Contacts of the helix formed by residues 44 - 55 (chain A) in PDB entry 3AZJ
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 44 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO* 1.3 70.5 - - - +
45A THR* 1.3 63.2 + - - +
46A VAL 3.2 1.3 - - - -
47A ALA* 3.3 15.9 - - - +
48A LEU* 3.1 27.4 + - - +
44B GLN* 5.4 1.1 - - - -
228J A 2.8 20.3 + - - -
229J A 2.9 7.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 4.3 11.9 - - + -
42A ARG* 2.6 33.8 + - - +
43A PRO 3.2 1.5 + - - -
44A GLY* 1.3 74.1 - - - +
46A VAL* 1.3 63.9 + - - +
48A LEU* 3.6 7.7 + - - +
49A ARG* 3.3 25.3 + - - +
142I T 3.8 23.8 - - - +
143I T 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 4.0 9.9 - - + -
45A THR* 1.3 75.8 - - - +
47A ALA* 1.3 55.5 + - - +
49A ARG* 2.7 55.8 + - - +
50A GLU* 2.8 34.1 + - + +
229J A 2.9 36.0 + - + +
230J C 3.9 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY* 3.3 22.4 - - - +
46A VAL* 1.3 74.4 - - - +
48A LEU* 1.3 64.6 + - - +
50A GLU* 2.9 16.2 + - - +
51A ILE* 3.0 17.4 + - - +
39B ARG* 3.7 24.9 + - - +
44B GLN* 3.6 28.7 - - + +
228J A 4.8 1.3 - - - +
229J A 2.9 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY 3.1 11.3 + - - +
45A THR* 3.8 11.2 - - - +
47A ALA* 1.3 78.1 - - - +
49A ARG* 1.3 62.7 + - - +
51A ILE* 3.1 24.0 + - + +
52A ARG* 3.0 50.4 + - - +
44B GLN* 5.1 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TYR* 3.2 54.4 + - - -
45A THR* 3.3 17.1 + - - +
46A VAL* 2.7 42.0 + - + +
48A LEU* 1.3 75.2 - - - +
50A GLU* 1.3 55.0 + - + +
52A ARG* 3.1 15.9 + - + +
53A ARG* 2.9 27.2 + - + +
142I T 5.5 4.2 - - - -
154J T 3.5 24.0 + - - -
155J C 2.9 32.7 + - - +
230J C 5.3 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 2.8 39.9 + - + +
47A ALA* 2.9 5.4 + - - +
49A ARG* 1.3 69.0 - - + +
51A ILE* 1.3 57.4 + - - +
53A ARG* 4.1 10.1 + - - +
54A TYR* 2.7 59.2 + - + -
35B ARG* 4.8 7.6 + - - +
36B ARG* 5.9 1.5 - - - +
39B ARG* 2.8 36.7 + - - +
229J A 5.4 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA 3.0 17.4 + - - +
48A LEU* 3.3 24.2 - - + +
50A GLU* 1.3 76.3 - - - +
52A ARG* 1.3 65.6 + - + +
55A GLN* 2.8 57.7 + - - +
39B ARG* 3.7 30.1 - - - +
42B GLY* 3.6 26.2 - - - +
43B VAL 3.8 10.5 - - - +
44B GLN* 4.2 13.7 - - + +
110G ASN 5.4 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.0 54.8 + - - +
49A ARG* 3.3 14.6 - - + +
51A ILE* 1.3 81.1 - - + +
53A ARG* 1.3 65.3 + - - +
55A GLN* 3.5 6.7 + - - +
56A LYS* 3.5 26.5 + - - +
109G PRO* 6.1 0.2 - - - +
142I T 5.8 1.8 + - - -
155J C 5.8 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 2.9 12.7 + - + +
50A GLU* 3.5 13.0 + - - +
52A ARG* 1.3 76.9 - - - +
54A TYR* 1.3 102.7 + - + +
56A LYS* 3.0 27.0 + - - +
57A SER* 3.3 12.0 + - - +
59A GLU* 5.1 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 2.7 51.9 + - + +
51A ILE 4.4 0.4 - - - +
53A ARG* 1.3 112.6 + - + +
55A GLN* 1.3 58.5 - - - +
56A LYS 3.1 1.2 + - - -
57A SER* 3.6 5.9 - - - +
59A GLU* 4.0 14.6 - - - -
61A LEU* 3.4 34.1 - - + -
36B ARG* 3.0 35.0 - - + +
39B ARG* 4.1 8.7 - - + -
40B ARG* 2.9 52.5 + - + +
107G VAL* 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 2.8 37.9 + - + +
52A ARG* 4.0 3.9 - - - +
54A TYR* 1.3 73.4 - - - +
56A LYS* 1.3 57.4 + - - +
57A SER 4.5 0.7 - - - -
105A GLU* 5.1 2.2 + - - -
39B ARG 3.9 4.3 - - - +
40B ARG 3.0 28.3 + - - +
41B GLY 4.0 1.6 - - - -
42B GLY* 3.5 21.2 - - - +
81G ARG* 3.3 5.3 + - - -
107G VAL* 3.2 34.4 - - + +
108G LEU 4.4 4.6 + - - -
109G PRO* 3.4 20.3 - - + +
110G ASN 2.6 38.7 + - - +
----------------------------------------------------------
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