Contacts of the helix formed by residues 41 - 58 (chain b) in PDB entry 3J7Y
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 ARG 41 (chain b).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38b ALA* 3.3 21.6 + - + +
39b SER 3.7 1.0 + - - -
40b SER* 1.3 73.8 - - - +
42b GLY* 1.3 62.2 + - - +
43b ALA 3.2 0.9 - - - -
44b ARG* 3.2 19.6 + - - +
45b GLU* 2.9 37.5 + - + +
91b CYS* 5.9 0.4 - - - +
92b LYS 6.0 0.2 + - - -
93b SER* 6.2 1.8 - - - +
93o ASP 5.5 0.6 + - - -
96o ASN* 3.3 38.0 + - - +
97o VAL* 3.7 28.7 - - - +
99o LYS* 4.7 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 42 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39b SER 5.4 0.4 + - - -
40b SER* 4.5 0.2 - - - +
41b ARG* 1.3 81.4 - - - +
43b ALA* 1.3 56.1 + - - +
45b GLU* 3.2 4.6 + - - +
46b PHE* 2.9 29.1 + - - +
89b ILE 6.0 0.2 - - - -
91b CYS* 6.1 0.8 - - - +
92b LYS 3.4 25.9 + - - +
93b SER* 5.1 0.2 - - - -
94b VAL* 4.0 16.3 - - - +
97b ILE* 3.3 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31b PHE* 5.5 2.2 - - + -
33b VAL* 4.0 12.6 - - + -
40b SER* 3.9 24.1 - - - +
41b ARG 3.2 1.2 - - - +
42b GLY* 1.3 74.9 - - - +
44b ARG* 1.3 58.4 + - - +
46b PHE* 3.2 9.2 + - - +
47b VAL* 2.9 34.8 + - + +
73b PRO* 4.6 1.3 - - + -
89b ILE* 4.1 30.6 + - + +
97b ILE* 3.4 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33b VAL* 3.8 9.6 - - + -
34b SER 2.9 16.5 + - - +
35b ARG 2.7 20.7 + - - -
36b ASP* 3.5 2.4 - - - +
37b GLY 2.7 42.0 + - - +
38b ALA* 5.5 0.2 - - - +
40b SER 3.1 28.4 + - - +
41b ARG* 3.2 31.1 + - - +
43b ALA* 1.3 78.8 - - - +
45b GLU* 1.3 57.4 + - - +
47b VAL* 3.2 4.5 + - - +
48b GLU* 2.9 26.2 + - - +
99o LYS* 2.8 30.5 + - + +
100o LYS* 4.3 1.4 - - - +
101o TRP* 3.3 57.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41b ARG* 2.9 23.1 + - + +
42b GLY* 3.2 3.3 + - - +
44b ARG* 1.3 76.6 - - - +
46b PHE* 1.3 62.3 + - - +
48b GLU* 3.2 18.8 + - - +
49b ARG* 3.0 49.8 + - - +
94b VAL* 3.3 33.6 - - + +
99o LYS* 3.9 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 46 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31b PHE* 3.4 39.3 - + - -
42b GLY 2.9 12.6 + - - +
43b ALA* 3.3 9.2 - - - +
45b GLU* 1.3 75.9 - - - +
47b VAL* 1.3 63.4 + - - +
50b GLU* 2.9 58.9 + - + +
51b VAL* 3.0 35.3 + - + -
54b PHE* 4.8 5.2 - + + -
94b VAL* 4.3 10.7 - - + +
97b ILE* 4.0 17.7 - - + -
98b SER* 3.9 28.5 - - - -
101b VAL* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31b PHE* 5.0 5.4 - - + -
33b VAL* 4.1 15.0 - - + -
43b ALA 2.9 19.2 + - - +
44b ARG* 3.4 9.4 - - - +
46b PHE* 1.3 82.3 - - + +
48b GLU* 1.3 63.5 + - - +
51b VAL* 3.1 28.9 - - + +
52b ILE* 4.9 2.8 - - - +
65b VAL* 3.9 35.7 - - + -
143h LEU* 4.2 22.0 - - + +
154h ILE* 5.0 4.6 - - + +
101o TRP* 3.8 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44b ARG 2.9 11.9 + - - +
45b GLU* 3.2 22.6 + - - +
47b VAL* 1.3 80.8 - - - +
49b ARG* 1.3 65.3 + - + +
52b ILE* 4.6 10.7 - - - +
139h LYS* 2.6 38.1 + - - +
142h GLU* 5.5 2.2 - - - +
143h LEU* 4.6 12.2 - - + +
99o LYS* 5.6 4.7 + - - +
101o TRP* 4.7 4.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 49 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45b GLU* 3.0 44.6 + - - +
46b PHE* 3.3 0.4 + - - -
48b GLU* 1.3 85.4 - - + +
50b GLU* 1.3 89.8 + - + +
51b VAL 3.5 2.3 + - - -
52b ILE* 4.5 5.1 + - - +
53b ASP* 3.6 19.1 - - - +
94b VAL* 4.7 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46b PHE* 2.9 31.3 + - + -
49b ARG* 1.3 100.8 + - + +
51b VAL* 1.3 61.9 + - - +
52b ILE 3.6 0.4 - - - -
53b ASP* 4.3 7.0 - - - -
54b PHE* 3.5 19.6 + - - +
57b ARG* 4.1 13.6 + - - +
94b VAL* 3.6 22.1 - - + +
95b GLU* 4.8 6.8 - - - +
98b SER* 3.3 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31b PHE* 4.9 3.6 - - + -
46b PHE* 3.0 36.6 + - + +
47b VAL* 3.1 37.5 - - + +
50b GLU* 1.3 76.9 - - - +
52b ILE* 1.3 74.4 + - + +
53b ASP 3.2 0.2 - - - -
54b PHE* 3.2 5.6 + - + +
55b ALA* 2.9 28.1 + - - +
63b ILE* 4.1 28.9 - - + -
65b VAL* 5.0 4.7 - - + -
152h LEU* 4.2 15.9 - - + -
154h ILE* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47b VAL 4.9 3.4 - - - +
48b GLU 4.6 15.0 - - - +
49b ARG 4.5 3.7 + - - +
51b VAL* 1.3 85.6 - - + +
53b ASP* 1.3 66.6 + - - +
55b ALA* 3.2 4.5 + - - +
56b ARG* 2.9 58.9 + - - +
143h LEU* 5.6 5.4 - - + -
146h SER* 3.9 33.0 - - - +
147h ASN* 4.4 3.1 - - - +
148h LEU* 4.2 8.7 - - + -
149h PRO* 4.0 13.2 - - + +
152h LEU* 3.4 25.6 - - + -
154h ILE* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 53 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49b ARG 3.6 16.7 - - - +
50b GLU* 4.1 7.2 + - - +
51b VAL 3.2 0.4 - - - -
52b ILE* 1.3 83.9 - - - +
54b PHE* 1.3 57.0 + - - +
56b ARG* 3.2 17.9 + - - +
57b ARG* 2.9 49.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 54 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26b LEU* 4.5 3.1 - - + -
29b LEU* 3.4 26.5 - - + -
31b PHE* 6.2 0.2 - + - -
46b PHE* 4.8 6.1 - + + -
50b GLU 3.5 13.5 + - - +
51b VAL* 3.2 12.9 + - + +
53b ASP* 1.3 79.3 - - - +
55b ALA* 1.3 57.6 + - - +
57b ARG* 3.2 30.6 + - + +
58b ASN* 2.4 64.7 + - - +
61b VAL* 4.3 2.7 - - + -
63b ILE* 4.0 20.0 - - + -
101b VAL* 3.5 29.2 - - + -
102b GLN* 4.8 10.3 - - + -
105b ALA* 3.9 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51b VAL 2.9 11.9 + - - +
52b ILE* 3.3 11.4 - - - +
54b PHE* 1.3 76.5 - - - +
56b ARG* 1.3 63.4 + - - +
58b ASN* 3.1 26.6 - - - +
59b PRO* 3.9 0.2 - - - +
63b ILE* 3.7 25.1 - - + -
149h PRO* 4.3 10.3 - - + -
151h ASN* 3.2 25.9 - - + +
152h LEU* 4.5 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52b ILE* 2.9 33.5 + - - +
53b ASP* 3.4 18.4 + - - +
55b ALA* 1.3 77.6 - - - +
57b ARG* 1.3 63.7 + - - +
59b PRO* 4.1 9.5 - - - +
147h ASN* 3.1 45.9 + - - +
149h PRO* 4.2 17.1 - - + +
151h ASN* 4.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50b GLU* 4.1 18.2 + - - +
53b ASP* 2.9 27.9 + - - +
54b PHE* 3.2 47.3 + - + +
56b ARG* 1.3 78.8 - - + +
58b ASN* 1.3 60.1 + - - +
59b PRO* 3.6 6.4 - - - +
98b SER* 5.4 5.3 + - - -
102b GLN* 4.9 18.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 58 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24b GLN* 3.1 35.5 - - + +
54b PHE* 2.4 69.2 + - - +
55b ALA* 3.1 8.9 - - - +
57b ARG* 1.3 78.6 - - - +
59b PRO* 1.4 65.6 - - - +
60b GLY 3.3 1.6 - - - +
61b VAL* 3.3 23.8 + - + +
102b GLN* 5.9 1.0 - - - +
105b ALA* 3.8 4.4 - - - +
----------------------------------------------------------
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