Contacts of the helix formed by residues 30 - 42 (chain A) in PDB entry 1XPU
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 ARG 30 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A MET* 1.3 75.3 - - - +
31A LYS* 1.3 67.3 + - - +
32A GLN* 3.0 34.3 - - + +
33A ASP* 2.8 43.1 + - - +
34A ILE* 3.1 9.6 + - - +
76A PRO* 5.2 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU 4.8 0.4 - - - -
7A LYS* 2.7 39.7 + - - +
8A ASN 5.1 1.6 + - - -
9A THR 4.1 13.9 + - - -
10A PRO* 5.5 2.2 - - - +
11A VAL* 3.8 37.9 - - + +
14A LEU* 5.2 4.7 - - + -
29A MET 3.8 1.2 + - - -
30A ARG* 1.3 71.6 - - - +
32A GLN* 1.3 62.2 + - - +
34A ILE* 3.3 15.3 + - - +
35A ILE* 3.1 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 2.9 42.1 + - + +
31A LYS* 1.3 80.2 - - - +
33A ASP* 1.3 64.3 + - - +
35A ILE* 3.3 13.1 + - - +
36A PHE* 3.2 51.3 + - + -
76A PRO* 3.5 26.6 - - + +
77A ASP* 3.2 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A MET* 4.0 23.9 - - + +
30A ARG* 2.8 42.2 + - - +
32A GLN* 1.3 76.7 - - - +
34A ILE* 1.3 52.5 + - - +
36A PHE* 3.3 8.5 + - - +
37A ALA* 2.7 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 4.4 10.5 - - + -
14A LEU* 3.9 23.1 - - + +
15A ILE* 4.3 18.4 - - + -
26A LEU* 3.5 28.0 - - + +
27A ALA* 5.5 0.4 - - - -
29A MET* 3.3 35.4 - - + +
30A ARG 3.1 8.2 + - - +
31A LYS* 3.5 16.2 - - - +
33A ASP* 1.3 76.9 - - - +
35A ILE* 1.3 56.6 + - - +
37A ALA* 3.2 7.1 + - - +
38A ILE* 2.9 52.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.3 12.6 - - + -
6A LEU* 4.0 17.5 - - + -
7A LYS* 3.8 32.5 - - + +
14A LEU* 3.7 24.0 - - + -
31A LYS* 3.1 33.7 + - + +
32A GLN* 3.3 17.2 + - - +
34A ILE* 1.3 75.1 - - - +
36A PHE* 1.3 63.0 + - + +
38A ILE* 3.1 5.4 + - - +
39A LEU* 2.9 49.5 + - + +
77A ASP* 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 5.6 0.7 - - + -
32A GLN* 3.2 38.7 + - + +
33A ASP* 3.6 11.2 - - - +
35A ILE* 1.3 84.1 - - + +
37A ALA* 1.3 57.5 + - - +
40A LYS* 2.9 34.9 + - - +
76A PRO* 3.6 22.4 - - + -
77A ASP* 3.6 13.2 - - + -
104A PRO* 4.8 10.8 - - + -
109A ARG 3.9 19.5 - - - -
110A TYR* 5.6 0.2 - - - -
111A PHE* 3.5 42.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.7 12.7 - - + +
26A LEU* 4.4 16.6 - - + -
29A MET* 4.6 6.7 - - + -
33A ASP 2.7 22.6 + - - +
34A ILE* 3.6 8.1 - - - +
36A PHE* 1.3 73.1 - - - +
38A ILE* 1.3 57.7 + - - +
40A LYS* 4.5 7.0 - - - +
41A GLN* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 5.8 2.2 - - - +
6A LEU* 3.9 17.7 - - + -
14A LEU* 3.5 45.3 - - + +
17A LEU* 4.7 13.2 - - + -
18A GLY* 4.1 10.5 - - - +
21A MET* 4.5 18.2 - - + +
23A LEU* 3.7 19.3 - - + -
34A ILE* 2.9 24.1 + - + +
35A ILE 3.5 4.7 - - - +
37A ALA* 1.3 76.1 - - - +
39A LEU* 1.3 66.9 + - + +
40A LYS 3.2 0.2 - - - -
41A GLN* 3.0 20.1 + - - +
42A HIS* 3.3 14.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 4.4 15.9 - - - +
2A ASN 4.5 0.4 - - - -
3A LEU* 3.6 42.0 - - + +
6A LEU* 3.7 20.0 - - + -
35A ILE* 2.9 31.5 + - + +
38A ILE* 1.3 74.3 - - + +
40A LYS* 1.3 62.3 + - - +
42A HIS* 3.4 10.2 + - - +
49A ILE* 3.2 51.7 - - + +
103A PRO* 4.4 1.8 - - - -
111A PHE* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A PHE 2.9 21.9 + - - +
37A ALA* 4.5 6.5 - - - +
39A LEU* 1.3 74.9 - - - +
41A GLN* 1.3 58.1 + - - +
42A HIS 3.1 0.8 - - - -
43A ALA* 2.9 27.8 + - + +
103A PRO* 4.0 25.7 - - + +
104A PRO 4.9 10.0 + - - +
106A GLU* 4.4 14.8 + - - -
111A PHE* 5.1 1.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 4.1 35.1 + - + +
22A GLY 6.1 0.2 - - - -
23A LEU* 4.0 21.5 - - + +
37A ALA 3.2 20.3 + - - +
38A ILE* 3.0 12.0 + - - +
40A LYS* 1.3 73.4 - - - +
42A HIS* 1.3 52.3 + - - +
43A ALA* 2.6 22.1 + - - +
44A LYS* 3.6 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.4 21.4 + - - +
21A MET* 3.7 28.6 - - + +
38A ILE* 3.3 14.4 + - + +
39A LEU* 3.4 16.6 - - - +
40A LYS 3.1 3.2 - - - -
41A GLN* 1.3 72.4 - - - +
43A ALA* 1.3 54.4 + - - +
44A LYS* 2.8 25.1 + - - +
45A SER* 4.3 1.6 + - - -
46A GLY 5.4 0.2 + - - -
47A GLU* 3.1 53.2 + - + +
48A ASP 4.0 16.3 + - - -
49A ILE* 3.8 17.6 - - + +
103A PRO* 6.0 0.7 - - - -
----------------------------------------------------------
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