Contacts of the helix formed by residues 43 - 54 (chain A) in PDB entry 1JQI
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 PRO 43 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.9 24.0 - - + -
41A LEU* 3.4 6.9 - - + +
42A PHE* 1.3 90.0 - - + +
44A THR* 1.3 66.7 + - - +
45A SER 3.4 2.5 - - - -
46A GLN* 3.2 27.2 + - + +
47A VAL* 3.0 35.1 + - + +
88A THR* 3.7 19.3 - - - +
91A ILE* 4.0 13.5 - - + -
211A ALA* 4.4 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 5.3 1.4 - - - +
42A PHE* 2.8 35.8 + - + +
43A PRO* 1.3 71.6 - - - +
45A SER* 1.3 66.1 + - - +
47A VAL* 3.3 2.9 + - - +
48A LYS* 3.2 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO 3.4 0.4 - - - -
44A THR* 1.3 78.9 - - - +
46A GLN* 1.3 74.7 + - - +
48A LYS* 3.3 12.5 + - - +
49A LYS* 3.1 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.9 4.3 - - + -
28A GLU* 4.0 21.4 - - + +
29A LEU* 3.9 22.9 - - + -
32A ILE* 3.1 33.3 - - + +
36A LEU* 5.6 0.8 - - - +
43A PRO* 3.4 34.9 + - + +
44A THR 4.2 0.2 - - - +
45A SER* 1.3 82.9 - - - +
47A VAL* 1.3 66.0 + - - +
49A LYS* 3.2 9.4 + - - +
50A MET* 2.9 28.5 + - - +
88A THR* 5.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PHE* 3.8 28.0 - - + -
43A PRO* 3.0 28.6 + - + +
44A THR 3.7 4.7 - - - +
46A GLN* 1.3 75.0 - - - +
48A LYS* 1.3 58.4 + - - +
50A MET* 3.2 10.9 + - - +
51A GLY 2.9 23.7 + - - -
56A LEU* 3.6 26.6 - - + +
88A THR* 5.0 7.9 - - + -
91A ILE* 4.5 12.6 - - + -
122A GLY 4.5 6.3 - - - +
125A ILE* 4.3 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 3.2 28.1 + - + +
45A SER* 3.5 11.4 - - - +
47A VAL* 1.3 74.9 - - + +
49A LYS* 1.3 66.1 + - + +
51A GLY* 3.1 10.7 + - - -
52A GLU* 3.1 24.1 + - - +
121A ASN 3.8 3.2 - - - +
122A GLY* 4.0 21.5 - - - +
123A ASP* 4.6 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.9 16.4 - - + -
28A GLU* 3.9 32.6 + - + +
45A SER* 3.1 23.3 + - - +
46A GLN* 3.7 8.1 - - + +
48A LYS* 1.3 79.5 - - + +
50A MET* 1.3 62.3 + - - +
52A GLU* 3.2 17.5 + - - +
53A LEU* 3.1 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 3.5 24.7 - - + -
46A GLN* 2.9 19.5 + - - +
47A VAL* 3.3 15.7 - - - +
49A LYS* 1.3 77.0 - - - +
51A GLY* 1.3 62.6 + - - +
53A LEU* 3.0 14.7 + - - +
55A LEU* 3.0 42.2 + - + +
56A LEU* 4.3 8.5 - - + -
81A ILE* 4.0 14.6 - - + -
88A THR* 3.3 28.0 - - + -
92A MET* 3.3 45.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL 2.9 11.1 + - - -
48A LYS 3.1 1.5 + - - -
50A MET* 1.3 77.9 - - - +
52A GLU* 1.3 56.3 + - - +
54A GLY* 2.8 20.1 + - - -
56A LEU* 3.5 25.3 - - - +
120A THR 3.7 10.4 - - - +
121A ASN* 3.4 25.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS* 3.1 24.8 + - - +
49A LYS* 3.2 18.4 + - - +
51A GLY* 1.3 75.4 - - - +
53A LEU* 1.3 61.6 + - + +
54A GLY* 3.0 1.1 + - - -
121A ASN* 4.5 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 4.8 22.2 - - + -
21A CYS* 6.1 1.3 - - - -
24A PHE* 4.1 32.1 - - + -
49A LYS* 3.1 14.1 + - + +
50A MET* 3.0 10.5 + - - +
52A GLU* 1.3 78.1 - - + +
54A GLY* 1.3 60.4 + - - +
55A LEU* 3.6 27.5 + - + +
67A ALA* 5.3 1.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLY 2.8 16.1 + - - -
52A GLU 3.0 1.6 - - - -
53A LEU* 1.3 80.8 - - - +
55A LEU* 1.3 63.5 + - - +
56A LEU 3.2 3.8 + - - -
57A ALA* 3.6 7.4 + - - -
58A MET* 3.6 7.2 - - - +
66A GLY 6.1 0.4 - - - -
67A ALA* 3.4 30.3 - - - +
120A THR 4.9 5.2 - - - -
----------------------------------------------------------
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