Contacts of the helix formed by residues 30 - 42 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ARG* 5.0 7.9 - - - +
131E ILE* 4.8 5.1 - - + +
133E PHE* 3.3 57.6 - - + +
134E GLU* 3.4 10.8 - - - +
299E ARG* 4.8 8.9 - - - +
29F MET* 1.3 76.7 - - - +
31F LYS* 1.3 66.2 + - - +
32F GLN* 4.4 10.1 - - + +
33F ASP* 2.8 31.2 + - - +
34F ILE* 3.1 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E GLU* 3.1 26.3 + - + +
6F LEU 4.5 1.1 - - - -
7F LYS* 3.4 28.2 + - + +
9F THR 2.7 28.5 + - - -
10F PRO* 4.4 1.2 - - - +
11F VAL* 3.8 26.9 - - + +
14F LEU* 4.0 10.7 - - + +
30F ARG* 1.3 70.4 - - - +
32F GLN* 1.3 77.8 + - - +
34F ILE* 3.1 20.4 + - - +
35F ILE* 3.2 28.0 - - + +
69F ASP* 4.7 6.3 - - - +
70F SER* 5.8 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F LYS* 3.4 18.1 - - - +
30F ARG* 3.2 9.4 - - + +
31F LYS* 1.3 90.8 - - - +
33F ASP* 1.3 61.6 + - - +
35F ILE* 4.8 0.7 - - - -
36F PHE* 3.4 14.6 + - - +
70F SER* 2.9 30.2 + - - -
73F LEU* 5.5 10.5 - - + +
75F GLY* 4.1 8.7 - - - -
76F PRO* 3.8 23.2 - - + +
77F ASP* 2.9 39.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F MET* 3.8 27.2 - - + +
30F ARG* 2.8 31.4 + - - +
32F GLN* 1.3 76.2 - - - +
34F ILE* 1.3 60.0 + - - +
36F PHE* 4.0 6.4 - - - +
37F ALA* 3.0 29.5 + - - +
76F PRO* 3.4 23.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134E GLU* 5.4 0.2 - - - +
11F VAL* 5.1 9.4 - - + -
14F LEU* 3.9 26.9 - - + +
15F ILE* 4.9 7.2 - - + +
26F LEU* 3.3 48.2 - - + +
29F MET* 3.6 17.9 - - + +
30F ARG 3.2 12.3 - - - +
31F LYS* 3.1 15.2 + - - +
33F ASP* 1.3 75.4 - - - +
35F ILE* 1.3 63.0 + - + +
37F ALA* 3.1 6.0 + - - +
38F ILE* 2.8 49.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F LEU* 3.8 23.1 - - + -
6F LEU* 3.7 44.8 - - + +
7F LYS* 4.3 11.2 - - + +
14F LEU* 4.1 17.3 - - + -
31F LYS* 3.2 34.6 + - + +
32F GLN* 3.7 0.4 + - - -
34F ILE* 1.3 78.0 - - - +
36F PHE* 1.3 58.9 + - - +
38F ILE* 3.3 6.7 + - - +
39F LEU* 2.8 41.7 + - + +
77F ASP* 3.4 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F GLN 3.4 14.2 + - - +
33F ASP* 4.0 7.9 - - - +
34F ILE 3.3 0.4 - - - -
35F ILE* 1.3 79.4 - - - +
37F ALA* 1.3 58.6 + - - +
39F LEU* 4.0 4.4 - - - +
40F LYS* 3.0 62.7 + - + +
76F PRO* 3.3 33.4 - - + +
77F ASP* 4.2 11.0 - - + -
104F PRO* 4.6 1.8 - - + -
109F ARG* 3.3 30.1 - - + -
110F TYR* 4.6 0.7 - - - -
111F PHE* 3.9 27.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F LEU* 4.3 9.9 - - + +
26F LEU* 4.0 29.2 - - + -
29F MET* 5.1 2.7 - - - -
33F ASP 3.0 20.2 + - - +
34F ILE 3.1 4.5 + - - +
36F PHE* 1.3 79.2 - - - +
38F ILE* 1.3 62.6 + - - +
40F LYS* 3.7 5.1 + - - +
41F GLN* 3.2 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 38 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET* 6.1 1.1 - - + -
6F LEU* 4.4 18.2 - - + -
14F LEU* 3.5 39.0 - - + +
17F LEU* 4.0 27.6 - - + -
18F GLY* 4.4 14.4 - - - +
21F MET* 4.1 9.9 - - + -
23F LEU* 4.4 6.5 - - + -
26F LEU* 5.0 1.1 - - + -
34F ILE* 2.8 30.9 + - + +
35F ILE* 3.8 4.7 - - - +
37F ALA* 1.3 74.8 - - - +
39F LEU* 1.3 55.1 + - + +
41F GLN* 3.1 7.2 + - - +
42F HIS* 2.6 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET 5.1 5.8 - - - +
3F LEU* 3.7 30.7 - - + -
6F LEU* 4.0 20.4 - - + -
35F ILE* 2.8 34.1 + - + +
36F PHE* 4.0 3.6 - - - +
38F ILE* 1.3 73.4 - - + +
40F LYS* 1.3 61.4 + - - +
42F HIS* 3.5 7.3 + - + +
43F ALA* 3.2 18.0 + - - +
49F ILE* 3.8 31.0 - - + +
50F PHE 5.9 0.2 - - - +
77F ASP* 4.9 5.8 - - + +
101F ILE* 4.6 9.4 - - + -
111F PHE* 3.3 38.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F PHE* 3.0 50.2 + - + +
37F ALA* 4.0 5.6 - - - +
39F LEU* 1.3 76.5 - - - +
41F GLN* 1.3 58.9 + - - +
43F ALA* 3.2 21.9 - - + +
44F LYS* 4.9 6.8 - - - +
103F PRO* 5.9 1.5 - - + +
104F PRO* 4.2 28.8 + - + +
111F PHE* 3.8 7.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 41 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F MET* 2.9 48.3 + - + +
22F GLY 5.2 0.8 - - - -
23F LEU* 3.7 29.1 - - + +
37F ALA 3.2 13.8 + - - +
38F ILE 3.1 4.8 + - - +
40F LYS* 1.3 76.0 - - - +
42F HIS* 1.3 55.9 + - - +
43F ALA 3.1 7.8 + - - -
44F LYS* 3.8 37.4 + - - +
45F SER* 5.0 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 42 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET* 4.2 21.8 + - + +
17F LEU* 6.6 0.2 - - + -
21F MET* 3.8 15.0 - - + +
38F ILE* 2.6 26.7 + - + +
39F LEU* 3.5 8.0 + - + +
40F LYS 3.4 0.2 - - - -
41F GLN* 1.3 70.4 - - - +
43F ALA* 1.3 54.9 + - - +
44F LYS 3.2 9.8 + - - -
45F SER* 3.3 30.0 + - - +
46F GLY* 3.9 14.3 - - - -
47F GLU 4.2 4.4 + - - -
48F ASP* 5.3 2.0 - - + -
49F ILE* 3.2 29.2 - - + +
----------------------------------------------------------
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