Contacts of the helix formed by residues 54 - 76 (chain B) in PDB entry 3CJD
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 54 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 6.0 0.7 - - - -
49B TYR* 3.8 15.9 - - + -
52B PHE* 3.2 7.9 + - - +
53B GLN* 1.3 85.3 - - - +
55B LEU* 1.3 67.1 + - - +
56B ASN* 3.6 18.6 + - - +
57B ALA* 3.1 32.4 + - - +
58B LEU* 3.3 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.8 29.7 - - + +
33B ARG* 4.2 1.1 - - - -
34B ALA* 3.8 31.2 - - + +
37B LEU* 4.1 25.4 - - + -
48B ILE* 4.4 9.2 - - + -
49B TYR* 4.0 16.6 - - + +
54B ASP* 1.3 71.5 - - - +
56B ASN* 1.3 55.3 + - - +
58B LEU* 3.2 16.3 + - + +
59B THR* 2.8 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASP* 3.6 18.1 + - - +
55B LEU* 1.3 75.1 - - - +
57B ALA* 1.3 52.9 + - - +
59B THR* 3.1 10.1 + - - -
60B LEU* 2.8 45.2 + - - +
114B VAL* 3.1 26.9 - - - +
115B GLU* 3.3 35.5 + - + +
116B MSE 5.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 4.2 6.9 - - + -
53B GLN* 4.0 23.1 - - + +
54B ASP* 3.1 22.5 + - - +
56B ASN* 1.3 80.2 - - - +
58B LEU* 1.3 58.3 + - - +
60B LEU* 3.4 14.8 + - + +
61B GLU* 3.4 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 4.0 15.5 - - + +
17B ILE* 3.9 16.6 - - + -
20B ALA* 3.8 14.8 - - + -
32B LEU* 4.8 3.1 - - + -
37B LEU* 3.5 32.5 - - + -
48B ILE* 4.5 11.4 - - + -
52B PHE* 3.5 46.1 - - + +
54B ASP 3.3 6.8 + - - +
55B LEU* 3.2 19.2 + - + +
57B ALA* 1.3 74.6 - - - +
59B THR* 1.3 65.2 + - - +
61B GLU* 3.2 13.5 + - - +
62B VAL* 3.2 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 4.6 5.4 - - + -
29B LEU* 3.3 37.9 - - + +
32B LEU* 3.6 12.2 - - - +
55B LEU* 2.8 22.4 + - - +
56B ASN* 3.1 11.5 + - - -
58B LEU* 1.3 73.6 - - - +
60B LEU* 1.3 55.2 + - - +
62B VAL* 3.2 8.5 + - - +
63B ASN* 2.9 35.3 + - - +
110B ALA* 4.8 1.3 - - + +
114B VAL* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASN* 2.8 30.4 + - - +
57B ALA* 3.7 13.2 - - - +
58B LEU 3.3 0.4 - - - -
59B THR* 1.3 72.4 - - - +
61B GLU* 1.3 56.6 + - - +
63B ASN* 3.4 1.2 + - - -
64B GLY 2.9 23.6 + - - -
114B VAL* 4.1 18.2 - - + -
116B MSE 3.4 36.8 - - + -
123B PRO* 3.9 22.4 - - + -
125B TRP* 3.4 17.0 - - + +
126B TYR* 3.5 37.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 3.3 24.9 + - - -
17B ILE* 3.9 29.2 - - + +
52B PHE* 3.9 19.6 - - + -
57B ALA 3.4 14.2 + - - +
58B LEU* 3.2 9.0 + - - +
60B LEU* 1.3 74.2 - - - +
62B VAL* 1.3 63.3 + - - +
64B GLY* 3.2 10.0 + - - -
65B ARG* 3.3 15.9 + - - +
125B TRP* 3.9 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 4.0 14.1 - - + +
20B ALA* 3.6 29.4 - - + -
21B GLU* 3.7 22.2 - - + +
24B ILE* 3.9 19.5 - - + -
58B LEU 3.2 14.1 + - - +
59B THR 3.6 6.3 - - - +
61B GLU* 1.3 75.4 - - - +
63B ASN* 1.3 66.8 + - - +
65B ARG* 3.1 9.4 + - - +
66B THR* 3.0 18.7 + - - +
107B LEU* 3.8 28.3 - - + -
110B ALA* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR* 2.9 23.6 + - - +
60B LEU* 3.6 4.6 - - - +
62B VAL* 1.3 77.9 - - - +
64B GLY* 1.3 51.4 + - - +
66B THR* 3.1 6.2 + - - -
67B PHE* 2.8 39.7 + - - -
107B LEU 4.5 1.6 - - - +
110B ALA* 3.2 43.0 + - - +
111B LEU* 3.6 17.9 + - + +
114B VAL* 3.3 17.2 - - - +
126B TYR* 3.1 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU 2.9 14.7 + - - -
61B GLU 3.5 5.8 - - - -
62B VAL 3.2 0.4 - - - -
63B ASN* 1.3 74.4 - - - +
65B ARG* 1.3 60.6 + - - +
67B PHE* 3.4 13.7 + - - +
68B ALA* 3.2 20.3 + - - +
125B TRP* 3.9 21.5 - - - -
126B TYR* 4.4 0.8 - - - -
129B ALA* 5.9 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 3.2 24.9 + - - +
17B ILE* 3.4 29.3 - - - +
18B ASP* 2.9 38.2 + - - +
21B GLU* 3.2 37.9 + - - +
61B GLU 3.3 9.0 + - - +
62B VAL* 3.1 10.1 + - - +
64B GLY* 1.3 70.1 - - - +
66B THR* 1.3 61.4 + - - +
68B ALA* 3.2 10.3 + - - +
69B ARG* 3.0 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLU* 5.2 0.9 + - - -
62B VAL* 3.0 13.8 + - - +
63B ASN* 3.1 10.6 + - - -
65B ARG* 1.3 73.1 - - - +
67B PHE* 1.3 66.0 + - - +
69B ARG* 3.1 11.2 + - - +
70B LEU* 3.0 20.8 + - - +
100B PHE* 3.4 33.0 - - + -
107B LEU* 3.7 42.0 + - + +
111B LEU* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE* 5.1 0.2 - - + -
201A STE 4.1 21.1 - - + -
63B ASN 2.8 18.8 + - - -
64B GLY* 3.5 11.9 - - - +
65B ARG 3.3 0.2 - - - -
66B THR* 1.3 72.0 - - - +
68B ALA* 1.3 51.1 + - - +
70B LEU* 3.1 6.5 + - + +
71B GLY* 2.7 33.1 + - - -
111B LEU* 3.6 25.1 - - + -
126B TYR* 3.5 60.6 - + - -
129B ALA* 3.8 24.2 - - + +
130B MSE 4.0 19.1 - - + -
133B LEU* 3.7 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B GLY 3.2 10.3 + - - +
65B ARG* 3.2 13.0 + - - +
67B PHE* 1.3 76.1 - - - +
69B ARG* 1.3 61.6 - - - +
71B GLY* 3.4 2.0 + - - +
72B ALA* 3.1 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLU* 3.3 25.9 + - - -
25B GLU* 3.3 19.8 + - - -
65B ARG* 3.0 17.6 + - + +
66B THR* 3.1 12.2 + - - +
68B ALA* 1.3 74.2 - - - +
70B LEU* 1.3 63.0 + - - +
72B ALA* 3.5 7.0 + - - +
73B ALA* 3.1 22.9 + - - +
100B PHE* 3.6 31.3 - - + -
104B HIS* 3.4 25.0 + - - -
107B LEU* 3.7 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A STE 4.1 27.4 - - + -
66B THR 3.0 15.3 + - - +
67B PHE* 3.4 8.7 - - + +
69B ARG* 1.3 77.6 - - - +
71B GLY* 1.3 57.0 + - - +
73B ALA* 3.2 6.2 + - + +
74B VAL* 2.9 38.5 + - + +
96B ALA 5.3 0.4 - - - +
97B TYR* 4.1 24.0 - - + -
100B PHE* 3.5 41.1 - - + -
111B LEU* 3.7 30.5 - - + -
133B LEU* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE 2.7 16.7 + - - -
68B ALA* 3.4 3.6 + - - -
70B LEU* 1.3 73.6 - - - +
72B ALA* 1.3 54.8 + - - +
74B VAL* 4.1 1.8 - - - +
75B GLY* 3.1 24.4 + - - -
133B LEU* 3.5 19.8 - - - +
136B TYR* 4.6 14.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ALA 3.1 16.6 + - - +
69B ARG* 3.8 6.5 - - - +
70B LEU 3.3 0.2 - - - -
71B GLY* 1.3 75.1 - - - +
73B ALA* 1.3 62.1 + - - +
75B GLY* 3.7 1.3 + - - -
76B ALA* 3.5 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ARG 3.1 17.0 + - - +
70B LEU* 3.2 8.7 + - + +
72B ALA* 1.3 78.7 - - - +
74B VAL* 1.3 61.5 + - + +
76B ALA* 3.8 16.0 - - - +
96B ALA* 3.8 27.5 - - + +
100B PHE* 5.5 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A STE 3.7 40.6 - - + -
70B LEU* 2.9 22.6 + - + +
71B GLY* 4.4 3.8 - - - +
73B ALA* 1.3 79.9 - - + +
75B GLY* 1.3 60.2 + - - +
76B ALA 3.4 4.5 + - - +
89B ARG* 5.4 4.9 + - - -
93B MSE 3.4 52.1 - - + +
96B ALA* 4.4 7.4 - - + -
97B TYR 5.2 1.6 - - - +
136B TYR* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLY 3.1 17.9 + - - -
72B ALA* 4.2 2.2 - - - -
73B ALA 3.5 0.2 - - - -
74B VAL* 1.3 76.3 - - - +
76B ALA* 1.3 63.1 + - - +
77B VAL* 4.0 8.7 - - - +
89B ARG* 5.6 2.1 + - - -
136B TYR* 5.7 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA 3.5 11.4 + - - +
73B ALA* 3.8 15.9 - - - +
74B VAL 3.3 5.8 - - - +
75B GLY* 1.3 79.5 - - - +
77B VAL* 1.3 66.5 + - - +
89B ARG* 4.9 6.2 + - - -
----------------------------------------------------------
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