Contacts of the helix formed by residues 35 - 50 (chain A) in PDB entry 2FAC
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 35 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY 3.5 3.0 + - - +
34A ALA* 1.3 74.1 - - - +
36A SER* 1.3 65.7 + - - +
37A LEU* 3.3 3.5 + - - -
38A ASP* 2.9 44.3 + - - +
39A THR* 3.2 9.9 + - - -
301A PM4 3.5 11.2 + - - -
404A ZN 1.8 37.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP* 1.3 77.0 - - - +
37A LEU* 1.3 63.3 + - - +
39A THR* 3.3 16.8 + - - -
40A VAL* 3.6 10.8 + - - +
301A PM4 1.5 62.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP* 3.3 7.8 + - - +
36A SER* 1.3 75.4 - - - +
38A ASP* 1.3 68.1 + - - +
40A VAL* 3.1 16.5 + - + -
41A GLU* 2.9 56.4 + - + +
404A ZN 4.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLN* 4.3 10.8 - - - +
15A LEU* 3.6 29.2 - - + +
33A GLY 4.2 2.3 - - - +
34A ALA* 3.4 9.2 - - + -
35A ASP* 2.9 49.4 + - - +
37A LEU* 1.3 78.2 - - - +
39A THR* 1.3 52.6 + - - +
41A GLU* 4.6 11.7 - - - +
42A LEU* 2.7 39.1 + - - +
404A ZN 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 5.2 2.6 - - - +
35A ASP 3.2 2.6 + - - -
36A SER 3.4 10.8 - - - -
37A LEU 3.2 0.2 - - - -
38A ASP* 1.3 80.6 - - - +
40A VAL* 1.3 69.8 + - + +
42A LEU* 3.8 3.5 - - - +
43A VAL* 3.0 33.4 + - + +
59A ALA* 6.1 0.9 - - + -
60A GLU* 6.0 2.7 - - - -
301A PM4 2.4 76.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER 3.6 12.3 + - - +
37A LEU* 3.1 19.2 + - + +
39A THR* 1.3 82.5 - - + +
41A GLU* 1.3 66.1 + - + +
43A VAL* 3.4 4.4 + - - +
44A MET* 3.0 46.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLN* 3.6 22.9 + - - +
37A LEU* 2.9 51.5 + - + +
38A ASP* 4.1 11.0 - - - +
40A VAL* 1.3 77.5 - - + +
42A LEU* 1.3 59.2 + - - +
44A MET* 3.9 4.5 - - - +
45A ALA* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.4 1.1 - - + -
11A ILE* 3.9 33.4 - - + +
14A GLN* 4.0 24.1 - - + +
15A LEU* 4.9 9.4 - - + -
28A PHE* 3.6 38.6 - - + -
38A ASP 2.7 23.2 + - - +
39A THR* 3.8 3.8 - - - +
41A GLU* 1.3 70.7 - - - +
43A VAL* 1.3 66.6 + - - +
45A ALA* 3.4 0.9 + - - +
46A LEU* 3.0 31.6 + - + +
301A PM4 3.9 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 3.0 25.0 + - + +
40A VAL* 3.7 5.2 - - - +
42A LEU* 1.3 77.4 - - - +
44A MET* 1.3 58.0 + - + +
46A LEU* 3.1 3.5 + - - +
47A GLU* 2.8 56.5 + - - +
54A ILE* 4.0 13.2 - - + -
56A ASP* 5.1 0.2 - - - +
59A ALA* 4.0 10.8 - - + -
301A PM4 3.6 44.8 - - + +
405A ZN 4.4 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 3.0 32.8 + - + +
41A GLU* 4.1 4.9 - - - +
43A VAL* 1.3 78.3 - - + +
45A ALA* 1.3 56.7 + - - +
47A GLU* 3.6 15.0 - - - +
48A GLU* 2.9 30.7 + - - +
406A ZN 4.3 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.0 12.6 - - + +
14A GLN* 3.8 28.3 - - + +
41A GLU 3.0 18.6 + - - +
42A LEU 3.6 4.9 - - - +
43A VAL 3.2 0.2 - - - -
44A MET* 1.3 77.0 - - - +
46A LEU* 1.3 59.4 + - - +
48A GLU* 3.4 5.6 + - - +
49A GLU* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.4 13.5 - - + +
10A ILE* 3.7 29.6 - - + -
11A ILE* 4.9 2.5 - - + -
42A LEU* 3.0 30.5 + - + +
43A VAL 3.1 3.1 + - - +
45A ALA* 1.3 75.3 - - - +
47A GLU* 1.3 65.1 + - - +
50A PHE* 3.0 53.4 + - + +
68A ALA* 4.5 12.3 - - + -
72A ILE* 4.3 6.5 - - + -
301A PM4 3.9 48.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 2.8 32.4 + - + +
44A MET* 3.6 23.9 - - - +
46A LEU* 1.3 76.9 - - - +
48A GLU* 1.3 58.0 + - - +
51A ASP* 2.9 23.7 + - - -
52A THR 2.9 27.8 + - - +
53A GLU* 3.3 24.2 - - - +
54A ILE* 3.0 35.9 + - + +
301A PM4 3.9 12.8 - - + -
405A ZN 4.1 7.4 - - - -
406A ZN 4.0 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A MET 2.9 17.7 + - - +
45A ALA* 3.8 6.1 - - - +
47A GLU* 1.3 75.8 - - - +
49A GLU* 1.3 69.0 + - - +
51A ASP* 3.3 10.4 + - - +
1B SER* 3.8 11.3 + - - -
5B GLU* 3.8 2.9 - - - +
407B ZN 2.3 35.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
6A ARG* 2.8 29.9 + - + +
10A ILE* 3.4 28.5 - - + -
45A ALA 3.0 18.0 + - - +
48A GLU* 1.3 78.5 - - - +
50A PHE* 1.3 78.8 + - + +
76A GLN* 4.8 1.4 - - - +
1B SER* 2.6 51.6 + - - -
6B ARG* 3.9 10.0 - - - +
9B LYS* 3.6 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 3.6 23.3 - - + -
6A ARG* 3.7 33.2 - - + -
7A VAL* 3.8 20.2 - - + -
10A ILE* 4.3 2.0 - - + -
46A LEU* 3.0 33.0 + - + +
47A GLU 3.8 0.2 - - - -
49A GLU* 1.3 95.0 - - + +
51A ASP* 1.3 62.7 + - - +
52A THR* 2.7 28.9 + - - +
72A ILE* 3.6 39.0 - - + -
76A GLN* 3.5 43.0 - - + +
77A ALA* 5.0 0.9 + - - +
301A PM4 5.1 0.7 - - + -
----------------------------------------------------------
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