Contacts of the helix formed by residues 156 - 162 (chain A) in PDB entry 1D8V
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 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A PHE* 5.5 6.3 - - + -
14A TYR* 6.3 0.4 - - + -
17A PHE* 4.2 28.9 - - + -
18A ILE* 4.7 1.6 - - - +
21A PHE* 5.2 3.5 - - - -
50A LEU* 4.6 14.4 - - + -
52A LEU* 4.5 15.3 - - + -
64A ILE* 6.4 0.7 - - - -
69A VAL* 5.0 0.2 - - - +
71A VAL* 5.1 1.6 - - - +
130A LEU* 5.3 2.9 - - + -
152A LEU* 2.2 61.2 + - + +
155A THR* 1.3 77.6 + - - +
157A ALA* 1.3 66.4 + - - +
158A GLU 3.5 0.2 - - - -
159A ALA* 3.8 1.5 - - - +
160A ALA* 3.2 21.7 + - - +
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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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21A PHE* 5.5 0.4 - - - -
64A ILE* 5.5 4.2 - - + +
69A VAL* 2.8 39.1 - - + +
70A TYR* 4.1 5.2 - - - -
71A VAL* 4.5 7.2 - - + +
153A ILE* 3.0 23.0 + - + +
156A THR* 1.3 81.0 + - - +
158A GLU* 1.3 63.7 + - - +
160A ALA 3.4 0.3 + - - -
161A ARG* 3.2 33.5 + - - +
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Residues in contact with GLU 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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109A TYR* 4.0 2.1 + - - -
153A ILE* 2.7 22.6 + - + +
154A GLN* 3.2 26.9 - - + +
157A ALA* 1.3 69.6 - - - +
159A ALA* 1.3 69.7 + - - +
161A ARG* 2.4 56.5 + - - +
162A PHE 3.2 9.4 + - - -
165A ILE* 3.8 29.3 - - + +
183A ILE* 5.8 2.9 - - + -
187A GLU* 2.9 39.7 - - - +
190A TRP* 5.0 1.2 - - - -
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Residues in contact with ALA 159 (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 TYR* 3.0 16.4 - - + +
18A ILE* 3.3 20.6 - - + +
154A GLN 3.4 5.3 + - - +
155A THR* 2.8 28.7 - - - +
156A THR* 3.5 2.0 + - - +
157A ALA 3.3 0.6 - - - -
158A GLU* 1.3 78.0 - - - +
160A ALA* 1.3 59.1 + - - +
162A PHE 2.7 22.3 - - - +
165A ILE* 4.0 12.8 - - + +
166A GLU* 3.7 10.4 - - - +
169A VAL* 5.3 0.9 - - + -
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Residues in contact with ALA 160 (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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18A ILE* 3.2 25.6 - - + +
21A PHE* 3.3 43.3 - - + -
69A VAL* 4.5 1.6 - - + -
156A THR 3.2 13.4 + - - +
157A ALA 3.7 3.8 - - - +
158A GLU 3.1 0.6 - - - -
159A ALA* 1.3 80.9 - - - +
161A ARG* 1.3 63.6 + - - +
162A PHE* 3.3 1.9 + - - -
236A LYS* 5.1 4.9 - - - +
237A LEU* 3.2 19.5 - - + +
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Residues in contact with ARG 161 (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 ASN* 2.7 32.9 + - - +
69A VAL* 3.5 21.5 + - + -
70A TYR* 4.3 10.3 - - - +
109A TYR* 4.3 5.7 + - - -
153A ILE* 4.1 7.5 - - - +
157A ALA* 3.3 20.7 - - - +
158A GLU* 2.4 52.3 + - - +
160A ALA* 1.3 80.0 - - - +
162A PHE* 1.3 70.8 + - + +
165A ILE* 5.5 0.4 - - + -
187A GLU* 4.9 1.4 + - - +
190A TRP* 3.4 47.9 + - + -
235A ILE* 5.4 1.0 - - - +
236A LYS* 4.7 6.8 + - - +
237A LEU* 3.7 26.1 - - + +
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Residues in contact with PHE 162 (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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18A ILE* 5.9 0.2 - - - -
158A GLU 3.2 2.6 + - - -
159A ALA 2.7 20.4 - - - +
160A ALA 4.6 1.3 - - - -
161A ARG* 1.3 89.6 - - + +
163A LYS* 1.3 63.7 + - - +
164A TYR* 4.1 5.4 - + + +
165A ILE* 3.4 22.7 + - + +
166A GLU 3.2 9.4 + - - -
186A LEU* 4.2 19.3 - - + -
190A TRP* 3.6 39.9 - + + -
193A LEU* 5.0 1.1 - - + -
230A VAL* 3.3 29.6 - - + -
234A ASN* 2.8 59.2 - - - -
235A ILE* 3.4 18.2 - - + -
236A LYS* 5.5 1.1 - - - +
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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