Contacts of the helix formed by residues 62 - 76 (chain E) in PDB entry 3ECS
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 62 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E SER* 5.3 2.7 - - - -
60E ASP* 3.2 25.1 + - - +
61E SER* 1.3 80.1 + - - +
63E VAL* 1.3 65.5 + - - +
64E ALA* 2.9 24.0 + - - +
65E VAL* 3.7 12.5 + - - +
66E SER* 3.7 8.0 + - - -
198E GLU* 4.1 26.6 - - - +
250E PHE* 3.9 7.2 - - - -
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Residues in contact with VAL 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E SER* 1.3 72.0 + - - +
64E ALA* 1.3 55.9 + - - +
65E VAL 3.1 0.7 - - - -
66E SER* 3.0 3.2 + - - -
67E SER* 2.7 36.6 + - - -
198E GLU* 3.1 41.3 - - + +
199E GLY* 3.7 10.1 - - - +
207E ILE* 3.8 26.9 - - + -
236E VAL* 4.8 9.9 - - + -
238E LEU* 4.4 5.4 - - + -
250E PHE* 3.3 49.4 - - + +
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Residues in contact with ALA 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E SER* 5.4 2.5 - - - -
23E ALA* 3.5 24.5 - - + +
62E SER* 2.9 11.3 + - - +
63E VAL* 1.3 81.6 - - - +
65E VAL* 1.3 54.8 + - + +
67E SER* 3.3 6.5 + - - -
68E GLY* 2.6 35.3 + - - -
198E GLU* 3.5 17.7 - - + +
233E PHE 4.4 0.3 - - - +
234E LYS* 4.1 21.8 - - + -
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Residues in contact with VAL 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E PHE* 4.7 2.7 - - + -
22E SER* 4.2 17.3 - - - -
23E ALA* 4.2 11.7 - - - +
26E ALA* 4.1 20.0 - - + +
27E ILE* 5.5 0.2 - - - +
54E GLU* 4.4 14.6 - - + +
57E CYS* 3.9 22.7 - - - +
58E GLY* 4.8 4.3 - - - -
60E ASP* 3.2 34.5 - - + +
62E SER* 3.7 10.9 + - - +
63E VAL 3.1 0.2 - - - -
64E ALA* 1.3 77.1 - - - +
66E SER* 1.3 58.2 + - - +
69E GLY* 2.9 26.5 + - - -
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Residues in contact with SER 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E GLU* 4.6 6.0 - - - +
62E SER 3.7 1.5 + - - -
63E VAL* 3.0 8.5 + - - -
65E VAL* 1.3 83.4 - - - +
67E SER* 1.3 58.1 + - - +
69E GLY* 3.8 0.6 - - - -
70E GLU* 2.9 28.8 + - - +
236E VAL* 5.2 5.1 - - - +
250E PHE* 4.1 27.8 - - - -
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Residues in contact with SER 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E VAL 2.7 23.0 + - - -
64E ALA* 3.3 4.3 + - - -
66E SER* 1.3 70.8 + - - +
68E GLY* 1.3 65.1 + - - +
70E GLU* 4.0 6.3 - - - +
71E LEU* 3.0 29.3 + - - +
233E PHE 3.0 14.1 + - - -
234E LYS* 3.6 11.4 + - - -
235E PHE 3.6 22.7 - - - -
236E VAL* 3.6 22.6 - - - +
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Residues in contact with GLY 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ALA* 4.7 0.9 - - - -
27E ILE* 3.8 18.9 - - - +
64E ALA 2.6 22.8 + - - -
67E SER* 1.3 74.8 + - - +
69E GLY* 1.3 57.0 + - - +
71E LEU* 3.3 3.0 + - - +
72E PHE* 3.0 28.2 + - - +
100E PHE* 4.4 2.3 - - - -
233E PHE* 3.6 22.7 - - - -
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Residues in contact with GLY 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ALA* 6.5 0.4 - - - -
27E ILE* 4.1 4.9 - - - +
30E LEU* 4.4 7.9 - - - -
54E GLU* 2.8 25.3 - - - +
65E VAL 2.9 18.6 + - - -
66E SER 3.8 0.2 - - - -
68E GLY* 1.3 74.9 - - - +
70E GLU* 1.3 65.2 + - - +
72E PHE* 3.1 7.1 + - - +
73E LEU* 3.0 22.2 + - - +
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Residues in contact with GLU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E GLU* 3.4 4.9 + - - -
66E SER* 2.9 18.5 + - - +
67E SER* 4.0 6.5 - - - +
69E GLY* 1.3 73.4 - - - +
71E LEU* 1.3 63.8 + - + +
73E LEU* 3.6 5.8 + - + +
74E ARG* 2.6 81.3 + - + +
237E ARG* 3.3 31.4 - - - +
304E TYR* 3.3 4.2 + - - +
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Residues in contact with LEU 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E SER 3.0 18.8 + - - +
68E GLY 3.5 4.3 - - - +
70E GLU* 1.3 76.0 - - + +
72E PHE* 1.3 62.0 + - - +
74E ARG* 3.6 4.0 + - - +
75E PHE* 3.1 23.6 + - - +
100E PHE* 3.9 16.1 - - + -
232E SER 3.7 8.7 - - - +
233E PHE* 3.4 41.5 - - + +
235E PHE* 4.4 11.4 - - + +
300E LEU* 6.2 1.3 - - + -
303E LEU* 4.0 20.0 - - + -
304E TYR* 3.1 40.8 - - + +
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Residues in contact with PHE 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ILE* 3.7 36.3 - - + -
30E LEU* 3.7 38.8 - - + -
31E LEU* 4.2 18.2 - - + -
34E LEU* 5.1 4.0 - - + -
68E GLY 3.0 13.9 + - - +
69E GLY* 3.1 8.7 + - - +
71E LEU* 1.3 72.3 - - - +
73E LEU* 1.3 67.1 + - + +
74E ARG 3.0 0.9 - - - -
75E PHE* 2.8 25.3 + - - +
76E ILE* 3.0 36.7 + - + +
97E GLY* 3.4 34.3 - - - -
100E PHE* 3.7 22.4 - + + -
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Residues in contact with LEU 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E ALA* 4.7 10.3 - - + +
50E THR* 3.8 21.5 - - - +
51E SER* 4.0 16.8 - - - -
54E GLU* 3.3 28.3 - - - +
69E GLY 3.0 6.6 + - - +
70E GLU* 4.1 5.2 - - + +
72E PHE* 1.3 81.8 - - + +
74E ARG* 1.3 70.2 + - + +
76E ILE* 3.3 22.9 - - + +
77E SER* 2.8 23.1 + - - +
93E MSE 5.5 1.5 - - + +
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Residues in contact with ARG 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C LEU* 5.8 5.3 - - - +
70E GLU* 2.6 67.5 + - + +
71E LEU* 3.8 4.7 - - + +
72E PHE 3.0 1.0 - - - -
73E LEU* 1.3 84.3 - - + +
75E PHE* 1.3 64.5 + - - +
77E SER* 3.4 20.4 - - - +
237E ARG* 3.2 19.7 - - - +
304E TYR* 3.6 31.1 + - + -
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Residues in contact with PHE 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E LEU 3.1 14.2 + - - +
72E PHE 2.8 14.8 + - - +
74E ARG* 1.3 73.1 - - - +
76E ILE* 1.3 57.1 + - + +
77E SER 3.0 8.9 + - - +
96E ARG* 3.3 42.9 - - + +
99E LEU* 3.9 24.7 - - + -
100E PHE* 3.4 41.5 - + + -
103E ARG* 5.1 9.0 - - - -
306E ALA* 4.8 20.9 - - + -
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Residues in contact with ILE 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E LEU* 4.0 13.7 - - + -
50E THR* 6.1 4.9 - - + -
72E PHE* 3.6 38.6 - - + +
73E LEU* 3.3 22.9 - - + +
75E PHE* 1.3 78.7 - - + +
77E SER* 1.3 56.7 + - - +
78E LEU 5.5 0.7 - - - -
93E MSE 3.2 57.3 - - + +
96E ARG* 4.1 11.4 - - + -
97E GLY* 3.7 33.4 - - - +
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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