Contacts of the helix formed by residues 66 - 78 (chain B) in PDB entry 1ES0
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 TYR 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B TYR* 4.5 0.7 - - - +
60B TYR* 4.1 8.7 + + - -
61B TYR* 2.7 49.1 + + - +
64B GLN* 1.3 99.5 - - + +
68B LEU* 1.3 66.4 + - - +
69B GLU* 2.9 4.8 + - - -
70B ARG* 3.1 18.5 + - + +
71B THR* 2.9 22.1 + - - +
215B LEU* 3.4 46.4 - - + -
216B LEU* 2.5 42.5 + - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B PHE* 4.6 3.1 - - + -
45B GLY 3.4 23.6 - - - +
46B GLU* 3.8 7.9 - - + -
47B TYR* 4.8 3.1 - - + +
61B TYR 3.3 7.1 + - - -
62B ASN* 3.4 40.5 + - + +
64B GLN 4.0 0.4 - - - -
66B TYR* 1.3 74.6 - - - +
69B GLU* 1.3 63.9 + - - +
71B THR* 3.7 3.8 - - - -
72B ARG* 3.0 62.1 + - + +
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B TYR* 2.9 1.7 + - - -
68B LEU* 1.3 81.7 - - - +
70B ARG* 1.3 65.2 + - - +
71B THR 3.0 1.2 + - - -
72B ARG* 3.3 7.5 + - - +
73B ALA* 3.3 25.7 + - - +
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Residues in contact with ARG 70 (chain B).
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* 4.0 14.6 + - - -
64B GLN 5.9 0.2 - - - +
66B TYR* 3.1 21.7 + - + +
69B GLU* 1.3 79.8 - - - +
71B THR* 1.3 62.6 + - - +
73B ALA* 3.8 6.6 + - - +
74B GLU* 3.5 24.0 + - + +
213B PHE* 3.9 34.3 - - - +
215B LEU* 3.6 33.2 - - + +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.0 5.5 - - + +
28B THR* 4.8 4.7 - - + +
40B PHE* 3.3 38.1 - - + -
47B TYR* 2.6 36.2 + - + +
66B TYR 2.9 16.0 + - - -
68B LEU* 3.7 4.0 - - - -
70B ARG* 1.3 72.7 - - - +
72B ARG* 1.3 68.5 + - - +
73B ALA 3.1 1.8 - - - -
74B GLU* 2.9 35.7 + - - +
215B LEU* 3.4 10.3 - - - +
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 5.2 0.2 - - - +
40B PHE* 3.8 24.7 - - + -
45B GLY* 2.5 34.8 + - - +
46B GLU* 4.4 6.3 + - - +
68B LEU* 3.0 52.3 + - + +
69B GLU* 4.0 7.6 - - - +
71B THR* 1.3 75.5 - - - +
73B ALA* 1.3 61.0 + - - +
75B LEU* 3.2 23.2 + - - +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLU* 3.3 19.5 + - - +
70B ARG* 3.9 7.6 - - - +
71B THR 3.0 1.0 + - - -
72B ARG* 1.3 74.3 - - - +
74B GLU* 1.3 56.0 + - - +
75B LEU 2.9 5.6 - - - -
76B ASP* 2.8 25.1 + - - +
77B THR* 3.1 21.7 + - + +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 3.9 12.9 - - + +
28B THR* 4.9 2.3 + - - +
70B ARG* 3.5 19.9 + - + +
71B THR* 2.9 28.0 + - - +
73B ALA* 1.3 76.8 - - - +
75B LEU* 1.3 58.4 + - - +
77B THR* 3.5 13.7 - - - +
78B ALA* 2.8 40.0 + - + +
79B CYS* 3.1 2.8 + - - +
211B PRO 4.1 0.9 - - - +
212B VAL* 3.5 18.2 - - + +
213B PHE* 2.8 48.9 + - + +
215B LEU* 5.4 4.3 - - - +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 3.4 42.4 - - + +
25B ARG* 3.9 2.2 - - - +
26B LEU* 3.6 23.6 - - + +
40B PHE* 6.3 0.2 - - + -
42B SER* 3.4 31.2 - - - +
72B ARG 3.2 15.5 + - - +
73B ALA 2.9 1.0 - - - -
74B GLU* 1.3 78.5 - - - +
76B ASP* 1.3 63.2 + - - +
79B CYS* 3.1 9.8 - - - +
80B ARG* 3.1 27.2 + - - +
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Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ALA* 2.8 10.3 + - - +
75B LEU* 1.3 84.9 - - - +
77B THR* 1.3 63.1 + - + +
78B ALA 3.2 1.6 - - - -
80B ARG* 2.5 47.3 + - + +
81B HIS* 2.9 29.8 + - - +
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Residues in contact with THR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ALA* 3.1 15.7 + - + +
74B GLU* 3.5 19.6 - - - +
76B ASP* 1.3 78.1 - - + +
78B ALA* 1.3 59.4 + - - +
81B HIS* 3.3 16.1 - - - +
210B ALA* 3.2 20.6 - - - +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B CYS* 4.5 0.7 - - - -
74B GLU* 2.8 27.7 + - + +
77B THR* 1.3 80.0 + - - +
79B CYS* 1.3 59.5 + - - +
82B ASN* 2.9 42.7 + - - +
210B ALA* 4.1 6.7 - - + -
211B PRO 4.3 11.0 - - - +
212B VAL* 3.9 28.5 - - + -
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Residues in contact with CYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A TYR* 4.5 0.9 - - - -
15B CYS* 2.0 54.1 - - + -
17B PHE* 3.4 15.4 - - + -
24B ILE* 3.6 15.7 - - + -
26B LEU* 4.0 28.0 - - - -
74B GLU 3.1 2.8 + - - -
75B LEU* 3.1 19.3 - - - +
78B ALA* 1.3 80.5 - - - +
80B ARG* 1.3 64.7 + - - +
82B ASN* 4.1 0.5 - - - +
83B TYR* 3.1 19.1 + - - +
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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