Contacts of the helix formed by residues 154 - 161 (chain A) in PDB entry 3DAG
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 LYS 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A PRO* 4.4 18.8 - - + +
151A LYS 4.2 9.4 - - - +
152A GLY 3.0 2.6 - - - +
153A ASN* 1.3 96.3 + - - +
155A GLN* 1.3 63.5 + - - +
156A PRO* 3.5 0.7 - - - -
157A ASP* 3.5 9.9 + - - +
158A ILE* 3.4 34.9 + - + +
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Residues in contact with GLN 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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147A THR* 4.8 1.2 + - - -
149A LEU* 3.7 25.9 + - + +
150A PRO 3.0 27.6 + - - +
152A GLY* 3.5 12.8 - - - +
154A LYS* 1.3 77.4 - - - +
156A PRO* 1.4 69.1 - - + +
158A ILE* 3.1 6.4 + - + -
159A ILE* 2.8 37.7 + - + +
177A THR* 3.1 21.0 + - - -
178A ILE* 3.7 35.1 - - + +
183A PHE* 3.7 15.9 - - - -
186A ILE* 4.2 7.4 - - + -
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Residues in contact with PRO 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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152A GLY 3.7 10.8 - - - +
153A ASN* 3.7 11.7 - - - +
154A LYS 3.6 3.6 - - - -
155A GLN* 1.4 91.5 - - + +
157A ASP* 1.3 60.8 + - - +
159A ILE* 3.4 0.5 + - - +
160A LYS* 2.9 32.7 + - - +
186A ILE* 3.8 33.7 - - + +
190A LEU* 5.1 0.2 - - - +
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Residues in contact with ASP 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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153A ASN 5.4 3.0 + - - +
154A LYS* 3.5 9.3 + - - +
155A GLN 3.2 0.6 - - - -
156A PRO* 1.3 77.7 - - - +
158A ILE* 1.3 67.6 + - + +
160A LYS* 2.7 46.0 + - - +
161A LYS* 3.1 29.1 + - - +
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Residues in contact with ILE 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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135A ASP* 4.0 2.3 - - - +
149A LEU* 3.9 20.4 - - + -
150A PRO* 3.8 22.4 - - + -
154A LYS* 3.4 27.6 + - + +
155A GLN* 3.1 10.4 + - - +
157A ASP* 1.3 77.9 - - + +
159A ILE* 1.3 63.9 + - - +
161A LYS* 3.3 19.9 + - - +
162A PHE* 3.4 19.6 - - + -
501A FEG 3.4 53.4 - - + +
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Residues in contact with ILE 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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147A THR* 5.9 0.2 - - + -
149A LEU* 4.2 11.0 - - + -
155A GLN* 2.8 30.0 + - + +
158A ILE* 1.3 72.4 - - - +
160A LYS* 1.3 64.6 + - - +
161A LYS 3.0 3.2 + - - -
162A PHE* 3.0 24.4 + - + -
163A ALA* 2.9 25.1 + - + +
183A PHE* 3.7 29.8 - - + -
186A ILE* 3.7 37.2 - - + -
187A PHE* 3.6 32.1 - - + -
190A LEU* 3.9 6.1 - - + -
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Residues in contact with LYS 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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156A PRO 2.9 13.9 + - - +
157A ASP* 2.7 50.3 + - - +
159A ILE* 1.3 76.2 - - - +
161A LYS* 1.3 72.2 + - + +
162A PHE 3.4 0.7 + - - -
163A ALA* 4.2 5.2 + - - +
164A ASP* 4.6 5.7 + - - +
190A LEU* 3.9 32.7 - - + +
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Residues in contact with LYS 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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135A ASP* 6.5 0.4 - - + -
136A ARG* 2.8 36.2 + - - +
157A ASP* 3.1 32.0 + - - +
158A ILE* 3.3 11.8 + - - +
159A ILE 3.0 1.6 + - - -
160A LYS* 1.3 95.9 - - + +
162A PHE* 1.3 52.9 + - + +
501A FEG 6.2 0.9 - - - +
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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