Contacts of the helix formed by residues 34 - 52 (chain A) in PDB entry 3ROT
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 ASP 34 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER 3.7 1.3 - - - +
33A GLN* 1.3 77.6 - - - +
35A PRO* 1.3 69.4 - - - +
36A TYR* 2.8 30.9 + - - +
37A TRP* 2.9 38.9 + - + +
38A THR* 3.9 2.3 + - - +
63A ALA* 5.9 0.2 - - - +
215A THR* 4.3 6.1 - - - -
216A SER* 2.5 34.3 + - - -
217A GLN* 3.7 31.3 - - + +
244A ASP* 4.6 2.4 - - - +
246A THR* 3.9 0.9 - - - +
317A GOL 4.7 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN 3.5 7.9 - - - +
34A ASP* 1.3 90.5 - - - +
36A TYR* 1.3 57.9 + - - +
37A TRP 3.2 0.2 - - - -
38A THR* 2.7 27.4 + - + +
39A SER* 3.4 4.2 + - - -
216A SER* 4.3 4.9 - - - +
220A ASP* 5.0 10.5 - - - +
246A THR* 3.8 25.4 - - + -
247A PRO* 4.2 13.2 - - + -
191B PRO* 6.2 0.9 - - + -
220B ASP* 6.1 0.9 - - + +
224B GLN* 3.2 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 2.8 21.9 + - - +
35A PRO* 1.3 79.2 - - - +
37A TRP* 1.3 90.4 + + - +
39A SER* 3.3 9.5 + - - -
40A LEU* 3.2 18.6 + - + +
112A ASP* 2.7 28.3 + - + -
244A ASP* 3.5 39.7 - - + +
246A THR* 4.1 5.4 - - - +
264A GLN* 3.6 12.6 + - - -
266A PRO* 3.5 35.8 - - + +
269A MSE 3.3 25.2 - - - +
317A GOL 3.6 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A THR* 3.8 23.1 - - + -
30A HIS* 3.4 43.7 - + - -
31A GLY* 3.4 32.6 - - - -
32A SER* 3.5 10.5 - - - -
34A ASP* 2.9 38.9 + - + +
36A TYR* 1.3 91.8 - + - +
38A THR* 1.3 53.9 + - - +
39A SER 3.0 1.8 - - - -
40A LEU* 2.9 24.6 + - + +
41A PHE* 2.7 55.3 + + + -
63A ALA* 5.4 2.2 + - - +
87A THR* 4.1 6.5 - - + -
112A ASP* 3.7 14.8 - - - -
158A GLN* 6.3 0.2 - - - -
217A GLN* 5.7 2.4 - - - +
317A GOL 3.9 13.7 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
32A SER 4.7 5.2 - - - +
34A ASP 3.9 3.0 + - - +
35A PRO* 2.7 22.7 + - + +
37A TRP* 1.3 75.2 - - - +
39A SER* 1.3 54.8 + - - +
41A PHE* 3.8 10.1 - - + +
42A GLN* 3.0 29.6 + - - +
191B PRO* 3.2 37.7 - - + -
192B ASN* 3.8 16.1 - - + +
195B GLN* 4.0 12.4 - - - +
224B GLN* 2.5 28.0 + - - +
232B TYR* 3.6 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO 3.4 7.4 + - - -
36A TYR* 3.3 12.1 + - - -
37A TRP 3.0 0.4 - - - -
38A THR* 1.3 80.3 + - - +
40A LEU* 1.3 64.6 + - - +
42A GLN* 3.5 3.0 + - - +
43A GLY 3.2 15.9 + - - -
266A PRO* 3.5 20.1 - - - +
267A PHE* 3.5 24.1 + - - +
224B GLN* 4.3 4.7 - - - -
231B ARG* 4.7 7.8 + - - -
232B TYR* 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
----------------------------------------------------------
27A LEU* 4.5 17.7 - - + -
29A THR* 4.2 13.5 - - + -
36A TYR* 3.2 10.9 + - + +
37A TRP* 2.9 38.2 + - + +
39A SER* 1.3 80.7 - - - +
41A PHE* 1.3 63.4 + - + +
43A GLY 3.3 1.7 + - - -
44A ALA* 3.1 18.4 + - - +
111A VAL* 4.9 10.8 - - + -
112A ASP* 5.5 0.9 - - + -
266A PRO* 3.1 34.0 - - + +
269A MSE 3.6 24.0 - - + -
270A GLY* 3.3 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.8 13.7 - - + -
29A THR* 3.7 36.1 - - + -
31A GLY 4.0 3.6 - - - -
32A SER* 4.2 16.2 - - - -
37A TRP* 2.7 44.8 + - + +
38A THR* 3.8 10.1 - - + +
40A LEU* 1.3 78.6 - - + +
42A GLN* 1.3 56.5 + - - +
44A ALA* 3.2 2.9 + - - +
45A LYS* 2.9 35.6 + - - +
57A ILE* 3.6 41.5 - - + +
59A ALA* 4.2 5.2 - - + -
190B ASP* 5.9 0.2 - - - -
192B ASN* 3.9 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR 3.0 19.8 + - - +
39A SER 3.9 3.6 - - - +
41A PHE* 1.3 75.7 - - - +
43A GLY* 1.3 59.2 + - - +
45A LYS* 3.0 29.3 - - - +
46A LYS* 2.8 37.6 + - - +
49A GLU* 4.9 1.9 + - - +
267A PHE* 3.9 7.6 - - + -
195B GLN* 5.1 0.4 + - - +
199B LYS* 3.5 23.2 + - - +
231B ARG 2.9 28.6 - - - +
232B TYR* 3.5 36.8 - - + -
233B ASP* 4.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER 3.2 9.1 + - - -
40A LEU 3.3 2.2 + - - -
42A GLN* 1.3 79.7 - - - +
44A ALA* 1.3 61.2 + - - +
46A LYS* 3.8 0.2 - - - +
47A ALA 3.1 17.2 + - - -
267A PHE* 3.5 41.2 - - - -
271A TYR* 3.2 20.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.5 31.6 - - + -
40A LEU 3.1 8.5 + - - +
41A PHE 3.5 4.9 - - - +
43A GLY* 1.3 77.2 - - - +
45A LYS* 1.3 56.1 + - - +
47A ALA* 3.3 3.6 + - - +
48A ALA* 2.9 28.4 + - - +
55A LEU* 3.5 11.8 - - + +
57A ILE* 5.3 0.2 - - + -
270A GLY* 3.6 16.0 - - - +
271A TYR* 4.5 0.2 - - - +
273A SER* 5.4 0.2 - - - +
274A ILE* 3.7 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE 2.9 25.7 + - - +
42A GLN* 3.0 33.0 - - - +
44A ALA* 1.3 73.4 - - - +
46A LYS* 1.3 59.2 + - - +
48A ALA* 3.3 8.0 + - - +
49A GLU* 2.9 39.3 + - + +
55A LEU* 4.1 11.2 - - + -
57A ILE* 3.9 17.9 - - + -
192B ASN* 2.9 36.3 + - - +
195B GLN* 4.7 9.5 + - - +
196B SER* 4.7 12.9 - - - +
199B LYS* 5.4 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 2.8 26.1 + - - +
43A GLY 3.8 4.5 - - - +
45A LYS* 1.3 75.9 - - - +
47A ALA* 1.3 62.1 + - - +
49A GLU* 3.3 16.1 + - - +
50A GLU* 3.0 65.1 + - - +
267A PHE* 4.3 15.9 - - + -
271A TYR* 4.1 15.0 - - + -
230B ASP 5.6 2.1 + - - +
231B ARG 4.7 2.9 - - - +
233B ASP* 3.3 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY 3.1 15.9 + - - +
44A ALA 3.5 4.3 - - - +
45A LYS 3.3 0.2 - - - -
46A LYS* 1.3 73.7 - - - +
48A ALA* 1.3 66.4 + - - +
50A GLU* 3.3 1.3 + - - +
51A LEU* 3.0 31.3 + - + +
271A TYR* 3.5 44.3 - - + +
274A ILE* 4.0 11.4 - - + -
275A THR* 3.9 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA 2.9 14.5 + - - +
45A LYS* 3.3 10.7 + - - +
47A ALA* 1.3 77.7 - - - +
49A GLU* 1.3 57.5 + - + +
51A LEU 3.6 0.3 - - - -
52A LYS* 2.9 24.6 + - - -
53A VAL* 3.1 40.2 + - + +
55A LEU* 3.8 26.0 - - + +
274A ILE* 4.1 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 4.9 1.2 - - - +
45A LYS* 2.9 25.1 + - + +
46A LYS* 3.5 17.8 + - - +
48A ALA* 1.3 77.8 - - + +
50A GLU* 1.3 64.4 + - + +
52A LYS* 3.3 17.3 + - - +
53A VAL 5.4 0.2 - - - -
199B LYS* 4.8 9.5 + - - -
233B ASP* 4.3 13.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 3.0 48.3 + - - +
47A ALA 4.0 2.2 - - - +
49A GLU* 1.3 75.1 - - - +
51A LEU* 1.3 63.4 + - + +
52A LYS* 3.0 22.4 + - - -
271A TYR* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA* 3.0 21.4 + - - +
48A ALA 4.2 1.3 - - - +
50A GLU* 1.3 81.4 - - + +
52A LYS* 1.3 65.7 + - - +
53A VAL* 4.6 2.5 - - + -
271A TYR* 5.8 2.9 - - - +
274A ILE* 4.5 0.9 - - + +
275A THR* 3.8 42.0 - - + +
278A VAL* 3.8 29.2 - - + -
279A LEU* 5.8 6.7 - - + -
282A ARG* 2.4 51.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 3.8 14.9 - - - +
23A ASP 5.2 0.2 + - - -
48A ALA 2.9 9.6 + - - -
49A GLU 3.3 12.7 + - - +
50A GLU 3.0 25.1 + - - -
51A LEU* 1.3 84.3 + - - +
53A VAL* 1.3 59.0 + - - +
282A ARG* 4.0 8.9 + - - +
----------------------------------------------------------
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