Contacts of the helix formed by residues 54 - 75 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ILE* 6.0 0.9 - - - -
49A TYR* 3.8 15.9 - - + -
52A PHE* 3.3 8.1 - - - +
53A GLN* 1.3 91.2 + - + +
55A LEU* 1.3 64.6 + - - +
56A ASN* 3.3 13.7 + - - +
57A ALA* 2.8 44.9 + - - +
58A LEU* 3.2 10.0 + - - +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LEU* 3.7 37.3 - - + +
33A ARG* 4.3 0.9 - - - -
34A ALA* 4.1 24.2 - - + +
37A LEU* 4.0 27.1 - - + -
48A ILE* 4.7 7.9 - - + -
49A TYR* 4.0 15.6 + - - +
54A ASP* 1.3 72.3 - - - +
56A ASN* 1.3 59.1 + - - +
58A LEU* 3.3 12.7 + - + +
59A THR* 2.9 32.4 + - - -
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Residues in contact with ASN 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASP* 3.2 14.6 + - - +
55A LEU* 1.3 77.1 - - - +
57A ALA* 1.3 56.5 + - - +
59A THR* 3.1 9.7 + - - -
60A LEU* 2.9 37.4 + - - +
114A VAL* 3.2 11.0 - - - +
115A GLU* 2.8 65.0 + - + +
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A PHE* 4.3 6.6 - - + -
53A GLN* 4.0 24.7 - - + +
54A ASP* 2.8 26.2 + - - +
56A ASN* 1.3 70.9 - - - +
58A LEU* 1.3 64.3 + - - +
60A LEU* 3.3 24.4 + - + +
61A GLU* 3.4 16.8 + - - +
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.0 7.9 - - + +
17A ILE* 3.9 24.7 - - + -
20A ALA* 3.6 17.3 - - + -
32A LEU* 4.9 2.7 - - + -
37A LEU* 3.8 28.7 - - + -
48A ILE* 4.7 7.6 - - + -
52A PHE* 3.6 49.9 - - + +
54A ASP 3.2 9.4 + - - +
55A LEU* 3.3 17.9 + - + +
57A ALA* 1.3 74.7 - - - +
59A THR* 1.3 63.1 + - - +
61A GLU* 3.2 4.0 + - - +
62A VAL* 3.2 18.8 + - - +
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Residues in contact with THR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 4.3 7.6 - - + +
29A LEU* 3.2 40.9 - - + +
32A LEU* 3.6 10.7 - - - +
55A LEU 2.9 17.8 + - - -
56A ASN* 3.4 10.6 - - - -
58A LEU* 1.3 76.5 - - - +
60A LEU* 1.3 50.0 + - - +
62A VAL* 3.1 10.0 + - - +
63A ASN* 2.8 40.6 + - - +
110A ALA* 4.5 1.8 - - + -
114A VAL* 3.7 23.6 - - + -
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ASN* 2.9 25.6 + - - +
57A ALA* 3.5 15.3 - - + +
58A LEU 3.3 0.4 - - - -
59A THR* 1.3 74.6 - - - +
61A GLU* 1.3 57.1 + - - +
63A ASN* 3.3 1.9 + - - -
64A GLY 2.9 23.6 + - - -
114A VAL* 3.7 25.4 - - + -
115A GLU 4.4 1.3 - - - +
116A MSE 3.5 36.1 - - + -
123A PRO* 4.6 13.7 - - + -
125A TRP* 3.2 17.7 - - + -
126A TYR* 3.5 32.5 - - + +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 3.4 26.1 + - - -
17A ILE* 4.0 26.8 - - + +
52A PHE* 3.9 20.5 - - + -
57A ALA 3.4 12.6 + - - +
58A LEU 3.2 9.3 + - - +
60A LEU* 1.3 72.9 - - - +
62A VAL* 1.3 65.0 + - - +
64A GLY* 3.2 10.0 + - - -
65A ARG* 3.3 15.9 + - - +
125A TRP* 3.4 32.9 + - + -
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 3.9 13.5 - - + +
20A ALA* 3.6 15.3 - - + -
21A GLU* 3.6 37.5 - - + +
24A ILE* 4.0 16.2 - - + -
58A LEU 3.2 12.9 + - - +
59A THR* 3.1 9.7 + - - +
61A GLU* 1.3 75.7 - - - +
63A ASN* 1.3 58.8 + - - +
65A ARG* 3.1 10.6 + - - +
66A THR* 3.0 28.0 + - - +
107A LEU* 3.9 27.8 - - + -
110A ALA* 5.8 0.4 - - + -
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Residues in contact with ASN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR* 2.8 18.4 + - - +
60A LEU* 3.5 7.4 - - - +
62A VAL* 1.3 75.5 - - - +
64A GLY* 1.3 58.5 + - - +
66A THR* 3.6 3.9 + - - -
67A PHE* 2.8 35.7 + - - -
107A LEU 4.5 1.4 - - - +
110A ALA* 3.2 41.8 + - - +
111A LEU* 3.6 20.0 - - + +
114A VAL* 3.3 20.4 - - - +
126A TYR* 3.2 28.7 + - - +
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Residues in contact with GLY 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU 2.9 10.5 + - - -
61A GLU 3.2 6.4 + - - -
63A ASN* 1.3 75.0 - - - +
65A ARG* 1.3 61.6 + - - +
67A PHE* 3.5 12.1 + - - +
68A ALA* 3.2 21.3 + - - +
125A TRP* 3.7 25.4 - - - -
126A TYR* 4.4 0.2 - - - -
129A ALA* 5.6 1.3 - - - +
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 3.2 24.7 + - - -
17A ILE* 3.4 29.4 - - - +
18A ASP* 2.9 36.6 + - - +
21A GLU* 3.1 38.9 + - - +
61A GLU 3.3 8.4 + - - +
62A VAL* 3.1 10.5 + - - +
64A GLY* 1.3 74.2 - - - +
66A THR* 1.3 62.9 + - - +
68A ALA* 3.2 10.2 + - - +
69A ARG* 3.0 26.5 + - - +
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Residues in contact with THR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU* 5.3 0.5 + - - -
62A VAL* 3.0 15.5 + - - +
63A ASN* 3.2 8.2 + - - -
65A ARG* 1.3 71.7 - - - +
67A PHE* 1.3 66.4 + - - +
69A ARG* 3.2 11.5 + - - +
70A LEU* 3.0 21.5 + - - +
100A PHE* 3.5 30.0 - - + -
107A LEU* 3.8 39.4 + - + +
111A LEU* 3.8 25.6 - - + -
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Residues in contact with PHE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ASN 2.8 17.9 + - - -
64A GLY* 3.6 12.1 - - - +
66A THR* 1.3 75.3 - - - +
68A ALA* 1.3 51.8 - - - +
70A LEU* 3.2 8.3 + - + +
71A GLY* 2.8 32.7 + - - -
111A LEU* 4.0 20.4 - - + -
125A TRP* 5.5 0.2 - + - -
126A TYR* 3.4 61.9 - + - -
129A ALA* 3.7 25.8 - - + -
130A MSE 4.0 18.4 - - + -
133A LEU* 3.6 26.9 - - + +
203A STE 4.0 23.8 - - + -
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A GLY 3.2 9.4 + - - +
65A ARG* 3.2 14.7 + - - +
67A PHE* 1.3 76.9 - - - +
69A ARG* 1.3 62.9 - - - +
71A GLY* 3.3 2.6 + - - -
72A ALA* 3.0 24.0 + - - +
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Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU* 3.2 27.3 + - - -
25A GLU* 3.4 19.2 + - - -
65A ARG* 3.0 19.1 + - + +
66A THR* 3.2 9.5 + - - +
68A ALA* 1.3 74.1 - - - +
70A LEU* 1.3 57.5 + - - +
72A ALA* 3.3 8.0 + - - +
73A ALA* 3.0 27.7 + - - +
100A PHE* 3.6 29.3 - - + -
104A HIS* 3.3 25.8 + - - +
107A LEU* 3.7 17.8 - - - +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A THR 3.0 12.4 + - - +
67A PHE* 3.5 9.0 - - + +
69A ARG* 1.3 76.4 - - - +
71A GLY* 1.3 58.5 + - - +
73A ALA* 3.2 6.8 + - + +
74A VAL* 2.9 45.3 + - + +
96A ALA 5.1 0.2 - - - +
97A TYR* 4.0 28.7 - - + -
100A PHE* 4.1 31.8 - - + -
111A LEU* 4.7 13.2 - - + -
133A LEU* 4.2 7.9 - - + -
203A STE 3.3 48.2 - - + -
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Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PHE 2.8 17.0 + - - -
68A ALA* 3.7 2.9 - - - -
69A ARG 3.3 0.2 - - - -
70A LEU* 1.3 70.7 - - - +
72A ALA* 1.3 58.7 + - - +
74A VAL* 4.3 0.8 - - - +
75A GLY* 3.0 29.3 + - - -
133A LEU* 3.6 19.0 - - - +
136A TYR* 4.4 14.0 + - - -
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA 3.0 13.5 + - - +
69A ARG* 3.3 10.7 + - - +
71A GLY* 1.3 76.8 - - - +
73A ALA* 1.3 61.1 + - - +
75A GLY* 3.7 9.1 + - - -
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG 3.0 13.7 + - - +
70A LEU* 3.2 17.0 + - + +
72A ALA* 1.3 78.6 - - - +
74A VAL* 1.3 61.6 + - + +
96A ALA* 3.9 27.2 - - + +
100A PHE* 5.0 8.3 - - + -
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 2.9 29.6 + - + +
71A GLY 4.3 1.8 - - - +
73A ALA* 1.3 80.4 - - + +
75A GLY* 1.3 59.6 + - - +
93A MSE 3.5 48.8 - - + +
96A ALA* 4.8 5.2 - - + -
97A TYR 5.4 0.2 - - - +
136A TYR* 3.9 23.3 - - + -
203A STE 3.7 35.9 - - + -
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Residues in contact with GLY 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLY 3.0 17.3 + - - -
72A ALA 3.7 7.6 + - - -
73A ALA 3.6 1.8 - - - -
74A VAL* 1.3 80.7 - - - +
93A MSE 6.0 0.2 - - - +
136A TYR* 3.9 33.0 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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