Contacts of the helix formed by residues 188 - 199 (chain L) in PDB entry 1I43
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 188 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184L ILE* 3.5 23.2 - - - +
185L ASP* 3.2 27.6 + - + +
186L PRO 5.1 0.7 - - - -
187L ALA* 1.3 73.4 - - - +
189L VAL* 1.3 59.6 + - - +
190L GLY* 3.2 6.1 + - - -
191L ALA* 2.8 41.9 + - + +
192L LEU 3.6 1.9 + - - -
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Residues in contact with VAL 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186L PRO 5.6 0.7 - - - +
187L ALA 2.6 19.4 + - - +
188L ASP* 1.3 70.6 - - - +
190L GLY* 1.3 66.2 + - - +
192L LEU* 3.2 11.0 + - + +
193L GLU* 2.9 23.4 + - + +
218L ASP* 6.1 2.0 - - + -
221L LEU* 4.1 24.2 - - + -
222L VAL* 5.6 7.4 - - + -
225L LEU* 3.5 27.8 - - + -
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Residues in contact with GLY 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188L ASP* 3.2 5.0 + - - -
189L VAL* 1.3 76.8 - - - +
191L ALA* 1.3 54.0 + - - +
193L GLU* 3.0 12.1 + - - +
194L LEU* 2.8 36.2 + - - +
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Residues in contact with ALA 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184L ILE* 3.7 25.8 - - + +
188L ASP* 2.8 37.6 + - - +
190L GLY* 1.3 71.6 - - - +
192L LEU* 1.3 57.7 + - - +
194L LEU* 3.4 9.3 + - - +
195L ALA* 2.9 31.9 + - - +
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Residues in contact with LEU 192 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157L VAL* 3.9 25.8 - - + -
184L ILE* 3.7 15.4 - - + +
188L ASP 3.6 2.6 + - - +
189L VAL* 3.2 12.0 + - + +
190L GLY 3.1 0.4 - - - -
191L ALA* 1.3 81.3 - - - +
193L GLU* 1.3 56.8 + - - +
195L ALA* 3.4 3.8 + - - +
196L LEU* 2.9 56.4 + - + +
204L PHE* 4.0 22.4 - - + -
222L VAL* 3.8 33.4 - - + +
225L LEU* 4.0 22.0 - - + -
226L CYS* 4.3 7.0 - - - -
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Residues in contact with GLU 193 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L VAL* 2.9 14.7 + - - +
190L GLY* 3.5 12.8 - - - +
192L LEU* 1.3 76.3 - - - +
194L LEU* 1.3 64.9 + - - +
196L LEU* 3.3 10.7 - - + +
197L ASN* 3.2 36.4 + - - +
225L LEU* 4.7 24.4 - - + +
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Residues in contact with LEU 194 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L GLY 2.8 19.7 + - - +
191L ALA* 3.6 8.7 - - - +
193L GLU* 1.3 69.9 - - - +
195L ALA* 1.3 58.0 + - - +
197L ASN* 2.7 29.1 + - + +
198L GLN* 2.9 49.8 + - + +
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Residues in contact with ALA 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155L HIS* 5.5 0.2 - - - +
157L VAL* 4.5 12.6 - - + -
182L THR* 3.9 32.5 - - + +
184L ILE* 5.2 0.2 - - + -
191L ALA 2.9 17.9 + - - +
192L LEU* 3.8 4.7 - - - +
194L LEU* 1.3 76.5 - - - +
196L LEU* 1.3 58.1 + - - +
197L ASN 3.2 0.3 + - - -
198L GLN* 4.0 13.2 - - - +
199L LYS* 3.0 34.6 + - + +
201L VAL* 3.6 7.1 - - + +
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Residues in contact with LEU 196 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192L LEU* 2.9 54.4 + - + +
193L GLU* 3.3 13.0 - - + +
194L LEU 3.0 0.2 - - - -
195L ALA* 1.3 78.3 - - - +
197L ASN* 1.3 58.6 + - - +
199L LYS 3.6 7.7 - - - +
200L LYS* 5.3 0.9 - - - -
201L VAL* 3.7 31.1 + - + +
225L LEU* 4.3 9.2 - - + +
226L CYS* 4.2 14.6 - - - +
229L LYS* 3.7 47.9 - - + +
231L ALA* 3.9 14.6 - - + -
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Residues in contact with ASN 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193L GLU* 3.2 29.1 + - - +
194L LEU* 2.7 12.6 + - + +
196L LEU* 1.3 81.8 - - - +
198L GLN* 1.3 68.1 + - + +
199L LYS 4.1 1.3 - - - +
229L LYS* 3.4 31.6 + - - +
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Residues in contact with GLN 198 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194L LEU* 2.9 51.8 + - + +
195L ALA* 4.0 5.5 - - - +
197L ASN* 1.3 79.7 - - - +
199L LYS* 1.3 86.6 + - + +
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Residues in contact with LYS 199 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155L HIS* 3.7 34.5 - - + +
180L THR* 5.5 0.2 - - - -
182L THR* 3.0 29.6 + - - +
195L ALA* 3.0 24.1 + - - +
196L LEU 3.6 9.9 - - - +
197L ASN 4.1 0.5 - - - -
198L GLN* 1.3 106.5 + - + +
200L LYS* 1.3 60.2 + - - +
201L VAL 3.3 3.9 + - - -
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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