Contacts of the helix formed by residues 188 - 199 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184I ILE* 3.4 22.3 - - - +
185I ASP* 3.0 30.5 + - + +
186I PRO 5.1 0.7 - - - -
187I ALA* 1.3 72.4 - - - +
189I VAL* 1.3 60.2 + - - +
190I GLY* 3.2 6.1 + - - -
191I ALA* 2.8 41.8 + - + +
192I LEU 3.4 2.9 + - - -
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Residues in contact with VAL 189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186I PRO 5.5 1.8 - - - +
187I ALA* 2.7 20.8 + - - +
188I ASP* 1.3 71.4 - - - +
190I GLY* 1.3 59.9 + - - +
192I LEU* 3.3 10.9 + - + +
193I GLU* 3.0 28.0 + - + +
218I ASP* 6.1 2.2 - - + -
221I LEU* 3.9 27.4 - - + -
222I VAL* 5.5 7.4 - - + -
225I LEU* 3.4 28.0 - - + +
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Residues in contact with GLY 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I ASP* 3.2 5.3 + - - -
189I VAL* 1.3 76.9 - - - +
191I ALA* 1.3 55.3 + - - +
193I GLU* 3.1 11.0 + - - +
194I LEU* 2.8 36.0 + - - +
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Residues in contact with ALA 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184I ILE* 3.5 26.4 - - + +
188I ASP* 2.8 33.4 + - - +
190I GLY* 1.3 75.3 - - - +
192I LEU* 1.3 58.2 + - - +
194I LEU* 3.2 9.9 + - - +
195I ALA* 2.9 32.2 + - - +
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Residues in contact with LEU 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157I VAL* 3.9 13.9 - - + -
184I ILE* 3.7 16.7 - - + +
188I ASP 3.4 3.8 + - - +
189I VAL* 3.3 10.0 + - + +
190I GLY 3.2 0.4 - - - -
191I ALA* 1.3 80.4 - - - +
193I GLU* 1.3 56.0 + - - +
195I ALA* 3.8 4.6 - - - +
196I LEU* 2.9 54.5 + - + +
204I PHE* 3.8 36.3 - - + -
222I VAL* 3.6 41.1 - - + +
225I LEU* 4.2 20.4 - - + -
226I CYS* 4.4 1.8 - - - -
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Residues in contact with GLU 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I VAL* 3.0 15.3 + - - +
190I GLY* 3.1 11.8 + - - +
192I LEU* 1.3 77.7 - - - +
194I LEU* 1.3 62.1 + - - +
196I LEU* 3.5 9.0 - - + +
197I ASN* 3.1 39.4 + - - +
225I LEU* 4.5 24.8 - - + +
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Residues in contact with LEU 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190I GLY 2.8 16.4 + - - +
191I ALA* 3.5 8.7 - - - +
193I GLU* 1.3 73.8 - - - +
195I ALA* 1.3 57.6 + - - +
197I ASN* 2.7 29.6 + - + +
198I GLN* 2.8 48.8 + - + +
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Residues in contact with ALA 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155I HIS* 5.6 0.2 - - - +
157I VAL* 4.5 14.1 - - + -
182I THR* 4.0 29.8 - - + +
191I ALA 2.9 17.0 + - - +
192I LEU* 3.8 5.6 - - - +
194I LEU* 1.3 75.5 - - - +
196I LEU* 1.3 61.9 + - - +
197I ASN 3.2 0.5 + - - -
198I GLN* 4.1 13.0 + - - +
199I LYS* 3.0 30.3 + - + +
201I VAL* 3.6 7.0 - - + +
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Residues in contact with LEU 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192I LEU* 2.9 53.6 + - + +
193I GLU* 3.5 11.0 - - + +
195I ALA* 1.3 77.5 - - - +
197I ASN* 1.3 58.8 + - - +
199I LYS 3.4 9.9 - - - +
200I LYS* 5.1 0.9 - - - -
201I VAL* 3.7 31.4 + - + +
225I LEU* 4.2 9.2 - - + +
226I CYS* 4.2 15.9 - - - +
229I LYS* 3.6 49.0 - - + +
231I ALA* 3.9 13.9 - - + -
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Residues in contact with ASN 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193I GLU* 3.1 30.1 + - - +
194I LEU* 2.7 18.6 + - + +
196I LEU* 1.3 75.4 - - - +
198I GLN* 1.3 68.4 + - + +
199I LYS 4.1 0.7 - - - +
229I LYS* 3.3 31.0 + - - +
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Residues in contact with GLN 198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194I LEU* 2.8 54.3 + - + +
195I ALA* 4.1 6.3 - - - +
197I ASN* 1.3 79.2 - - + +
199I LYS* 1.3 87.0 + - + +
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Residues in contact with LYS 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155I HIS* 3.7 33.9 - - + +
180I THR* 5.4 0.2 - - - -
182I THR* 3.1 31.8 + - - +
195I ALA* 3.0 23.6 + - - +
196I LEU 3.4 11.3 - - - +
197I ASN 4.0 0.7 - - - +
198I GLN* 1.3 107.9 + - + +
200I LYS* 1.3 61.3 + - - +
201I VAL 3.4 2.0 + - - -
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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