Contacts of the helix formed by residues 34 - 48 (chain D) in PDB entry 3GBA
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 GLY 34 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PRO 3.3 13.7 - - - -
16D TYR 3.3 3.1 - - - -
18D MET* 4.3 1.3 - - - -
33D GLU* 1.3 78.2 - - - +
35D TYR* 1.3 67.1 + - - -
36D CYS 3.2 3.1 - - - -
37D LEU* 3.1 3.0 + - - +
38D ASP* 2.9 24.2 + - - -
250D TRP* 3.4 25.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PRO 3.0 15.5 + - - +
16D TYR* 3.9 20.0 - + + -
34D GLY* 1.3 70.3 - - - -
36D CYS* 1.3 63.0 + - - +
38D ASP* 3.2 1.9 + - - -
39D LEU* 2.9 31.0 + - + +
105D PHE* 3.5 45.6 + + - -
106D MET* 3.3 26.0 - - + +
243D LEU* 3.9 18.8 + - - +
246D MET* 3.5 41.2 - - + +
247D LYS* 3.6 20.6 - - - -
250D TRP* 3.5 20.0 - - + +
251D TRP* 4.0 10.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D TYR* 2.9 40.6 + - - +
17D VAL* 3.8 13.2 - - + -
35D TYR* 1.3 86.1 - - - +
37D LEU* 1.3 59.6 + - + +
39D LEU* 4.2 4.0 - - - -
40D LEU* 2.8 29.5 + - - +
86D VAL* 3.6 19.2 - - + +
87D ALA* 3.6 32.8 - - - -
105D PHE* 4.7 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D THR* 5.8 2.2 - - + -
16D TYR 3.9 8.7 - - - +
17D VAL* 4.0 18.4 - - + -
20D ARG* 6.0 0.2 - - - +
29D ASN* 4.7 6.1 - - + +
32D PHE* 3.7 39.0 - - + +
33D GLU* 3.8 20.2 - - - +
34D GLY 3.1 12.8 + - - +
36D CYS* 1.3 74.7 - - - +
38D ASP* 1.3 64.3 + - - +
40D LEU* 3.4 10.1 + - + +
41D LYS* 2.9 43.4 + - - +
51D TYR* 5.4 4.7 - - + +
53D VAL* 4.1 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLU* 6.0 0.3 - - - -
34D GLY 2.9 10.3 + - - +
35D TYR 3.5 8.3 - - - +
37D LEU* 1.3 79.3 - - - +
39D LEU* 1.3 60.8 + - - +
41D LYS* 3.4 18.0 + - - +
42D GLU* 3.1 27.5 + - + +
246D MET* 3.9 19.5 - - + +
249D LYS* 2.8 34.7 + - - +
250D TRP* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D TYR* 2.9 20.5 + - + +
36D CYS* 3.7 5.6 - - - +
38D ASP* 1.3 74.4 - - - +
40D LEU* 1.3 59.1 + - - +
42D GLU* 3.2 6.0 + - - +
43D LEU* 2.9 40.6 + - + +
86D VAL* 4.1 13.9 - - + -
105D PHE* 3.8 45.3 - - + -
218D VAL* 4.5 5.2 - - + -
234D ILE* 3.9 15.0 - - + -
237D LEU* 3.8 27.1 - - + -
243D LEU* 4.1 13.5 - - + -
246D MET* 3.4 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D VAL* 3.9 30.3 - - + -
36D CYS 2.8 18.5 + - - +
37D LEU* 3.7 11.4 - - + +
39D LEU* 1.3 77.1 - - - +
41D LYS* 1.3 56.2 + - - +
43D LEU* 3.3 5.5 + - + +
44D SER* 2.9 31.0 + - - -
49D PHE* 4.0 23.1 - - + -
51D TYR* 3.3 35.9 - - + -
53D VAL* 3.6 19.1 - - + -
84D LEU* 4.6 0.9 - - + -
86D VAL* 4.1 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ARG* 4.2 20.2 - - - +
32D PHE 6.0 0.4 - - - -
37D LEU* 2.9 29.5 + - + +
38D ASP* 3.6 15.8 + - - +
39D LEU 3.3 0.2 - - - -
40D LEU* 1.3 75.3 - - - +
42D GLU* 1.3 63.3 + - + +
44D SER* 2.7 25.0 + - - +
45D ASN* 3.0 22.0 + - - +
51D TYR* 3.3 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ASP* 3.1 18.4 + - + +
39D LEU* 3.5 8.5 - - - +
41D LYS* 1.3 77.8 - - + +
43D LEU* 1.3 57.5 + - - +
45D ASN* 3.2 9.2 + - - +
46D ILE* 2.9 46.2 + - - +
237D LEU* 3.8 38.0 - - + +
242D LYS* 4.3 16.7 + - - +
246D MET* 4.6 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LEU* 2.9 31.9 + - + +
40D LEU* 3.7 4.7 - - - +
42D GLU* 1.3 75.6 - - - +
44D SER* 1.3 57.7 + - - +
46D ILE* 4.6 2.9 - - - +
47D LEU* 2.9 40.0 + - + +
49D PHE* 3.6 13.2 - - + -
84D LEU* 5.0 5.2 - - + -
86D VAL* 4.5 14.1 - - + -
218D VAL* 4.1 28.9 - - + -
230D ILE* 4.2 13.2 - - + +
233D ALA* 3.6 28.0 - - + -
234D ILE* 4.2 17.5 - - + +
237D LEU* 4.6 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LEU 2.9 14.5 + - - -
41D LYS* 2.7 22.3 + - - +
43D LEU* 1.3 76.8 - - - +
45D ASN* 1.3 63.0 + - - +
48D GLY* 2.8 24.6 + - - -
49D PHE* 3.1 36.1 + - - +
51D TYR* 3.4 29.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 45 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LYS* 3.0 26.1 + - - +
42D GLU* 3.8 10.6 + - - +
44D SER* 1.3 87.7 + - - +
46D ILE* 1.3 65.4 + - + +
48D GLY* 3.8 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D GLU* 2.9 31.4 + - - +
43D LEU 4.0 1.8 - - - +
45D ASN* 1.3 79.8 - - + +
47D LEU* 1.3 63.3 + - + +
233D ALA* 3.9 25.8 - - + +
236D GLN* 3.8 35.2 - - - +
237D LEU* 3.9 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 2.9 21.6 + - + +
46D ILE* 1.3 82.3 - - + +
48D GLY* 1.3 63.5 + - - +
49D PHE* 3.7 21.1 - - + -
226D TYR* 4.4 16.6 - - + -
229D LYS* 3.7 41.6 - - + +
230D ILE* 3.9 24.7 - - + -
233D ALA* 3.5 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D SER 2.8 15.0 + - - -
45D ASN 3.8 5.5 + - - -
46D ILE 3.5 1.6 - - - -
47D LEU* 1.3 81.0 - - - +
49D PHE* 1.3 58.2 + - - +
----------------------------------------------------------
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