.3 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain e).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33e VAL* 3.3 6.1 - - - +
34e TRP* 2.7 91.5 + - + +
84e ILE* 3.7 2.8 - - - +
85e THR* 1.3 84.4 - - + +
87e LEU* 1.3 72.7 - - - +
88e GLN* 4.1 4.9 - - + +
21g LEU* 4.4 5.2 - - + -
27g VAL* 4.5 7.6 - - + -
57g ILE* 4.9 4.0 - - + -
60g VAL* 3.6 24.7 - - + -
61g VAL 3.3 11.2 - - - +
62g ILE* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain e).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21e ILE* 4.0 33.7 - - + -
24e TYR* 3.9 11.6 + - + -
31e ILE* 3.8 13.9 - - + -
32e GLN 3.6 0.2 - - - -
33e VAL* 3.7 30.1 - - + -
47e ILE* 4.8 6.5 - - + -
54e MET* 4.9 4.5 - - - -
56e LEU* 4.2 17.5 - - + -
84e ILE* 4.1 17.7 - - + -
86e LEU* 1.3 76.8 - - - +
88e GLN* 1.3 55.8 + - - +
60g VAL* 2.5 33.3 - - - +
61g VAL* 2.7 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 88 (chain e).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24e TYR* 4.9 3.8 - - - -
31e ILE* 3.1 22.0 - - - +
32e GLN* 2.9 49.0 + - + +
34e TRP* 2.6 37.4 + - - -
42e ARG* 3.6 6.0 + - - +
86e LEU* 4.1 4.3 - - + -
87e LEU* 1.3 74.4 - - - +
89e SER* 1.3 69.4 + - - +
90e VAL 5.3 3.0 + - - -
47g GLU* 4.8 3.8 + - - -
57g ILE* 2.8 43.8 - - + +
59g MET 5.1 0.2 - - - -
60g VAL* 4.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain e).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24e TYR* 4.4 10.7 - - - -
29e SER* 4.1 20.1 - - - -
30e ARG 3.7 1.8 - - - -
31e ILE* 4.2 4.4 - - - +
32e GLN 5.2 0.2 - - - -
88e GLN* 1.3 86.5 + - - +
90e VAL* 1.3 82.7 + - - +
57g ILE* 4.2 13.8 + - - +
59g MET 4.9 4.6 + - - -
----------------------------------------------------------
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