Contacts of the helix formed by residues 22 - 36 (chain F) in PDB entry 1UW9
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 THR 22 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F PRO 4.6 4.0 - - - +
21F LEU* 1.3 75.6 - - - +
23F ASP* 1.3 60.9 + - - +
24F GLU* 3.5 10.5 + - - +
25F GLN* 2.9 46.6 + - - +
26F ILE* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 23 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F LEU 5.3 0.3 - - - +
22F THR* 1.3 73.3 - - - +
24F GLU* 1.3 56.7 + - - +
26F ILE* 3.3 18.3 + - - +
27F ALA* 2.9 29.6 + - - +
90F LEU* 5.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F THR* 3.2 8.9 - - - +
23F ASP* 1.3 79.2 - - - +
25F GLN* 1.3 57.0 + - + +
27F ALA* 3.5 7.4 + - + +
28F ALA* 3.0 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429E GLN* 3.7 19.6 + - - +
433E GLU* 4.0 15.8 - - - +
19F PRO* 5.0 1.8 + - - +
20F PRO 3.8 4.4 + - - -
21F LEU* 3.4 24.2 - - + +
22F THR* 2.9 54.0 + - - +
24F GLU* 1.3 73.5 - - + +
26F ILE* 1.3 65.8 + - - +
28F ALA* 3.4 8.8 + - - +
29F GLN* 3.2 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F LEU* 3.8 31.4 - - + +
22F THR 2.9 19.2 + - - +
23F ASP* 3.6 18.2 - - - +
25F GLN* 1.3 76.1 - - - +
27F ALA* 1.3 63.1 + - - +
29F GLN* 3.0 12.0 + - - +
30F VAL* 3.0 25.8 + - + +
90F LEU* 4.3 18.4 - - + -
93F ILE* 4.6 11.9 - - + -
107F LEU* 5.4 0.2 - - + -
121F PHE* 4.3 15.3 - - + -
122F LEU 5.9 0.7 - - - +
123F VAL* 4.8 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ASP 2.9 18.0 + - - +
24F GLU* 3.7 8.3 - - + +
25F GLN 3.4 0.2 - - - -
26F ILE* 1.3 74.9 - - - +
28F ALA* 1.3 57.3 + - - +
30F VAL* 3.2 10.6 + - - +
31F ASP* 2.9 36.8 + - - +
86F PRO* 5.5 0.3 - - - +
90F LEU* 4.5 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432E ASN 4.3 5.6 - - - +
433E GLU* 4.0 27.8 - - + +
24F GLU 3.0 15.3 + - - +
25F GLN* 3.5 11.2 - - - +
26F ILE 3.2 0.2 - - - -
27F ALA* 1.3 77.6 - - - +
29F GLN* 1.3 62.0 + - - +
31F ASP* 3.3 12.3 + - - +
32F TYR* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429E GLN* 4.0 22.1 + - - +
432E ASN* 3.0 42.4 + - - +
433E GLU* 4.4 7.1 - - - +
15F PHE* 3.5 20.7 - - + -
21F LEU* 4.6 6.7 - - + -
25F GLN 3.2 15.1 + - - +
26F ILE 3.0 8.3 + - - +
28F ALA* 1.3 72.6 - - - +
30F VAL* 1.3 65.4 + - - +
32F TYR* 3.2 8.5 + - - +
33F ILE* 3.1 26.3 + - - +
119F MET* 4.1 11.2 - - + +
121F PHE* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F ILE* 3.0 20.5 + - + +
27F ALA* 3.2 8.7 + - - +
29F GLN* 1.3 73.4 - - - +
31F ASP* 1.3 62.4 + - - +
33F ILE* 3.1 12.5 + - + +
34F VAL* 3.1 22.5 + - + +
86F PRO* 3.7 25.8 - - + +
89F VAL* 3.7 33.9 - - + -
90F LEU* 4.1 20.0 - - + -
93F ILE* 4.9 0.4 - - + -
107F LEU* 3.8 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 31 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F ALA* 2.9 19.9 + - - +
28F ALA* 3.5 14.5 - - - +
30F VAL* 1.3 75.0 - - - +
32F TYR* 1.3 52.5 + - - +
34F VAL* 3.3 5.8 + - - +
35F ALA* 2.8 38.2 + - - +
86F PRO* 3.5 25.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 32 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396E ASP* 4.7 3.3 + - - -
431E ARG* 3.6 21.8 + - - -
432E ASN* 3.2 68.9 + - + +
28F ALA 3.1 8.7 + - - +
29F GLN* 3.4 15.9 - - - +
30F VAL 3.2 0.2 - - - -
31F ASP* 1.3 73.6 - - - +
33F ILE* 1.3 65.2 + - - +
35F ALA* 4.3 4.9 - - + -
36F ASN* 2.9 52.8 + - - +
38F TRP* 3.3 34.0 - + - -
118F ILE 5.8 0.4 - - - -
119F MET* 4.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 33 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F GLN 3.1 13.1 + - - +
30F VAL* 3.4 14.4 - - + +
32F TYR* 1.3 77.9 - - + +
34F VAL* 1.3 64.7 + - + +
36F ASN* 3.3 1.4 + - - -
37F GLY 3.2 3.5 + - - -
38F TRP* 3.1 53.2 + - + +
40F PRO* 4.0 19.3 - - + -
107F LEU* 3.9 27.4 - - + -
108F VAL 4.6 0.4 - - - +
109F ALA* 3.8 20.9 - - + -
119F MET* 3.6 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F VAL* 3.1 15.3 + - + +
31F ASP* 3.8 5.2 - - - +
33F ILE* 1.3 77.8 - - + +
35F ALA* 1.3 67.8 + - - +
37F GLY* 3.0 15.0 + - - +
38F TRP 5.3 2.2 - - - +
40F PRO* 5.5 1.6 - - + -
83F CYS* 4.7 12.6 - - - +
84F ARG* 3.7 32.6 - - + +
85F ASP 4.4 5.8 - - - +
86F PRO* 4.0 34.8 - - + -
89F VAL* 5.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F ASP 2.8 22.3 + - - +
32F TYR* 3.8 7.9 - - + +
33F ILE 3.4 0.2 - - - -
34F VAL* 1.3 73.5 - - - +
36F ASN* 1.3 64.1 + - - +
37F GLY 3.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F TYR* 2.9 55.1 + - - +
33F ILE 3.3 0.4 + - - +
34F VAL 3.1 0.4 - - - -
35F ALA* 1.3 80.7 - - - +
37F GLY* 1.3 62.8 + - - +
38F TRP* 3.4 43.6 + - + -
----------------------------------------------------------
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