Contacts of the helix formed by residues 242 - 258 (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 242 (chain A).
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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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Residues in contact with THR 243 (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 LYS* 3.4 49.4 - - + +
22A LEU* 3.6 14.5 - - + +
25A ALA* 4.1 9.0 - - + -
238A LEU 3.4 2.4 + - - -
239A GLN* 2.7 22.8 + - - +
240A LEU* 3.3 14.9 + - - -
241A THR 3.8 1.2 + - - -
242A LYS* 1.3 71.4 - - - +
244A GLU* 1.3 67.6 + - - +
246A VAL* 3.8 1.1 - - - +
247A ALA* 3.0 21.7 + - - +
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Residues in contact with GLU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.9 12.7 - - - +
28A ARG* 2.7 34.0 + - - -
242A LYS 3.3 0.6 - - - -
243A THR* 1.3 80.9 - - - +
245A GLU* 1.3 51.9 + - - +
247A ALA* 3.2 8.4 + - - +
248A HIS* 2.8 34.2 + - - +
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Residues in contact with GLU 245 (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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230A GLN 4.9 0.7 - - - +
231A VAL* 3.5 41.7 - - + +
232A GLN* 4.3 5.9 + - - +
242A LYS* 3.0 29.3 + - + +
244A GLU* 1.3 74.8 - - - +
246A VAL* 1.3 66.1 + - - +
248A HIS* 3.0 9.0 + - + +
249A ILE* 2.9 30.7 + - + +
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Residues in contact with VAL 246 (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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22A LEU* 4.0 23.3 - - + -
103A HIS* 4.0 24.0 - - + +
203A ILE* 4.7 8.3 - - + -
231A VAL* 4.9 5.6 - - + -
238A LEU* 3.5 37.9 - - + +
239A GLN* 5.0 0.7 - - - -
242A LYS* 2.9 18.8 + - + +
243A THR* 3.8 3.4 - - - +
245A GLU* 1.3 77.5 - - + +
247A ALA* 1.3 56.3 + - - +
249A ILE* 3.2 10.6 + - - +
250A LEU* 2.9 36.8 + - + +
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Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.8 10.5 - - + +
25A ALA* 4.1 25.6 - - + +
26A LEU* 4.1 15.9 - - + +
31A HIS* 5.5 0.3 + - - -
243A THR 3.0 15.6 + - - +
244A GLU* 3.2 15.0 + - - +
246A VAL* 1.3 76.4 - - - +
248A HIS* 1.3 56.2 + - - +
250A LEU* 3.2 3.1 + - - +
251A GLN* 3.0 25.6 + - - +
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Residues in contact with HIS 248 (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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244A GLU 2.8 15.9 + - - +
245A GLU* 3.0 11.7 + - - +
247A ALA* 1.3 70.3 - - - +
249A ILE* 1.3 68.5 + - - +
251A GLN* 3.2 14.9 + - + +
252A GLU* 3.2 44.7 + - + +
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Residues in contact with ILE 249 (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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203A ILE* 3.6 26.0 - - + -
229A TYR* 3.5 55.0 - - + -
230A GLN 5.7 0.4 - - - +
231A VAL* 3.7 31.2 - - + -
245A GLU* 2.9 21.9 + - + +
246A VAL* 3.5 11.2 - - - +
248A HIS* 1.3 77.6 - - - +
250A LEU* 1.3 63.1 + - - +
252A GLU* 3.0 19.4 + - - +
253A VAL* 3.0 15.2 + - + +
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Residues in contact with LEU 250 (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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6A PHE* 3.3 31.5 - - + -
22A LEU* 4.0 24.9 - - + -
26A LEU* 4.0 23.6 - - + -
77A VAL* 3.8 33.4 - - + -
101A VAL* 3.9 26.2 - - + -
203A ILE* 4.6 3.8 - - + -
246A VAL* 2.9 26.6 + - + +
247A ALA 3.6 4.9 - - - +
248A HIS 3.2 0.2 - - - -
249A ILE* 1.3 77.6 - - - +
251A GLN* 1.3 61.2 + - - +
253A VAL* 3.2 7.7 + - + +
254A ALA 3.0 17.3 + - - -
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Residues in contact with GLN 251 (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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1A MET* 3.9 29.1 - - + +
2A VAL 3.0 15.7 + - - +
3A THR* 5.9 1.0 - - - +
29A ALA* 4.1 15.1 + - + +
31A HIS* 3.1 31.2 + - - +
247A ALA 3.0 13.1 + - - +
248A HIS* 3.2 21.5 + - + +
250A LEU* 1.3 76.9 - - - +
252A GLU* 1.3 57.2 + - + +
254A ALA* 3.2 3.7 + - - +
255A ASP* 2.9 61.6 + - - +
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Residues in contact with GLU 252 (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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227A LYS* 5.6 0.2 - - - -
229A TYR* 2.9 35.5 + - - +
248A HIS* 3.2 39.5 + - + +
249A ILE* 3.0 11.0 + - - +
251A GLN* 1.3 74.5 - - + +
253A VAL* 1.3 59.9 + - - +
255A ASP* 3.4 11.9 + - - +
256A ALA* 3.0 29.5 + - - +
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Residues in contact with VAL 253 (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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75A ILE* 4.1 16.3 - - + +
99A ALA* 4.3 1.3 - - + -
101A VAL* 3.7 27.4 - - + -
201A VAL* 3.8 28.9 - - + -
229A TYR* 4.4 5.2 - - + -
249A ILE* 3.0 20.8 + - + +
250A LEU* 3.4 15.7 - - + +
252A GLU* 1.3 73.2 - - - +
254A ALA* 1.3 64.1 + - - +
256A ALA* 3.4 1.2 + - - -
257A TYR* 2.9 45.7 + - + +
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Residues in contact with ALA 254 (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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2A VAL* 3.8 20.3 - - + +
4A ALA* 3.8 23.8 - - + -
6A PHE* 4.1 1.8 - - + -
31A HIS* 4.1 8.1 - - + -
75A ILE* 3.8 3.8 - - - +
250A LEU 3.0 12.7 + - - +
251A GLN 3.2 9.8 + - - +
253A VAL* 1.3 74.9 - - - +
255A ASP* 1.3 63.0 + - - +
258A ALA* 2.8 39.5 + - + +
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Residues in contact with ASP 255 (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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-1A LYS* 3.3 42.1 + - + +
1A MET* 3.4 13.7 - - - +
2A VAL* 2.8 33.2 + - - +
251A GLN* 2.9 37.1 + - - +
252A GLU* 3.6 11.3 - - - +
253A VAL 3.4 0.2 - - - -
254A ALA* 1.3 77.2 - - - +
256A ALA* 1.3 59.6 + - - +
258A ALA 4.7 0.3 - - - +
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Residues in contact with ALA 256 (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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-1A LYS* 4.8 5.1 + - - -
252A GLU 3.0 17.4 + - - +
253A VAL* 3.9 3.6 - - - +
255A ASP* 1.3 79.5 - - - +
257A TYR* 1.3 85.1 + - + +
258A ALA 5.1 0.4 - - - -
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Residues in contact with TYR 257 (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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73A LYS* 5.5 1.9 + - - +
75A ILE* 5.2 1.1 - - + -
98A ALA* 3.5 19.3 - - + +
99A ALA* 3.7 29.4 - - + -
199A LYS* 3.3 45.1 + - + +
201A VAL* 3.6 23.4 - - + +
226A ASP* 3.6 26.3 + - - +
227A LYS* 4.6 7.4 - - + +
253A VAL* 2.9 29.3 + - + +
256A ALA* 1.3 92.1 - - + +
258A ALA* 1.3 66.6 + - - +
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Residues in contact with ALA 258 (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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-1A LYS* 4.8 6.1 + - - -
2A VAL* 3.7 23.7 - - + +
3A THR 4.8 0.7 - - - +
4A ALA* 3.7 31.6 - - + -
75A ILE* 3.7 15.3 - - + -
98A ALA* 4.3 8.2 - - + +
254A ALA* 2.8 19.5 + - - +
255A ASP 4.7 1.7 - - - +
257A TYR* 1.3 83.6 + - - +
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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