Contacts of the helix formed by residues 203 - 213 (chain B) in PDB entry 4IYM
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 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B ARG* 3.4 30.0 + - - -
35B LEU* 3.8 17.9 - - + +
171B LYS* 4.5 1.6 - - - +
174B GLU* 3.3 20.9 - - - +
202B GLY* 1.3 73.8 - - - -
204B LYS* 1.3 68.4 + - - +
205B GLY* 3.0 17.2 + - - -
206B ALA* 3.2 3.1 + - - +
207B VAL* 3.2 25.3 + - - +
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Residues in contact with LYS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B ASP* 1.3 78.6 - - + +
205B GLY* 1.3 56.4 + - - +
207B VAL* 3.3 8.7 + - + +
208B ASP* 2.9 51.6 + - - +
230B TYR* 3.1 33.3 + - + -
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Residues in contact with GLY 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG* 5.9 2.5 - - - -
36B ALA 5.0 4.7 - - - -
38B ASP* 5.2 1.5 - - - +
203B ASP* 3.0 12.3 + - - -
204B LYS* 1.3 78.3 - - - +
206B ALA* 1.3 60.7 + - - +
208B ASP* 3.4 4.6 + - - +
209B ALA* 3.1 22.8 + - - +
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ALA* 4.3 25.9 + - + +
37B SER 5.9 0.7 - - - -
41B LEU* 5.0 2.3 - - + +
171B LYS* 3.9 19.7 - - + -
200B VAL* 4.7 4.3 - - + -
201B ASN 4.4 0.9 - - - +
202B GLY* 4.0 17.7 - - - -
203B ASP* 3.2 10.9 + - - +
205B GLY* 1.3 74.0 - - - +
207B VAL* 1.3 57.8 + - - +
209B ALA* 3.3 8.8 + - - +
210B ILE* 2.9 34.4 + - + +
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Residues in contact with VAL 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ILE* 3.9 31.9 - - + -
171B LYS* 3.8 22.7 - - + +
203B ASP 3.2 15.9 + - - +
204B LYS* 3.3 10.7 + - + +
206B ALA* 1.3 75.8 - - - +
208B ASP* 1.3 60.2 + - - +
210B ILE* 3.0 9.5 + - - +
211B LEU* 2.8 52.4 + - + +
221B PHE* 6.0 0.2 - - + -
227B ILE* 6.1 1.6 - - + -
230B TYR* 5.1 3.4 - - + -
231B VAL* 4.2 11.7 - - + -
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Residues in contact with ASP 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B LYS* 2.9 46.7 + - - +
205B GLY* 3.8 4.6 - - - +
207B VAL* 1.3 73.1 - - - +
209B ALA* 1.3 63.8 + - - +
211B LEU* 3.2 7.5 + - - +
212B THR* 2.9 35.1 + - + +
230B TYR* 2.6 34.5 + - - -
234B THR* 5.3 1.0 - - - +
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B SER 5.4 2.0 - - - +
38B ASP* 3.9 21.5 - - - +
41B LEU* 3.4 22.6 - - + +
205B GLY 3.1 14.0 + - - +
206B ALA* 3.3 12.8 + - - +
208B ASP* 1.3 77.2 - - - +
210B ILE* 1.3 61.2 + - - +
212B THR* 3.6 6.1 + - - -
213B HIS* 3.0 27.0 + - - +
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Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.7 29.2 - - + -
142B ALA* 3.6 32.3 - - + -
144B ILE* 4.6 13.9 - - + -
169B ILE* 5.0 7.2 - - + +
171B LYS* 3.6 35.2 - - + +
200B VAL* 5.7 1.3 - - + -
206B ALA* 2.9 18.8 + - + +
207B VAL* 3.0 10.5 + - - +
209B ALA* 1.3 76.4 - - - +
211B LEU* 1.3 64.8 + - + +
212B THR 3.3 0.5 + - - -
213B HIS 3.4 4.2 + - - -
216B ILE* 3.7 12.7 - - + +
219B VAL* 4.3 13.5 - - + -
240B LYS* 3.4 14.2 - - - -
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ILE* 4.7 4.7 - - + -
207B VAL* 2.8 36.8 + - + +
208B ASP* 3.2 8.7 + - - +
210B ILE* 1.3 77.3 - - + +
212B THR* 1.3 59.3 + - + +
213B HIS 3.5 0.2 - - - -
219B VAL* 4.1 15.5 - - + -
230B TYR* 4.1 14.6 - - + -
231B VAL* 4.0 22.7 - - + -
234B THR* 3.8 35.8 - - + +
235B ALA* 3.9 26.5 - - + +
238B ASN* 3.3 16.9 + - - +
240B LYS* 3.2 20.4 + - - +
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Residues in contact with THR 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B ASP* 2.9 24.8 + - + +
209B ALA* 3.6 6.8 + - - -
211B LEU* 1.3 80.2 - - + +
213B HIS* 1.3 63.6 + - - +
214B PRO* 3.4 9.8 - - - +
234B THR* 5.1 4.9 - - + -
238B ASN* 3.6 26.8 - - - +
240B LYS* 4.3 1.1 - - - -
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Residues in contact with HIS 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 3.9 17.5 - - + -
42B ALA* 4.7 12.3 - - + +
45B VAL* 3.3 33.1 - - + +
46B GLU* 5.8 0.6 + - - -
209B ALA 3.0 15.7 + - - +
210B ILE 3.4 1.6 + - - -
212B THR* 1.3 77.3 - - - +
214B PRO* 1.4 69.2 - - + +
215B ASP* 3.1 38.4 + - + +
216B ILE* 3.3 22.0 + - + -
240B LYS* 2.7 25.4 + - - -
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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