Contacts of the helix formed by residues 52 - 72 (chain A) in PDB entry 1ECD
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A PHE* 5.3 1.0 - - - -
48A SER 3.6 19.5 - - - +
49A ILE* 2.7 30.7 + - + +
50A LYS 3.5 1.1 - - - +
51A GLY* 1.3 80.0 - - - +
53A ALA* 1.3 65.9 + - - +
54A PRO* 3.9 9.6 - - - +
55A PHE* 3.3 18.0 + - - +
56A GLU* 3.3 12.1 + - - +
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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
----------------------------------------------------------
52A THR* 1.3 72.3 - - - +
54A PRO* 1.3 68.4 - - + +
56A GLU* 3.4 8.0 + - - +
57A THR* 3.0 33.7 + - - +
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Residues in contact with PRO 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLN* 4.2 31.4 - - + +
41A PHE* 3.9 5.8 - - + -
52A THR* 3.5 11.4 - - - +
53A ALA* 1.3 96.1 - - + +
55A PHE* 1.3 64.1 + - - +
57A THR* 3.4 5.5 + - - +
58A HIS* 3.1 32.7 + - + +
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Residues in contact with PHE 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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21A VAL* 3.5 33.0 - - + -
24A LEU* 3.9 14.3 - - + +
25A TYR* 3.8 24.7 - - + -
28A PHE* 3.7 26.2 - + - -
41A PHE* 3.6 18.5 - + + -
46A LEU* 4.1 6.5 - - + -
49A ILE* 3.2 48.5 - - + +
50A LYS* 3.4 24.5 - - + +
52A THR* 3.3 9.2 + - - +
54A PRO* 1.3 77.8 - - - +
56A GLU* 1.3 59.9 + - - +
58A HIS* 3.5 3.1 + - - +
59A ALA* 2.9 29.5 + - - +
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Residues in contact with GLU 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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20A PRO* 5.1 5.2 - - + +
21A VAL* 4.0 27.1 - - + +
52A THR 3.3 9.5 + - - +
53A ALA* 3.7 10.5 - - - +
54A PRO 3.3 0.2 - - - -
55A PHE* 1.3 78.3 - - - +
57A THR* 1.3 61.5 + - - +
59A ALA* 3.7 1.1 - - - +
60A ASN* 2.9 54.8 + - - +
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Residues in contact with THR 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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53A ALA 3.0 17.8 + - - -
54A PRO* 3.6 8.5 - - - +
55A PHE 3.3 0.2 - - - -
56A GLU* 1.3 79.8 - - - +
58A HIS* 1.3 66.1 + - + +
60A ASN* 3.4 6.5 + - - +
61A ARG* 3.2 53.5 + - - +
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Residues in contact with HIS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.1 6.7 - - + -
38A PHE* 4.0 18.5 - + + -
40A GLN* 4.8 15.0 - - + -
41A PHE* 3.7 27.1 - + + -
54A PRO* 3.1 24.3 + - + +
55A PHE 3.7 3.8 - - - +
57A THR* 1.3 80.7 - - + +
59A ALA* 1.3 66.3 + - - +
61A ARG* 3.3 24.9 + - + +
62A ILE* 3.0 34.1 + - + +
137A HEM 2.9 36.5 + - + +
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Residues in contact with ALA 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 PRO* 3.6 30.3 - - + +
21A VAL* 4.0 8.5 - - + +
24A LEU* 3.3 22.4 - - + -
55A PHE* 2.9 18.6 + - + +
56A GLU* 3.7 6.3 - - - +
58A HIS* 1.3 76.8 - - - +
60A ASN* 1.3 58.9 + - - +
62A ILE* 4.6 2.0 - - - +
63A VAL* 3.0 35.7 + - - +
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Residues in contact with ASN 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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20A PRO* 3.3 27.3 - - - +
56A GLU* 2.9 42.1 + - - +
57A THR* 3.6 6.8 - - - +
59A ALA* 1.3 79.3 - - - +
61A ARG* 1.3 57.3 + - - +
64A GLY* 2.9 27.5 + - - +
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Residues in contact with ARG 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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57A THR* 3.2 33.0 + - + +
58A HIS* 3.6 37.0 + - + +
60A ASN* 1.3 79.4 - - + +
62A ILE* 1.3 64.4 + - + +
64A GLY* 3.9 0.3 - - - -
65A PHE* 3.2 17.3 + - - +
137A HEM 3.4 45.7 + - + +
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Residues in contact with ILE 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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24A LEU* 3.9 23.6 - - + -
38A PHE* 3.8 33.9 - - + -
58A HIS* 3.0 24.3 + - + +
59A ALA* 4.1 3.1 - - - +
61A ARG* 1.3 78.6 - - + +
63A VAL* 1.3 71.0 + - + +
65A PHE* 3.3 1.9 + - - +
66A PHE* 3.2 4.6 + - + -
100A PHE* 4.5 17.5 - - + -
137A HEM 3.0 82.2 - - + +
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Residues in contact with VAL 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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13A PHE* 4.5 13.7 - - + -
17A LYS* 4.8 8.5 - - + +
20A PRO* 3.9 33.9 - - + +
23A ILE* 4.0 37.0 - - + -
24A LEU* 5.0 4.0 - - + +
59A ALA* 3.0 17.9 + - - +
62A ILE* 1.3 80.4 - - + +
64A GLY* 1.3 61.1 + - - +
66A PHE* 3.6 9.4 - - + +
67A SER* 2.8 28.9 + - - -
100A PHE* 6.3 0.7 - - + -
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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 ASN* 2.9 23.4 + - - +
61A ARG 3.9 1.1 - - - -
62A ILE 3.3 0.2 - - - -
63A VAL* 1.3 79.2 - - - +
65A PHE* 1.3 55.2 + - - +
67A SER* 3.4 8.1 - - - -
68A LYS* 3.1 22.3 + - - +
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Residues in contact with PHE 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 ARG 3.2 17.0 + - - +
62A ILE 3.8 2.7 - - - +
64A GLY* 1.3 74.1 - - - +
66A PHE* 1.3 67.8 + - - +
68A LYS* 3.1 30.7 + - + +
69A ILE* 3.2 29.6 + - + +
79A ASP* 3.6 48.5 - - + -
82A THR* 4.4 17.0 - - + -
83A PHE* 4.4 12.8 - + + -
137A HEM 3.7 32.8 - - + -
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Residues in contact with PHE 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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13A PHE* 4.1 19.1 - + - -
23A ILE* 6.3 0.4 - - + -
62A ILE* 3.2 5.5 + - + +
63A VAL* 3.6 13.0 - - + +
65A PHE* 1.3 77.8 - - - +
67A SER* 1.3 58.4 + - - +
69A ILE* 2.9 24.6 + - + +
70A ILE* 3.0 40.5 + - + +
100A PHE* 4.9 17.0 - + + -
104A PHE* 3.7 44.9 - + - -
121A TRP* 4.5 0.9 - + - -
125A LEU* 4.5 12.3 - - + -
128A PHE* 4.0 32.8 - + - -
129A PHE* 6.0 0.7 - + - -
137A HEM 3.5 22.1 - - + +
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Residues in contact with SER 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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13A PHE* 3.7 28.2 - - - -
17A LYS* 5.0 9.1 - - - +
63A VAL* 2.8 20.0 + - - -
64A GLY* 3.4 10.5 - - - -
65A PHE 3.1 0.2 - - - -
66A PHE* 1.3 74.9 - - - +
68A LYS* 1.3 65.9 - - - +
70A ILE* 3.9 1.8 - - - +
71A GLY* 2.9 21.1 + - - -
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Residues in contact with LYS 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 3.1 9.0 + - - +
65A PHE* 3.1 28.8 + - + +
67A SER* 1.3 77.9 - - - +
69A ILE* 1.3 62.7 + - - +
71A GLY* 3.3 3.2 + - - -
72A GLU* 2.8 44.4 + - - +
79A ASP* 2.8 28.4 + - - +
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Residues in contact with ILE 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 PHE* 3.2 32.7 + - + +
66A PHE* 2.9 15.9 + - + +
68A LYS* 1.3 79.5 - - - +
70A ILE* 1.3 73.5 + - + +
72A GLU* 3.3 27.8 + - - +
73A LEU* 3.4 19.4 + - + +
76A ILE* 4.0 18.2 - - + -
79A ASP* 4.1 17.5 - - + +
80A VAL* 5.3 1.3 - - + -
83A PHE* 6.0 1.6 - - + -
128A PHE* 3.3 46.4 - - + -
137A HEM 5.1 2.2 - - + -
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Residues in contact with ILE 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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9A VAL* 4.1 12.8 - - + -
10A GLN* 3.2 30.7 - - + +
13A PHE* 4.4 24.7 - - + -
66A PHE* 3.0 43.5 + - + +
67A SER 3.9 4.7 - - - +
69A ILE* 1.3 86.0 - - + +
71A GLY* 1.3 61.3 + - - +
72A GLU 3.4 0.7 + - - -
73A LEU* 3.4 16.5 - - + +
121A TRP* 4.0 26.9 - - + -
124A THR* 4.2 17.3 - - + -
125A LEU* 6.2 0.2 - - + -
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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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10A GLN* 3.6 15.1 - - - +
67A SER 2.9 15.4 + - - -
68A LYS* 3.7 4.9 - - - -
69A ILE 3.2 0.2 - - - -
70A ILE* 1.3 79.2 - - - +
72A GLU* 1.3 56.2 + - - +
73A LEU 3.6 0.9 - - - +
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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
----------------------------------------------------------
68A LYS* 2.8 39.1 + - - +
69A ILE* 3.3 19.8 + - - +
71A GLY* 1.3 76.5 - - - +
73A LEU* 1.3 70.3 + - - +
74A PRO* 4.2 0.2 - - - +
75A ASN* 2.8 42.7 + - + +
76A ILE* 3.9 8.1 - - + -
79A ASP* 2.4 29.7 - - - +
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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
------------------------------------------------------------
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