Contacts of the helix formed by residues 50 - 72 (chain A) in PDB entry 2FD5
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 SER 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A PHE* 3.7 9.1 - - - -
45A TYR* 4.1 9.0 - - - -
48A PHE* 3.4 2.2 - - - +
49A GLN* 1.3 84.5 + - - +
51A LYS* 1.3 65.5 + - - +
52A ASP* 3.5 7.8 + - - +
53A ALA* 3.1 24.2 + - - +
54A LEU* 3.1 22.0 + - - +
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Residues in contact with LYS 51 (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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25A ALA 3.5 16.2 + - - -
26A VAL* 2.8 24.4 + - - +
28A PRO 2.7 30.4 + - - +
29A SER* 4.2 3.3 - - - +
30A VAL* 4.0 31.8 - - + +
33A VAL* 6.2 1.3 - - + -
44A PHE* 4.1 11.0 - - - -
45A TYR* 5.0 2.2 + - - +
50A SER* 1.3 74.4 - - - +
52A ASP* 1.3 70.5 + - - +
54A LEU* 3.3 8.5 + - + +
55A MET* 2.9 36.3 + - + +
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Residues in contact with ASP 52 (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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25A ALA 5.0 2.3 - - - +
50A SER* 3.2 7.6 + - - +
51A LYS* 1.3 92.3 - - - +
53A ALA* 1.3 59.8 + - - +
55A MET* 3.8 4.7 - - - +
56A LEU* 2.8 31.8 + - - +
116A LEU* 4.8 9.3 - - - +
117A PRO* 3.4 35.4 - - + +
120A PHE* 4.3 5.1 - - + -
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Residues in contact with ALA 53 (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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48A PHE* 5.0 3.6 - - + -
49A GLN* 3.8 31.9 - - + +
50A SER* 3.1 24.8 + - - +
52A ASP* 1.3 75.2 - - - +
54A LEU* 1.3 63.3 + - - +
56A LEU* 3.9 6.9 - - - +
57A GLU* 3.0 24.8 + - - +
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Residues in contact with LEU 54 (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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12A ILE* 3.9 6.5 - - + -
13A LEU* 4.0 6.9 - - + +
16A ALA* 3.7 31.2 - - + -
30A VAL* 5.9 0.7 - - + -
33A VAL* 4.3 18.4 - - + -
44A PHE* 3.6 22.7 - - + -
48A PHE* 3.6 48.8 - - + -
50A SER 3.1 13.8 + - - +
51A LYS* 3.4 15.5 - - + +
53A ALA* 1.3 75.5 - - - +
55A MET* 1.3 63.6 + - + +
57A GLU* 3.2 4.0 + - - +
58A ALA* 2.9 26.5 + - - +
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Residues in contact with MET 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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16A ALA* 3.9 37.9 - - - +
19A ALA* 4.6 0.4 - - + -
20A LEU* 4.1 11.7 - - + +
24A GLY 3.5 24.7 - - - +
25A ALA* 3.9 23.6 - - + +
28A PRO* 3.6 27.6 - - + +
33A VAL* 5.4 2.7 - - + -
51A LYS* 2.9 31.2 + - + +
52A ASP* 4.1 4.5 - - - +
54A LEU* 1.3 79.1 - - + +
56A LEU* 1.3 58.6 + - - +
58A ALA* 3.2 3.6 + - - +
59A PHE* 2.9 30.1 + - - +
120A PHE* 3.8 14.4 - - + -
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Residues in contact with LEU 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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52A ASP 2.8 18.8 + - - +
53A ALA* 3.9 6.7 - - - +
55A MET* 1.3 75.0 - - - +
57A GLU* 1.3 59.6 + - - +
59A PHE* 3.3 4.0 + - + +
60A GLU* 2.9 59.1 + - + +
117A PRO* 5.8 4.5 - - + -
119A GLY* 3.6 42.6 - - - +
120A PHE* 3.5 29.3 - - + +
123A VAL* 4.4 0.7 - - + -
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Residues in contact with GLU 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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9A ARG* 2.8 44.9 + - - -
13A LEU* 3.6 20.2 - - + +
48A PHE* 3.5 10.6 - - - -
53A ALA 3.0 17.2 + - - +
54A LEU* 3.7 4.3 - - - +
56A LEU* 1.3 77.8 - - - +
58A ALA* 1.3 57.9 + - - +
60A GLU* 3.4 14.7 + - + +
61A GLN* 2.9 32.1 + - + +
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Residues in contact with ALA 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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13A LEU* 3.8 10.2 - - + +
16A ALA* 4.4 5.4 - - + +
17A THR* 3.6 33.2 - - + +
20A LEU* 3.7 14.1 - - + -
54A LEU 2.9 13.2 + - - +
55A MET* 3.2 11.9 + - - +
57A GLU* 1.3 75.3 - - - +
59A PHE* 1.3 58.5 + - - +
61A GLN* 3.4 3.0 + - - +
62A LEU* 3.0 34.8 + - - +
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Residues in contact with PHE 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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20A LEU* 3.4 12.2 - - + +
55A MET 2.9 17.8 + - - +
56A LEU* 3.4 7.4 - - + +
58A ALA* 1.3 76.8 - - - +
60A GLU* 1.3 62.4 + - - +
62A LEU* 3.4 3.1 + - - +
63A LEU* 3.0 50.6 + - + +
105A PRO* 4.0 18.4 - - + -
106A LEU* 3.8 19.1 - - + -
109A THR* 3.2 31.6 - - + -
113A VAL* 4.6 10.5 - - + -
120A PHE* 3.6 57.7 - + + -
123A VAL* 4.1 9.9 - - + -
124A LEU* 4.4 4.7 - - + -
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Residues in contact with GLU 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 LEU* 2.9 40.8 + - + +
57A GLU* 3.8 14.6 - - + +
59A PHE* 1.3 74.7 - - - +
61A GLN* 1.3 57.2 + - - +
63A LEU* 3.8 1.8 - - - +
64A GLY* 2.9 26.7 + - - -
67A ARG* 5.1 2.4 + - - -
119A GLY* 5.7 0.3 - - - -
123A VAL* 3.4 42.6 - - + +
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Residues in contact with GLN 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 LEU* 3.4 27.7 - - + +
14A GLY* 6.0 0.3 - - - -
17A THR* 3.6 21.4 - - + +
57A GLU* 2.9 21.1 + - + +
58A ALA 3.7 3.8 - - - +
59A PHE 3.3 0.2 - - - -
60A GLU* 1.3 74.4 - - - +
62A LEU* 1.3 68.0 + - + +
64A GLY* 3.3 2.1 + - - -
65A LYS* 3.0 24.1 + - + +
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Residues in contact with LEU 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 THR* 3.8 25.4 - - + +
20A LEU* 3.7 22.4 - - + -
21A LEU* 3.7 37.9 - - + -
58A ALA 3.0 21.0 + - - +
59A PHE 3.9 3.1 - - - +
61A GLN* 1.3 76.9 - - + +
63A LEU* 1.3 62.9 + - - +
65A LYS* 3.2 7.0 + - + +
66A ARG* 3.0 28.0 + - - +
101A ASP 5.8 0.9 - - - +
102A ALA* 5.0 6.7 - - + +
103A GLY 3.6 20.4 - - - +
105A PRO* 4.0 15.7 - - + -
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Residues in contact with LEU 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 PHE* 3.0 50.2 + - + +
60A GLU* 3.9 3.4 - - - +
62A LEU* 1.3 75.5 - - - +
64A GLY* 1.3 63.6 + - - +
66A ARG* 3.2 3.8 + - + -
67A ARG* 3.1 26.2 + - - +
104A CYS* 4.6 2.9 - - - -
105A PRO* 3.7 26.0 - - + -
106A LEU* 3.9 15.0 - - + -
123A VAL* 3.6 18.4 - - + +
124A LEU* 4.8 1.6 - - - +
127A HIS* 3.4 50.3 - - + +
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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 GLU 2.9 17.3 + - - -
61A GLN* 3.7 2.7 - - - -
63A LEU* 1.3 75.0 - - - +
65A LYS* 1.3 57.9 + - - +
67A ARG* 3.2 26.4 + - - +
68A GLU* 3.0 27.8 + - - +
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Residues in contact with LYS 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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61A GLN* 3.0 15.2 + - + +
62A LEU* 3.5 11.9 - - + +
64A GLY* 1.3 73.9 - - - +
66A ARG* 1.3 59.3 + - - +
68A GLU* 3.1 27.6 + - + +
69A LEU* 2.9 44.8 + - + +
101A ASP* 6.5 0.2 - - - -
102A ALA* 3.5 33.4 - - + -
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Residues in contact with ARG 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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62A LEU 3.0 20.6 + - - +
63A LEU* 3.2 9.8 + - - +
65A LYS* 1.3 76.0 - - - +
67A ARG* 1.3 62.2 + - - +
69A LEU* 3.4 22.6 + - - +
70A LEU* 3.1 23.0 + - - +
86A ALA 5.5 0.4 + - - -
89A PHE* 5.0 7.7 + - - +
90A TYR* 3.5 34.9 - - - +
95A HIS* 4.1 23.4 + - - -
100A VAL* 5.2 2.2 - - - +
102A ALA* 2.8 29.7 + - - -
103A GLY* 3.9 8.9 - - - +
104A CYS* 3.9 25.5 - - + +
105A PRO* 4.8 0.2 - - + -
127A HIS* 4.2 12.1 - - + +
131A MET* 4.5 6.1 - - - +
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Residues in contact with ARG 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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60A GLU 5.1 2.0 + - - -
63A LEU* 3.1 21.7 + - - +
64A GLY* 3.5 25.9 - - - +
65A LYS 3.2 0.4 - - - -
66A ARG* 1.3 74.3 - - - +
68A GLU* 1.3 59.7 + - - +
70A LEU* 3.3 4.0 + - - +
71A GLY* 3.0 24.3 + - - -
123A VAL* 5.2 5.1 + - - +
126A ARG* 5.8 5.1 - - - +
127A HIS* 2.9 53.9 + - + +
130A ILE* 3.8 46.5 - - + +
131A MET* 4.0 16.2 - - + -
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Residues in contact with GLU 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 3.0 13.8 + - - +
65A LYS* 3.1 31.5 + - + +
67A ARG* 1.3 74.9 - - - +
69A LEU* 1.3 65.8 + - + +
71A GLY* 3.0 13.6 + - - +
72A GLU* 3.2 23.1 + - + +
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Residues in contact with LEU 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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65A LYS* 2.9 34.0 + - + +
66A ARG* 3.6 33.7 - - - +
68A GLU* 1.3 75.5 - - + +
70A LEU* 1.3 61.7 + - - +
72A GLU* 3.0 38.5 + - - +
73A LEU* 3.8 7.6 + - - +
102A ALA* 3.9 24.9 - - + +
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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 ARG 3.1 14.0 + - - +
67A ARG 3.7 7.6 - - - +
69A LEU* 1.3 76.1 - - - +
71A GLY* 1.3 60.4 + - - +
73A LEU* 3.2 31.3 + - + +
82A ARG* 5.7 0.3 - - - -
86A ALA* 3.7 30.7 - - + -
131A MET* 3.3 25.6 - - + -
134A SER* 3.1 30.1 - - - +
135A LEU* 4.0 23.3 - - + -
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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 ARG 3.0 14.7 + - - -
68A GLU* 3.0 8.6 + - - -
70A LEU* 1.3 75.8 - - - +
72A GLU* 1.3 60.0 + - - +
73A LEU 3.3 7.1 + - - +
75A PRO* 6.0 0.5 - - - +
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Residues in contact with GLU 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 GLU* 3.5 21.7 - - + +
69A LEU* 3.0 34.1 + - - +
71A GLY* 1.3 73.1 - - - +
73A LEU* 1.3 67.8 + - + +
74A ASP* 3.6 2.1 + - - -
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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