Contacts of the helix formed by residues 32 - 46 (chain A) in PDB entry 1QAG
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 VAL 32 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 1.3 83.9 - - + +
33A GLN* 1.3 58.6 + - + +
34A LYS 2.8 13.6 + - - -
35A LYS* 3.0 22.2 + - - +
36A THR* 3.1 24.8 + - + +
232B ASP* 4.6 29.2 - - + +
239B ASP* 4.3 23.3 - - + +
242B SER* 4.6 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP 4.7 2.7 - - - +
32A VAL* 1.3 78.6 - - + +
34A LYS* 1.3 56.8 + - - +
36A THR* 3.8 9.0 - - - -
37A PHE* 2.9 62.6 + - + +
124A LEU* 4.1 24.0 - - + +
128A TRP* 5.6 0.2 - - - +
239B ASP* 3.2 36.0 + - - +
241B LYS* 3.6 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 3.4 24.1 + - - +
32A VAL 2.8 1.4 + - - -
33A GLN* 1.3 76.8 - - - +
35A LYS* 1.3 59.3 + - + +
37A PHE* 3.0 2.3 + - - +
38A THR* 2.7 44.3 + - - +
54A ASN 5.9 0.7 - - - -
55A ASP* 3.2 28.3 + - - +
56A MSE 4.4 16.4 - - - +
57A PHE* 3.0 48.3 - - + -
124A LEU* 4.1 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP 4.2 10.5 - - - +
32A VAL* 3.0 13.2 + - - +
34A LYS* 1.3 81.1 - - + +
36A THR* 1.3 60.7 + - + +
38A THR* 3.5 6.3 - - - -
39A LYS* 2.9 48.1 + - - +
229B ASP* 3.7 16.5 + - - +
231B GLU* 5.6 0.8 + - - -
232B ASP* 2.6 39.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 3.1 19.1 + - + +
33A GLN 3.5 3.6 + - - -
35A LYS* 1.3 75.3 - - + +
37A PHE* 1.3 75.6 + - - +
39A LYS* 3.2 7.9 + - - +
40A TRP 2.8 25.5 + - - -
227B LEU 3.9 17.0 - - - +
228B LEU* 4.5 8.7 - - + -
232B ASP* 5.3 5.8 - - + +
242B SER* 2.6 35.1 + - - +
245B MSE 3.1 22.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 2.9 49.1 + - + +
34A LYS 3.7 1.3 - - - +
36A THR* 1.3 87.8 + - - +
38A THR* 1.3 66.7 + - - +
40A TRP* 3.4 6.5 + - - +
41A ILE* 3.0 24.8 + - - +
56A MSE 3.9 11.0 - - - -
124A LEU* 4.0 17.0 - - + -
127A LEU* 4.0 25.7 - - + +
128A TRP* 3.4 55.6 - + + -
131A ILE* 4.2 6.7 - - + -
241B LYS* 4.5 5.8 - - + -
242B SER* 4.5 5.4 - - - -
245B MSE 4.1 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LYS* 2.7 30.4 + - - +
35A LYS* 3.5 6.8 + - - -
37A PHE* 1.3 72.7 - - - +
39A LYS* 1.3 59.2 + - + +
41A ILE* 2.9 11.7 - - - +
42A ASN* 2.8 47.9 + - - +
53A ILE* 4.4 10.8 - - + -
54A ASN 4.3 17.2 + - - +
56A MSE 3.4 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 2.9 32.7 + - - +
36A THR* 3.4 8.5 - - - +
38A THR* 1.3 78.8 - - + +
40A TRP* 1.3 52.6 + - - +
42A ASN* 3.0 8.9 + - - +
43A ALA* 2.7 35.3 + - - +
226B LYS 3.7 13.9 + - - +
227B LEU* 3.3 33.6 + - + +
229B ASP* 3.1 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A THR 2.8 20.2 + - - +
37A PHE* 3.6 4.7 - - - +
38A THR 3.3 0.2 - - - -
39A LYS* 1.3 71.6 - - - +
41A ILE* 1.3 82.1 + - + +
43A ALA* 3.0 6.9 + - + +
44A ARG* 2.9 60.9 + - + +
69A LEU* 4.0 17.9 - - + -
73A LEU* 4.6 11.4 - - + -
127A LEU* 4.1 10.8 - - + -
130A ILE* 4.6 8.7 - - + -
131A ILE* 3.6 44.3 - - + +
134A TRP* 5.9 0.7 - - + -
135A GLN* 2.6 35.9 + - + -
227B LEU* 3.8 23.9 - - + +
245B MSE 3.8 27.6 - - + -
249B SER* 4.6 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE 3.0 14.5 + - - +
38A THR* 2.9 20.6 - - - +
40A TRP* 1.3 87.6 - - + +
42A ASN* 1.3 78.6 + - - +
44A ARG* 3.1 6.0 + - - +
45A PHE* 2.9 38.6 + - + -
53A ILE* 3.9 20.4 - - + -
60A LEU* 4.5 21.1 - - + -
66A LEU* 5.2 0.9 - - + -
69A LEU* 3.4 40.4 - - + -
127A LEU* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 2.8 37.8 + - - +
39A LYS* 3.4 7.2 - - - +
41A ILE* 1.3 72.6 - - - +
43A ALA* 1.3 57.7 + - - +
45A PHE* 3.5 6.4 - - - +
46A SER* 2.9 31.7 + - - -
52A PRO* 2.9 22.2 - - + +
53A ILE* 2.8 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS 2.7 15.7 + - - +
40A TRP* 3.1 15.5 - - + +
42A ASN* 1.3 71.7 - - - +
44A ARG* 1.3 72.0 + - - +
45A PHE 3.1 0.2 + - - -
46A SER* 3.0 8.8 + - - -
47A LYS* 3.0 32.8 + - - +
225B GLU* 3.7 36.1 - - + +
227B LEU* 4.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TRP* 2.9 49.6 + - + +
41A ILE 3.2 10.5 - - - +
43A ALA* 1.3 79.7 - - - +
45A PHE* 1.3 54.9 + - + +
47A LYS* 3.7 41.0 + - - +
48A SER* 2.7 26.9 + - - -
69A LEU* 4.1 16.2 - - + -
73A LEU* 5.1 13.3 - - + +
135A GLN* 3.9 17.8 + - - -
224B ILE* 6.1 2.4 - - - +
249B SER* 4.6 7.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 2.9 32.4 + - + -
42A ASN* 3.5 19.7 - - - +
44A ARG* 1.3 76.0 - - - +
46A SER* 1.3 58.1 + - - +
48A SER* 2.8 29.6 + - - -
50A LYS* 3.1 43.3 + - + +
51A PRO 3.3 19.1 - - - +
52A PRO* 4.4 0.7 - - + -
53A ILE* 4.2 11.9 - - + -
60A LEU* 5.8 0.2 - - + -
65A LYS* 3.6 42.8 - - + -
68A ASP* 4.0 8.5 - - + -
69A LEU* 3.6 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASN 2.9 16.5 + - - -
43A ALA* 3.0 13.5 + - - -
45A PHE* 1.3 72.2 - - - +
47A LYS* 1.3 69.8 + - - +
48A SER 2.9 6.4 + - - -
49A GLY* 3.2 12.2 + - - +
50A LYS 3.4 8.9 + - - +
51A PRO 5.5 0.2 - - - -
52A PRO* 6.0 4.5 - - - +
225B GLU* 3.9 10.9 + - - -
----------------------------------------------------------
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