Contacts of the helix formed by residues 39 - 58 (chain A) in PDB entry 3FH4
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 THR 39 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN* 2.5 29.4 + - - +
36A PHE* 3.1 19.3 + - + +
37A TYR 4.6 1.6 - - - +
38A THR* 1.3 84.5 - - - +
40A THR* 1.3 60.2 + - - +
41A SER* 3.3 3.4 + - - -
42A GLY* 3.1 14.7 + - - -
43A ALA* 3.0 25.1 + - - +
74A ASN* 5.6 1.6 - - - +
107A ASN* 3.6 31.6 - - - +
108A GLU* 3.2 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 1.3 73.0 - - - +
41A SER* 1.3 59.6 + - - +
43A ALA* 3.2 8.6 + - - +
44A GLN* 2.8 35.1 + - - +
108A GLU* 2.9 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 3.8 15.4 - - - -
33A THR* 4.5 11.6 - - - -
34A ASN* 2.7 46.1 + - - +
39A THR* 3.3 2.8 + - - -
40A THR* 1.3 79.1 + - - +
42A GLY* 1.3 60.2 + - - +
44A GLN* 4.2 6.7 - - - -
45A ALA* 3.0 30.7 + - - +
108A GLU* 5.0 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN 3.7 0.8 + - - -
35A ARG* 3.6 17.9 - - - -
36A PHE 3.2 23.6 - - - -
39A THR* 3.1 11.6 + - - -
41A SER* 1.3 79.9 + - - +
43A ALA* 1.3 59.5 + - - +
45A ALA* 3.7 6.6 + - - +
46A SER 3.7 5.5 + - - -
75A GLN* 3.0 24.6 + - - +
----------------------------------------------------------
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 THR 3.0 12.9 + - - +
40A THR* 3.5 10.8 - - - +
42A GLY* 1.3 73.6 - - - +
44A GLN* 1.3 69.2 + - + +
46A SER* 3.3 14.7 + - - -
47A ASP* 3.3 14.3 + - - +
74A ASN* 4.4 27.6 - - + +
75A GLN* 4.4 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 4.0 14.3 - - + -
40A THR* 2.8 24.0 + - - +
41A SER* 3.9 7.4 - - - +
42A GLY 3.5 0.2 - - - -
43A ALA* 1.3 75.8 - - + +
45A ALA* 1.3 55.8 + - - +
47A ASP* 3.1 30.5 + - - +
48A TRP* 2.8 28.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
29A LEU* 5.0 2.0 - - + -
32A PHE* 3.7 19.9 - - + -
35A ARG* 3.7 35.0 - - + -
41A SER 3.0 17.7 + - - +
42A GLY 3.9 5.8 - - - +
43A ALA 3.3 0.4 - - - -
44A GLN* 1.3 72.3 - - - +
46A SER* 1.3 65.2 + - - +
48A TRP* 3.2 2.3 + - - +
49A ILE* 3.0 33.5 + - + +
75A GLN* 5.4 0.4 - - - +
98A LEU* 4.9 3.1 - - + +
----------------------------------------------------------
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 GLY 3.7 7.7 + - - -
43A ALA 3.3 10.7 + - - -
44A GLN 3.3 0.2 - - - -
45A ALA* 1.3 76.0 - - - +
47A ASP* 1.3 65.2 + - - +
48A TRP 3.3 0.2 + - - -
49A ILE 3.3 1.2 + - - -
50A ALA 3.0 19.1 + - - -
67A GLN* 3.1 20.0 + - - -
75A GLN* 4.6 0.9 - - - -
76A LYS* 2.6 40.9 + - - +
78A VAL* 3.5 10.8 - - - +
98A LEU* 3.9 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA 3.3 8.4 + - - +
44A GLN* 3.1 37.1 + - - +
46A SER* 1.3 77.1 - - - +
48A TRP* 1.3 57.9 + - - +
50A ALA* 3.4 3.1 + - - +
51A SER* 3.0 29.5 + - - -
67A GLN* 2.8 25.8 + - - +
76A LYS* 5.1 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 4.3 19.5 - - + -
28A SER* 3.7 31.6 - - - -
29A LEU* 3.7 33.4 - - + -
32A PHE* 3.6 24.0 - + + -
44A GLN 2.8 13.4 + - - +
45A ALA 3.5 7.0 - - - +
46A SER 3.1 0.2 - - - -
47A ASP* 1.3 77.4 - - - +
49A ILE* 1.3 65.7 + - + +
51A SER* 3.3 7.0 + - - -
52A GLU* 2.9 67.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.1 13.0 - - + -
45A ALA* 3.0 22.6 + - + +
46A SER 3.8 3.6 - - - +
48A TRP* 1.3 90.1 - - + +
50A ALA* 1.3 59.4 + - - +
52A GLU* 3.3 3.7 + - - +
53A TRP* 2.9 66.1 + - + +
78A VAL* 4.2 13.0 - - + -
98A LEU* 3.6 35.7 - - + +
122A ILE* 3.9 19.7 - - + -
147A ALA* 4.2 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER 3.0 13.4 + - - +
47A ASP 3.5 8.3 - - - +
49A ILE* 1.3 76.8 - - - +
51A SER* 1.3 56.6 + - - +
54A GLN* 2.8 32.8 + - - +
65A VAL* 3.6 15.9 - - + +
66A LYS 5.8 0.2 - - - -
67A GLN* 3.6 31.6 - - + +
78A VAL* 3.9 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ASP 3.0 16.8 + - - -
48A TRP* 3.7 7.4 - - - -
50A ALA* 1.3 77.2 - - - +
52A GLU* 1.3 62.6 + - - +
54A GLN* 3.8 6.5 - - - +
55A ALA* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 5.3 4.7 + - + +
48A TRP* 2.9 54.8 + - + +
49A ILE* 3.3 8.9 + - - +
51A SER* 1.3 77.9 + - - +
53A TRP* 1.3 63.0 - - + +
55A ALA* 3.4 6.7 + - - +
56A LEU* 3.2 27.8 + - + +
126A THR* 4.7 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 2.9 36.0 + - + +
50A ALA 3.8 2.7 - - - +
52A GLU* 1.3 76.2 - - + +
54A GLN* 1.3 54.6 + - - +
56A LEU* 3.2 9.5 + - + +
57A SER* 2.8 35.5 + - - -
65A VAL* 3.8 13.2 - - + -
78A VAL* 3.5 30.3 - - + -
80A MET* 3.9 20.8 - - + +
122A ILE* 4.7 5.2 - - + -
125A VAL* 3.7 28.7 - - + -
126A THR* 3.0 37.5 + - + -
129A ILE* 3.6 17.3 - - + +
145A PHE* 3.3 23.1 - - + -
146A MET 3.7 22.7 - - - -
147A ALA* 3.7 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA 2.8 18.5 + - - +
51A SER* 3.8 7.9 - - - +
52A GLU 3.4 0.2 - - - -
53A TRP* 1.3 75.9 - - - +
55A ALA* 1.3 63.4 + - - +
57A SER* 2.9 25.7 + - - -
58A ALA* 3.1 13.9 + - - +
64A SER* 5.3 0.3 - - - -
65A VAL* 3.3 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A SER 3.1 17.4 + - - +
52A GLU* 3.7 7.4 - - - +
53A TRP 3.3 0.2 - - - -
54A GLN* 1.3 76.4 - - - +
56A LEU* 1.3 64.6 + - + +
58A ALA* 3.4 19.5 - - - +
59A SER* 4.4 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLU* 3.2 20.5 + - + +
53A TRP* 3.4 13.7 - - + +
55A ALA* 1.3 81.4 - - + +
57A SER* 1.3 61.9 + - - +
58A ALA 3.3 0.9 + - - -
59A SER* 3.4 9.9 + - - -
126A THR* 3.8 33.7 - - + +
129A ILE* 3.8 26.9 - - + -
130A ARG* 4.1 28.5 - - + +
133A SER* 3.3 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A TRP 2.8 18.5 + - - -
54A GLN* 2.9 30.5 + - - -
56A LEU* 1.3 71.5 - - - +
58A ALA* 1.3 64.8 + - - +
59A SER 3.2 0.4 - - - -
60A LEU* 3.1 27.2 + - - +
63A ALA* 3.9 27.0 + - - +
65A VAL* 4.1 7.4 - - - +
80A MET* 4.0 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN* 3.1 13.6 + - - +
55A ALA* 3.4 16.6 - - - +
56A LEU 3.2 0.6 - - - -
57A SER* 1.3 79.4 - - - +
59A SER* 1.3 56.8 + - - +
60A LEU 3.0 9.5 + - - +
----------------------------------------------------------
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