Contacts of the helix formed by residues 152 - 158 (chain A) in PDB entry 6E8Y
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 ILE 152 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A TRP* 4.9 2.9 - - - -
151A ASN* 1.3 83.1 - - - +
153A ALA* 1.3 66.3 + - - +
154A SER* 3.3 20.6 - - - +
155A GLU* 3.2 31.4 + - + +
156A VAL* 3.1 23.8 + - - +
162A CYS* 5.5 0.2 - - - -
222B ASN* 3.5 21.5 - - - +
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Residues in contact with ALA 153 (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 ASN* 3.2 28.9 - - - +
14A TRP* 3.5 48.6 - - + +
17A ALA* 3.6 9.0 - - + +
152A ILE* 1.3 74.4 - - - +
154A SER* 1.3 64.6 + - - +
155A GLU 3.1 0.3 + - - -
156A VAL* 3.2 1.4 + - - -
157A ALA* 3.0 21.7 + - - +
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Residues in contact with SER 154 (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 ASN* 4.1 12.1 + - - +
64A LEU* 5.6 1.6 - - - -
67A HIS* 4.9 0.7 + - - -
152A ILE* 3.3 20.8 - - - +
153A ALA* 1.3 78.5 - - - +
155A GLU* 1.3 60.7 + - - +
157A ALA* 3.6 5.4 + - - +
158A ASP* 3.0 36.7 + - - +
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Residues in contact with GLU 155 (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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151A ASN* 5.4 0.3 - - - -
152A ILE* 3.2 30.9 + - + +
153A ALA 3.2 0.4 - - - -
154A SER* 1.3 78.6 + - - +
156A VAL* 1.3 60.3 + - + +
158A ASP* 3.3 5.9 + - - +
159A GLU 3.0 7.8 + - - -
160A LYS* 2.9 62.1 + - + +
162A CYS* 5.4 5.0 - - - +
220B GLY* 4.5 16.7 - - - -
221B ASP 5.0 1.2 + - - -
222B ASN* 3.1 34.4 + - - +
223B THR* 4.9 4.6 + - - -
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Residues in contact with VAL 156 (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 TRP* 4.2 16.8 - - + -
17A ALA* 4.4 17.0 - - + +
18A ILE* 5.0 1.8 - - + -
20A LYS* 5.7 0.2 - - - -
21A ILE* 3.4 36.5 - - + +
151A ASN* 4.3 4.9 - - + -
152A ILE 3.1 14.5 + - - +
153A ALA 3.8 6.1 - - - +
155A GLU* 1.3 75.1 - - - +
157A ALA* 1.3 64.4 + - - +
159A GLU* 3.1 17.1 + - - +
160A LYS 5.1 2.9 - - - -
162A CYS* 4.1 13.7 - - - -
186A PHE* 4.0 26.7 - - + -
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Residues in contact with ALA 157 (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 ALA* 4.1 15.6 - - + +
20A LYS* 3.2 35.6 + - + +
64A LEU* 4.1 10.3 - - + -
67A HIS* 3.4 29.8 - - + +
153A ALA 3.0 16.1 + - - +
154A SER 3.8 3.1 - - - +
156A VAL* 1.3 78.3 - - - +
158A ASP* 1.3 62.7 + - - +
159A GLU* 3.2 7.3 + - - +
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Residues in contact with ASP 158 (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 HIS* 3.0 25.8 + - - -
154A SER* 3.0 24.7 + - - +
155A GLU* 3.8 5.3 - - - +
156A VAL 3.3 0.6 - - - -
157A ALA* 1.3 74.3 - - - +
159A GLU* 1.3 70.7 + - - +
160A LYS* 3.3 19.9 + - + +
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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