Contacts of the strand formed by residues 53 - 60 (chain Q) 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 VAL 53 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Q LYS* 3.5 1.6 - - - -
45Q MET* 2.9 45.3 + - + +
47Q LEU* 6.2 3.8 - - + -
51Q GLU 3.6 10.5 - - - +
52Q PRO* 1.3 82.8 - - - +
54Q GLN* 1.3 68.2 + - - +
55Q LEU* 3.7 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Q VAL 3.3 8.3 - - - +
44Q LYS* 3.5 33.9 - - + +
52Q PRO* 5.6 0.9 - - + -
53Q VAL* 1.3 80.5 - - - +
55Q LEU* 1.3 73.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P ARG* 6.4 0.2 - - - -
81P THR* 3.8 36.6 - - + +
82P VAL 6.1 0.2 - - - +
42Q ALA* 3.8 1.6 + - - -
43Q VAL* 2.8 43.0 + - + +
45Q MET* 4.2 23.8 - - + -
53Q VAL* 3.7 22.9 - - + +
54Q GLN* 1.3 91.1 - - - +
56Q GLU* 1.3 63.2 + - - +
57Q THR 3.3 11.0 + - - +
58Q LEU* 4.1 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81P THR* 5.0 0.4 + - - -
82P VAL* 6.1 0.9 - - - +
41Q LYS* 3.5 19.9 - - - +
42Q ALA* 3.5 7.0 + - - +
55Q LEU* 1.3 73.5 - - - +
57Q THR* 1.3 70.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P HIS* 3.9 21.5 + - + +
17P MET* 5.8 0.4 - - + +
81P THR* 2.7 38.7 + - - +
82P VAL* 4.0 29.1 - - + +
40Q LEU 3.4 12.2 + - - -
41Q LYS* 4.4 1.3 - - - +
43Q VAL* 4.5 2.7 - - - +
55Q LEU* 3.1 5.8 + - - +
56Q GLU* 1.3 92.8 - - + +
58Q LEU* 1.3 66.7 + - - +
59Q SER* 5.0 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P ILE* 5.5 1.3 - - + -
79P SER* 3.8 21.3 - - - +
80P MET 3.6 20.9 - - - +
81P THR* 4.2 2.2 - - + -
19Q LEU* 6.3 0.2 - - + -
25Q VAL* 3.7 40.8 - - + -
38Q THR 3.8 0.7 - - - +
39Q HIS* 3.4 1.7 - - - +
40Q LEU* 2.7 36.5 + - + +
43Q VAL* 4.0 18.8 - - + -
45Q MET* 3.9 21.8 - - - -
55Q LEU* 4.1 10.8 - - + -
57Q THR* 1.3 78.4 + - - +
59Q SER* 1.3 65.5 + - - +
60Q ILE* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P MET* 3.6 23.6 - - - +
12P HIS* 4.6 12.1 - - - -
79P SER* 3.1 7.4 - - - -
80P MET* 2.9 41.2 + - - +
38Q THR 3.2 4.5 - - - -
39Q HIS* 2.9 30.5 + - - +
57Q THR* 5.0 1.9 + - - -
58Q LEU* 1.3 75.5 + - - +
60Q ILE* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 60 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78P VAL 3.4 9.4 - - - +
79P SER* 4.5 4.3 - - - -
17Q ILE* 4.2 15.5 - - + -
19Q LEU* 3.9 33.0 - - + -
25Q VAL* 4.1 14.4 - - + -
36Q MET 4.4 0.2 - - - +
37Q ASN* 3.3 3.0 - - - +
38Q THR* 2.8 36.5 + - - +
40Q LEU* 3.8 24.7 - - + -
58Q LEU* 3.9 19.1 - - + -
59Q SER* 1.3 79.7 - - - +
61Q ARG* 1.3 75.3 + - - +
62Q GLY* 3.3 1.6 + - - -
64Q ASN* 4.4 2.0 - - + -
65Q ILE* 4.1 9.9 - - + -
----------------------------------------------------------
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