Contacts of the helix formed by residues 241 - 258 (chain A) in PDB entry 1DS1
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 ASP 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A ARG* 4.0 13.7 + - - +
240A GLU* 1.3 83.6 - - - +
242A PRO* 1.3 76.8 - - + +
243A ALA* 4.2 4.7 - - + +
244A ASP* 2.9 32.1 + - - +
245A LYS* 3.0 11.8 + - - +
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Residues in contact with PRO 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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240A GLU 3.7 3.1 - - - +
241A ASP* 1.3 88.4 - - + +
243A ALA* 1.3 56.1 + - - +
245A LYS* 3.2 11.0 + - + +
246A GLU* 3.0 36.7 + - + +
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Residues in contact with ALA 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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187A ARG* 4.2 14.6 + - - +
191A ARG* 3.6 35.2 - - - +
241A ASP* 3.2 1.8 - - + +
242A PRO* 1.3 80.9 - - - +
244A ASP* 1.3 61.6 + - - +
246A GLU* 3.6 8.2 + - - +
247A ALA* 3.1 23.9 + - - +
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Residues in contact with ASP 244 (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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191A ARG* 2.9 33.7 + - - +
195A ARG* 3.3 15.6 + - - +
196A ARG 5.4 1.0 - - - +
197A MET* 3.8 25.9 - - + +
239A PRO* 3.8 13.5 - - + -
240A GLU 4.6 2.9 + - - -
241A ASP* 2.9 25.9 + - - +
243A ALA* 1.3 76.0 - - - +
245A LYS* 1.3 57.4 + - - +
247A ALA* 3.8 2.7 - - - +
248A VAL* 2.9 34.1 + - - +
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Residues in contact with LYS 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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239A PRO* 2.8 42.3 + - + +
240A GLU* 2.5 44.0 + - - +
241A ASP 3.0 13.7 + - - +
242A PRO* 3.2 10.1 + - + +
244A ASP* 1.3 75.0 - - - +
246A GLU* 1.3 58.9 + - + +
248A VAL* 3.4 1.6 + - - +
249A ALA* 2.9 30.4 + - - +
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Residues in contact with GLU 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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242A PRO* 3.0 21.7 + - + +
243A ALA* 3.9 8.2 - - - +
245A LYS* 1.3 79.4 - - + +
247A ALA* 1.3 60.9 + - - +
249A ALA* 3.3 7.2 + - - +
250A ALA* 3.1 22.6 + - - +
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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
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187A ARG* 6.1 0.2 - - - +
188A THR* 3.9 22.3 - - + +
191A ARG* 4.1 17.3 - - + -
192A LEU* 3.7 25.6 - - + +
197A MET* 5.4 0.2 - - + -
243A ALA 3.1 18.8 + - - +
244A ASP* 3.3 3.8 + - - +
246A GLU* 1.3 73.1 - - - +
248A VAL* 1.3 66.7 + - - +
250A ALA* 3.2 4.0 + - - +
251A LEU* 3.0 22.9 + - - +
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Residues in contact with VAL 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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192A LEU* 4.1 7.4 - - + -
197A MET* 3.6 31.4 - - + -
220A PRO* 4.5 1.8 - - + -
232A TYR* 4.0 22.9 - - + +
237A LEU* 4.2 18.2 - - + +
239A PRO* 4.0 17.3 - - + -
244A ASP 2.9 20.1 + - - +
245A LYS 3.9 2.9 - - - +
247A ALA* 1.3 76.7 - - - +
249A ALA* 1.3 59.1 + - - +
251A LEU* 3.2 8.0 + - + +
252A SER* 2.8 27.6 + - - -
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Residues in contact with ALA 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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245A LYS 2.9 18.6 + - - +
246A GLU* 3.6 9.0 - - - +
247A ALA 3.3 0.4 - - - -
248A VAL* 1.3 77.2 - - - +
250A ALA* 1.3 54.8 + - - +
252A SER* 3.3 7.7 + - - -
253A LYS* 3.0 29.6 + - - +
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Residues in contact with ALA 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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184A LEU* 3.4 15.6 - - + +
188A THR* 4.0 22.0 - - + +
246A GLU 3.1 12.7 + - - +
247A ALA 3.2 7.4 + - - +
249A ALA* 1.3 71.7 - - - +
251A LEU* 1.3 65.6 + - - +
253A LYS* 3.4 8.7 + - - +
254A ALA* 3.0 19.1 + - - +
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Residues in contact with LEU 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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177A VAL* 5.5 2.2 - - + -
180A ALA* 5.1 6.3 - - + -
184A LEU* 3.9 24.1 - - + +
192A LEU* 4.0 15.9 - - + -
220A PRO* 4.1 24.7 - - + +
221A LEU* 4.7 7.2 - - + -
230A LEU* 4.0 25.1 - - + -
232A TYR* 4.2 16.6 - - + -
247A ALA 3.0 14.0 + - - +
248A VAL* 3.5 10.1 - - + +
250A ALA* 1.3 77.0 - - - +
252A SER* 1.3 63.0 + - - +
254A ALA* 3.2 2.8 + - - +
255A LEU* 2.9 47.8 + - + +
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Residues in contact with SER 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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232A TYR* 3.0 24.8 + - - -
234A ARG* 2.9 38.2 + - - +
248A VAL* 2.8 21.5 + - - -
249A ALA* 3.5 9.6 - - - -
251A LEU* 1.3 72.5 - - - +
253A LYS* 1.3 62.4 + - - +
255A LEU* 3.4 4.3 + - - +
256A ASP* 3.0 22.0 + - - -
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Residues in contact with LYS 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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249A ALA 3.0 16.4 + - - +
250A ALA* 3.6 8.1 - - - +
252A SER* 1.3 76.2 - - - +
254A ALA* 1.3 62.1 + - - +
256A ASP* 3.2 11.7 + - + +
257A GLU* 3.0 49.9 + - + +
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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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180A ALA* 3.8 24.0 - - + +
183A LEU* 4.2 10.5 - - + -
184A LEU* 3.7 19.1 - - + -
250A ALA 3.0 17.7 + - - +
251A LEU* 3.7 4.0 - - - +
253A LYS* 1.3 76.2 - - - +
255A LEU* 1.3 61.6 + - - +
257A GLU* 3.1 21.6 + - - +
258A VAL* 3.2 19.4 + - - +
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Residues in contact with LEU 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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143A PHE* 4.4 7.4 - - + -
175A ALA* 3.4 34.1 - - + +
176A SER 4.4 2.7 - - - +
177A VAL* 4.6 0.9 - - - +
180A ALA* 3.8 17.3 - - + -
230A LEU* 4.0 21.1 - - + -
232A TYR* 3.9 34.5 - - + -
234A ARG* 5.0 0.4 - - - +
251A LEU* 2.9 43.1 + - + +
252A SER* 3.7 4.7 - - - +
254A ALA* 1.3 76.1 - - - +
256A ASP* 1.3 63.9 + - - +
258A VAL* 3.2 4.0 + - - +
259A THR* 3.1 22.4 + - - -
278A THR* 4.3 6.3 - - + -
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Residues in contact with ASP 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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143A PHE* 3.6 7.6 - - - -
234A ARG* 2.8 42.8 + - - -
252A SER* 3.0 14.1 + - - +
253A LYS* 3.2 11.3 + - + +
255A LEU* 1.3 73.7 - - - +
257A GLU* 1.3 64.7 + - + +
259A THR* 3.1 25.4 + - - -
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Residues in contact with GLU 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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183A LEU* 3.7 25.5 - - + +
253A LYS* 3.0 47.1 + - + +
254A ALA* 3.1 12.7 + - - +
256A ASP* 1.3 77.8 - - + +
258A VAL* 1.3 59.6 + - - +
259A THR 3.5 0.6 - - - +
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Residues in contact with VAL 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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174A VAL 4.2 2.6 - - - +
175A ALA* 4.4 1.1 - - + -
176A SER 4.0 18.1 + - - +
179A LYS* 2.9 63.0 + - + +
180A ALA* 3.9 18.6 - - + +
183A LEU* 3.8 14.8 - - + -
254A ALA 3.2 15.7 + - - +
255A LEU* 3.6 9.0 - - - +
257A GLU* 1.3 79.7 - - - +
259A THR* 1.3 67.9 + - - +
260A GLU* 3.4 1.9 + - - +
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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