Contacts of the helix formed by residues 237 - 242 (chain A) in PDB entry 1DWQ
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 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A THR* 3.9 4.0 - - - +
14A HIS* 3.1 42.0 + - - -
18A ILE* 4.0 8.3 - - + +
79A GLU* 2.8 32.9 + - - +
158A LEU* 3.5 17.8 + - - +
159A PHE* 3.6 28.5 - - + -
162A CYS* 4.1 3.8 - - - -
235A ASP* 3.0 10.4 + - - +
236A HIS* 1.3 90.6 + - + +
238A LEU* 1.3 60.1 + - - +
239A GLN* 3.1 17.0 - - - +
240A LEU* 3.1 16.4 + - + -
241A THR* 2.8 26.5 + - - -
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Residues in contact with LEU 238 (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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103A HIS* 3.9 14.7 - - + +
104A ASN* 3.4 18.8 - - - +
203A ILE* 4.2 15.9 - - + -
204A TRP 4.1 21.5 - - - -
205A THR* 4.1 9.2 - - + -
231A VAL* 3.9 17.7 - - + -
233A GLY 4.2 6.3 - - - +
234A GLY* 4.2 0.2 - - - -
235A ASP 3.4 17.3 - - - +
236A HIS 3.1 5.1 + - - -
237A LYS* 1.3 75.1 - - - +
239A GLN* 1.3 56.6 + - - +
240A LEU 3.1 0.7 - - - -
241A THR* 3.5 5.4 - - - +
242A LYS* 2.8 59.7 + - + -
246A VAL* 3.5 9.4 - - + +
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Residues in contact with GLN 239 (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* 3.3 34.5 - - - +
19A TRP* 3.6 39.9 - - + -
21A LYS* 3.9 8.5 - - - +
22A LEU* 4.0 14.1 + - + -
79A GLU* 2.9 31.9 + - - -
103A HIS* 3.6 16.3 + - - +
237A LYS* 3.1 26.8 - - - +
238A LEU* 1.3 77.4 + - - +
240A LEU* 1.3 56.6 + - + +
243A THR* 2.7 31.1 + - - +
246A VAL* 4.7 4.0 - - - -
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Residues in contact with LEU 240 (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 TRP* 5.8 0.4 - - + -
18A ILE* 3.5 31.4 - - + +
20A HIS* 4.1 6.1 - - + -
21A LYS* 3.8 30.3 - - + +
159A PHE* 3.8 29.4 - - + -
162A CYS* 3.8 18.2 - - - -
166A GLU* 3.6 32.3 - - + +
237A LYS* 3.1 13.6 + - + +
239A GLN* 1.3 83.9 - - + +
241A THR* 1.3 62.1 + - - +
242A LYS 3.5 0.2 - - - -
243A THR* 3.3 11.9 + - - -
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Residues in contact with THR 241 (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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161A LYS* 3.5 26.7 - - + +
162A CYS* 3.8 9.9 - - - -
234A GLY* 3.6 12.4 - - - -
235A ASP* 2.8 50.5 + - - +
237A LYS 2.8 11.8 + - - -
238A LEU* 3.5 4.7 - - - -
240A LEU* 1.3 78.1 - - - +
242A LYS* 1.3 67.9 + - - +
243A THR 3.8 0.4 - - - -
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Residues in contact with LYS 242 (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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231A VAL* 3.5 12.6 - - + -
232A GLN 3.3 22.9 + - - -
233A GLY* 4.8 1.4 - - - -
234A GLY* 3.5 20.3 - - - +
238A LEU* 2.8 45.4 + - + +
241A THR* 1.3 77.9 + - - +
243A THR* 1.3 63.8 + - - +
244A GLU 3.3 2.5 - - - -
245A GLU* 3.0 25.0 + - + +
246A VAL* 2.9 21.4 + - + +
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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