Contacts of the helix formed by residues 31 - 49 (chain A) in PDB entry 1U32
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 GLN 31 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 4.9 5.0 + - - +
29A GLN 5.5 1.3 - - - +
30A LEU* 1.3 75.6 - - - +
32A GLU* 1.3 65.7 - - - +
33A ASN* 2.9 28.8 + - - +
34A GLU* 2.8 38.0 + - - +
35A ILE* 3.2 13.0 + - - +
144A TYR* 4.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU 3.9 0.8 + - - -
31A GLN* 1.3 73.4 - - - +
33A ASN* 1.3 63.3 + - - +
35A ILE* 3.3 6.1 + - - +
36A ARG* 3.0 27.3 + - + +
144A TYR* 4.3 19.1 - - + -
145A ASN* 2.8 33.0 + - - +
147A LYS* 5.3 9.0 + - - +
148A LEU* 4.4 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.9 1.4 - - - +
31A GLN* 2.9 33.9 + - - +
32A GLU* 1.3 79.5 - - - +
34A GLU* 1.3 73.2 + - - +
36A ARG* 3.9 7.2 - - - +
37A GLY* 3.0 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.9 13.0 - - + +
8A ASN* 5.8 2.4 - - - +
12A ILE* 3.9 19.7 - - + +
15A ARG* 2.6 48.2 + - - -
30A LEU* 3.7 8.3 - - + +
31A GLN* 2.8 40.8 + - + +
33A ASN* 1.3 95.2 + - - +
35A ILE* 1.3 64.5 + - - +
37A GLY* 3.1 1.7 + - - -
38A LEU* 2.9 28.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
30A LEU* 4.0 13.0 - - + -
31A GLN 3.2 9.0 + - - +
32A GLU 3.8 5.6 - - - +
34A GLU* 1.3 76.4 - - - +
36A ARG* 1.3 64.4 + - - +
38A LEU* 3.2 10.5 + - + +
39A CYS* 3.0 21.4 + - - -
101A LEU* 4.8 5.4 - - + -
105A CYS* 4.0 22.0 - - - -
144A TYR* 3.4 46.0 - - + +
148A LEU* 3.9 16.8 - - + -
152A PHE* 3.3 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU* 3.0 20.8 + - + +
33A ASN* 3.9 7.4 - - - +
35A ILE* 1.3 76.8 - - - +
37A GLY* 1.3 58.0 + - - +
39A CYS* 3.2 6.4 + - - +
40A LEU* 2.9 65.2 + - + +
147A LYS* 5.7 10.6 - - - +
148A LEU* 4.2 12.9 - - + +
151A THR* 3.1 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.7 17.3 - - - -
33A ASN 3.0 16.0 + - - -
34A GLU 3.1 4.0 + - - -
36A ARG* 1.3 74.7 - - - +
38A LEU* 1.3 58.9 + - - +
40A LEU* 4.5 6.5 - - - -
41A LYS* 2.8 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.8 1.9 - - + +
9A ILE* 4.0 13.9 - - + -
12A ILE* 4.1 15.7 - - + -
30A LEU* 4.2 11.9 - - + -
34A GLU 2.9 20.0 + - - +
35A ILE* 3.2 10.1 + - + +
37A GLY* 1.3 75.0 - - - +
39A CYS* 1.3 54.3 + - - +
42A SER* 2.7 37.5 + - - -
105A CYS* 3.8 42.8 - - + +
108A LEU* 4.2 12.6 - - + +
109A ALA* 3.8 30.7 - - + -
112A ILE* 3.5 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.0 18.5 + - - -
36A ARG 3.5 7.6 - - - +
38A LEU* 1.3 76.7 - - - +
40A LEU* 1.3 58.3 + - + +
42A SER* 3.1 5.9 + - - -
43A ARG* 3.0 32.2 + - - +
108A LEU* 4.2 5.6 - - - -
148A LEU* 5.4 0.4 - - - -
151A THR* 3.7 21.8 - - + +
152A PHE* 3.4 51.1 - - - -
155A CYS* 3.6 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 2.9 68.0 + - + +
37A GLY* 4.0 5.2 - - - +
39A CYS* 1.3 74.0 - - + +
41A LYS* 1.3 62.0 + - - +
43A ARG* 3.7 15.8 - - - +
44A GLU* 3.4 21.0 + - - +
151A THR* 4.6 8.1 - - + +
154A ASP* 6.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.5 7.6 - - + -
37A GLY 2.8 21.6 + - - +
40A LEU* 1.3 70.2 - - - +
42A SER* 1.3 65.6 + - - +
44A GLU* 3.3 33.0 + - - +
45A ILE* 3.2 42.8 + - - +
112A ILE* 3.6 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU 2.7 23.6 + - - -
39A CYS 3.1 8.0 + - - -
41A LYS* 1.3 73.5 - - - +
43A ARG* 1.3 54.4 + - - +
45A ILE* 3.0 8.5 + - - +
46A PHE* 2.8 54.6 + - - -
108A LEU* 3.6 16.9 - - - +
111A LYS* 4.8 3.1 - - - -
112A ILE* 3.8 17.3 - - - +
155A CYS* 3.3 15.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A CYS 3.0 20.3 + - - +
40A LEU* 3.7 18.2 - - - +
42A SER* 1.3 77.0 + - - +
44A GLU* 1.3 62.2 + - - +
46A PHE* 3.2 12.3 + - - +
47A LEU* 3.0 42.8 + - - +
154A ASP* 3.5 31.6 + - - +
155A CYS* 4.5 6.3 - - - +
158A CYS* 3.5 29.1 - - + -
192A PRO* 3.7 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU 3.4 10.1 + - - +
41A LYS* 3.3 39.2 + - - +
42A SER 3.2 0.2 - - - -
43A ARG* 1.3 82.1 - - - +
45A ILE* 1.3 58.1 + - - +
47A LEU* 3.5 8.4 + - - +
48A SER* 3.0 28.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 3.2 35.4 + - - +
42A SER* 3.0 8.1 + - - +
44A GLU* 1.3 76.8 - - + +
46A PHE* 1.3 66.7 + - - +
48A SER* 2.6 25.8 + - - +
49A GLN* 3.1 19.3 + - - +
111A LYS* 3.8 30.5 - - + +
112A ILE* 3.6 38.8 - - + +
115A PRO* 4.0 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A SER* 2.8 40.9 + - - -
43A ARG* 3.5 11.0 - - - +
45A ILE* 1.3 73.2 - - - +
47A LEU* 1.3 58.3 + - - +
49A GLN* 2.9 28.0 + - - +
50A PRO 4.7 0.3 - - - +
108A LEU* 4.0 16.8 - - + -
111A LYS* 3.7 38.6 - - + -
120A LEU* 4.1 12.3 - - + -
155A CYS* 3.9 20.4 - - - -
158A CYS 3.2 19.3 - - - +
159A LEU* 3.4 31.6 - - + -
160A PRO* 4.0 15.6 - - + +
191A ARG* 3.2 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG* 3.0 49.5 + - - +
44A GLU* 3.9 6.7 - - - +
46A PHE* 1.3 77.1 - - - +
48A SER* 1.3 59.6 + - - +
49A GLN 3.2 4.7 + - - +
158A CYS* 3.8 20.0 - - + -
191A ARG* 3.6 48.3 + - + +
192A PRO* 5.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU* 3.0 15.6 + - - -
45A ILE* 2.6 27.6 + - - +
47A LEU* 1.3 77.6 - - - +
49A GLN* 1.3 64.6 + - - +
50A PRO* 4.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 3.1 22.7 + - + +
46A PHE* 2.9 8.7 + - - +
47A LEU 3.7 2.4 - - - +
48A SER* 1.3 86.3 - - - +
50A PRO* 1.3 72.6 - - + +
53A LEU* 4.3 9.8 - - + +
111A LYS* 2.8 26.2 + - - +
115A PRO* 2.9 25.5 + - - +
116A GLU* 3.3 20.6 + - - +
119A PHE* 3.9 15.4 - - - -
191A ARG* 2.8 23.6 + - - -
----------------------------------------------------------
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