Contacts of the helix formed by residues 38 - 48 (chain U) in PDB entry 5JPQ
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 38 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843 G 2.6 20.6 - - - -
2643 G 3.4 7.4 - - - -
37U LYS* 1.3 73.7 - - - +
39U THR* 1.3 59.8 + - - -
40U ASN 3.4 2.2 - - - -
41U GLU 3.4 3.4 + - - -
42U THR* 2.9 29.8 + - - -
99U THR* 4.7 7.9 - - - -
101U SER 3.1 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 39 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843 G 2.9 14.8 + - - -
38U GLY* 1.3 71.1 - - - -
40U ASN* 1.3 56.4 + - - +
42U THR* 3.4 6.9 + - - -
43U THR* 2.9 29.5 + - - -
65U ILE* 4.7 17.7 - - - -
66U VAL* 5.7 3.1 - - - -
100U ALA* 5.0 12.3 - - - +
101U SER* 4.0 16.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 40 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843 G 4.8 0.8 + - - -
2623 C 4.5 5.1 + - + +
2633 U 3.6 15.9 + - + +
2643 G 4.8 6.7 + - - +
291S PRO* 3.8 20.7 - - + +
292S ALA* 4.5 14.6 - - + +
293S SER* 5.6 1.6 - - - +
38U GLY 3.4 0.4 - - - -
39U THR* 1.3 78.7 - - - +
41U GLU* 1.3 61.7 + - - +
43U THR* 3.4 7.6 + - - -
44U LYS* 3.2 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2623 C 4.1 0.4 - - - -
2633 U 2.1 50.8 + - + +
2643 G 2.9 22.9 + - - +
36U LYS* 4.1 10.2 - - + +
37U LYS 3.9 4.7 - - - +
38U GLY* 3.4 8.2 + - - +
40U ASN* 1.3 73.6 - - - +
42U THR* 1.3 63.9 + - - +
44U LYS* 3.6 2.2 + - - +
45U ALA* 3.2 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 42 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36U LYS* 4.8 1.7 - - - +
38U GLY 2.9 19.3 + - - -
39U THR* 3.7 7.6 - - - -
40U ASN 3.3 0.2 - - - -
41U GLU* 1.3 73.6 - - - +
43U THR* 1.3 65.0 + - - +
45U ALA* 3.1 17.8 + - - +
46U VAL* 3.1 14.1 + - - +
54U VAL* 6.2 2.2 - - - -
101U SER* 4.5 9.4 - - - -
102U ALA* 4.4 24.0 - - - -
103U ALA* 4.5 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 43 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289S LYS 5.0 7.6 - - - -
290S MET 5.4 0.7 - - - -
291S PRO* 4.3 17.9 - - - -
39U THR 2.9 18.8 + - - -
40U ASN* 3.4 9.6 - - - -
42U THR* 1.3 76.0 - - - +
44U LYS* 1.3 57.4 + - - +
46U VAL* 3.1 7.6 + - - +
47U GLU* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 44 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2613 U 4.2 5.5 + - - +
2623 C 2.2 46.6 + - - +
2633 U 4.9 1.1 - - - +
291S PRO* 5.0 0.6 - - - +
40U ASN 3.2 9.5 + - - +
41U GLU* 3.9 8.5 - - - +
42U THR 3.3 0.2 - - - -
43U THR* 1.3 79.5 - - - +
45U ALA* 1.3 57.5 + - - +
47U GLU* 3.8 7.1 - - - +
48U ARG* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36U LYS* 4.7 6.3 - - + -
41U GLU 3.2 13.0 + - - +
42U THR 3.1 10.7 + - - +
44U LYS* 1.3 78.9 - - - +
46U VAL* 1.3 58.6 + - - +
48U ARG* 4.8 2.7 - - - -
49U GLY* 3.3 2.1 + - - -
50U GLN* 2.9 35.2 + - + -
51U ALA* 3.3 25.0 + - + +
103U ALA* 4.3 10.5 - - + -
105U LEU* 6.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42U THR 3.1 9.9 + - - +
43U THR* 3.1 11.0 + - - +
45U ALA* 1.3 74.7 - - - +
47U GLU* 1.3 59.7 + - - +
48U ARG 3.1 1.6 - - - -
49U GLY* 2.8 21.7 + - - -
51U ALA* 4.8 5.8 - - + +
72U LEU* 4.9 23.8 - - + +
73U CYS* 5.3 7.0 - - + +
76U LYS* 4.1 17.7 - - + +
78U ILE* 5.7 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2613 U 2.8 31.3 + - + +
43U THR 2.9 15.5 + - - +
44U LYS* 3.8 8.7 - - - +
46U VAL* 1.3 78.3 - - - +
48U ARG* 1.3 56.7 - - - +
49U GLY 3.6 0.3 + - - -
72U LEU* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 48 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2603 G 4.9 6.7 - - - +
2613 U 2.9 27.8 + - - +
44U LYS 2.9 19.1 + - - +
45U ALA* 4.4 3.8 - - - +
47U GLU* 1.3 76.3 - - - +
49U GLY* 1.3 62.4 + - - +
50U GLN* 3.3 8.9 + - + +
----------------------------------------------------------
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