Contacts of the helix formed by residues 47 - 63 (chain A) in PDB entry 1A4I
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 ASP 47 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASN* 3.4 6.0 + - - +
46A ARG* 1.3 73.2 - - - +
48A ASP* 1.3 62.1 + - - +
50A ASN* 3.3 12.7 + - - +
51A LEU* 3.1 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 2.8 48.9 + - - +
47A ASP* 1.3 71.5 + - - +
49A SER* 1.3 73.8 + - - -
51A LEU* 3.1 12.1 + - - +
52A TYR* 2.9 49.0 + - + +
102A PRO* 5.8 0.8 - - - +
240A TYR* 5.6 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 3.7 18.8 - - - -
46A ARG* 3.4 21.0 + - - +
47A ASP 3.3 0.2 - - - -
48A ASP* 1.3 90.1 + - - +
50A ASN* 1.3 58.7 + - - +
52A TYR* 3.8 9.6 - - - +
53A ILE* 2.9 35.0 + - - +
100A GLN* 4.0 22.8 + - - +
101A LEU 4.4 8.3 + - - -
102A PRO* 4.6 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 2.9 17.0 + - - +
45A ASN* 3.0 24.9 + - - +
46A ARG 3.0 19.8 + - - -
47A ASP* 3.5 15.3 + - - +
48A ASP 3.2 0.2 - - - -
49A SER* 1.3 76.3 - - - +
51A LEU* 1.3 57.7 + - + +
53A ILE* 3.8 5.1 - - - +
54A ASN* 2.9 40.9 + - - +
69A HIS* 5.0 2.5 - - - -
71A LYS* 2.7 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP* 3.1 21.2 + - + +
48A ASP* 3.1 10.7 + - - +
50A ASN* 1.3 78.9 - - + +
52A TYR* 1.3 66.7 + - + +
54A ASN* 3.1 14.6 + - + +
55A VAL* 3.1 26.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASP* 2.9 44.1 + - + +
49A SER* 3.8 4.5 - - - +
51A LEU* 1.3 76.3 - - + +
53A ILE* 1.3 66.9 + - - +
55A VAL* 3.3 11.8 + - + +
56A LYS* 3.1 33.7 + - - +
100A GLN* 4.0 21.3 - - - +
101A LEU 6.0 0.2 - - - -
238A ILE* 4.2 15.9 - - + +
240A TYR* 3.8 18.3 + - - -
280A VAL* 5.7 0.3 - - - +
302A NDP 6.0 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 4.0 20.6 - - + -
42A GLN* 3.4 40.8 - - + +
49A SER 2.9 20.8 + - - +
50A ASN* 3.8 3.8 - - - +
52A TYR* 1.3 76.2 - - - +
54A ASN* 1.3 54.6 + - - +
56A LYS* 3.0 8.8 + - - +
57A LEU* 2.7 45.5 + - + +
69A HIS* 3.6 35.2 - - + +
100A GLN* 3.7 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN* 2.9 29.0 + - - +
51A LEU* 3.1 13.8 + - + +
53A ILE* 1.3 79.2 - - - +
55A VAL* 1.3 56.6 + - + +
57A LEU* 3.2 18.4 + - - +
58A LYS* 2.9 29.8 + - - +
69A HIS* 5.3 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 3.1 16.6 + - + +
52A TYR* 3.6 13.0 - - + +
53A ILE 3.2 0.2 - - - -
54A ASN* 1.3 76.8 - - + +
56A LYS* 1.3 62.8 + - - +
58A LYS* 3.3 8.0 + - - +
59A ALA* 3.0 23.5 + - + +
280A VAL* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 5.8 0.9 - - - -
40A ILE* 4.0 21.8 - - + -
52A TYR* 3.1 21.8 + - - +
53A ILE* 3.0 8.2 + - - +
55A VAL* 1.3 74.4 - - - +
57A LEU* 1.3 64.3 + - - +
59A ALA 3.4 0.9 + - - -
60A ALA* 3.0 21.4 + - - +
98A LEU* 4.2 14.1 - - + +
100A GLN* 2.7 34.1 + - - +
125A ASP* 4.9 4.8 + - - -
279A THR* 6.5 1.1 - - - -
280A VAL* 4.3 20.0 - - + -
283A LEU* 3.6 24.8 - - + +
284A MET* 3.5 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ILE* 4.2 15.5 - - + -
53A ILE* 2.7 36.8 + - + +
54A ASN* 3.2 19.0 + - - +
56A LYS* 1.3 72.9 - - - +
58A LYS* 1.3 56.1 + - - +
60A ALA* 3.4 4.6 + - - +
61A GLU* 3.0 31.6 + - - +
67A ALA* 3.5 37.2 - - + +
68A THR 4.7 1.1 - - - +
69A HIS* 4.1 23.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASN 2.9 16.3 + - - +
55A VAL* 3.6 7.6 - - - +
57A LEU* 1.3 72.1 - - - +
59A ALA* 1.4 67.7 + - - +
61A GLU* 3.3 7.2 + - - +
62A GLU* 3.1 46.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 4.2 15.5 - - - +
55A VAL* 3.0 11.7 + - + +
56A LYS 3.8 2.5 - - - +
58A LYS* 1.4 78.3 - - - +
60A ALA* 1.3 63.2 + - - +
62A GLU* 3.3 11.4 + - - +
63A ILE* 3.1 27.9 + - - +
280A VAL* 3.6 31.0 - - + -
284A MET* 4.1 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.8 2.7 - - + -
56A LYS 3.0 17.6 + - - +
57A LEU 3.8 4.0 - - - +
59A ALA* 1.3 76.0 - - - +
61A GLU* 1.3 63.8 + - - +
63A ILE* 3.1 2.4 + - - -
64A GLY 3.0 4.9 + - - -
65A ILE* 2.9 44.4 + - + +
67A ALA* 3.8 25.1 - - + -
284A MET* 3.7 20.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU 3.0 18.5 + - - +
58A LYS* 3.8 6.6 - - - +
59A ALA 3.3 0.2 - - - -
60A ALA* 1.3 76.4 - - - +
62A GLU* 1.3 64.7 + - + +
64A GLY* 3.2 12.6 + - - -
65A ILE 3.9 7.2 + - - -
67A ALA* 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 4.4 16.3 + - + +
21A LYS* 3.4 27.8 + - - +
58A LYS* 3.1 47.1 + - + +
59A ALA* 3.6 11.1 - - - +
60A ALA 3.2 0.2 - - - -
61A GLU* 1.3 81.2 - - + +
63A ILE* 1.3 64.1 + - + +
64A GLY 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 3.7 41.5 - - + +
20A LEU* 4.0 21.8 - - + -
21A LYS* 3.6 18.1 - - + +
24A VAL* 3.5 29.2 - - + +
25A THR* 5.3 0.5 + - - -
59A ALA 3.1 18.6 + - - +
60A ALA 3.8 3.1 - - - +
62A GLU* 1.3 79.7 - - + +
64A GLY* 1.3 57.5 + - - +
65A ILE* 3.7 22.7 - - + -
284A MET* 3.5 33.4 - - + -
288A VAL* 4.6 0.4 - - + -
----------------------------------------------------------
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