Contacts of the helix formed by residues 181 - 195 (chain A) in PDB entry 1IAX
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 THR 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A ASN* 3.9 24.7 - - - +
179A LYS* 3.5 4.9 + - + +
180A ILE* 1.3 75.6 - - - +
182A SER* 1.3 59.6 + - - +
183A LYS* 3.5 9.4 + - - +
184A ALA* 2.8 40.7 + - + +
185A VAL* 3.0 13.2 + - - +
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Residues in contact with SER 182 (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 ILE 4.0 1.4 + - - -
181A THR* 1.3 72.2 - - - +
183A LYS* 1.3 60.2 + - - +
185A VAL* 3.4 10.3 + - - +
186A LYS* 3.1 36.1 + - - +
222A SER* 3.3 34.3 + - - -
223A VAL* 4.7 2.9 + - - +
226A PHE* 5.5 6.2 - - - +
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Residues in contact with LYS 183 (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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181A THR* 3.0 8.8 + - - +
182A SER* 1.3 74.7 - - - +
184A ALA* 1.3 65.6 + - - +
186A LYS* 3.2 9.0 + - - +
187A GLU* 2.6 63.4 + - + +
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Residues in contact with ALA 184 (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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170A ILE* 3.7 18.0 - - + +
171A HIS* 3.8 29.8 + - + +
181A THR* 2.8 30.8 + - + +
183A LYS* 1.3 77.8 - - - +
185A VAL* 1.3 59.5 + - - +
187A GLU* 3.4 16.7 + - - +
188A ALA* 3.4 17.5 + - - +
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Residues in contact with VAL 185 (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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146A LEU* 4.5 2.9 - - + +
170A ILE* 4.3 16.6 - - + -
180A ILE* 3.6 25.1 - - + -
181A THR 3.0 14.7 + - - +
182A SER* 3.7 10.3 - - - +
183A LYS 3.1 0.2 - - - -
184A ALA* 1.3 75.9 - - - +
186A LYS* 1.3 65.1 + - - +
188A ALA* 3.4 3.8 + - - +
189A TYR* 3.1 21.3 + - - +
202A LEU* 3.9 21.3 - - + -
223A VAL* 4.9 9.9 - - + -
226A PHE* 3.3 33.7 - - + -
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Residues in contact with LYS 186 (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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182A SER* 3.1 25.6 + - - +
183A LYS* 3.2 10.1 + - - +
185A VAL* 1.3 76.0 - - - +
187A GLU* 1.3 64.7 + - + +
189A TYR* 3.2 7.1 + - - +
190A GLU* 2.9 43.8 + - + +
226A PHE* 4.0 32.3 - - + -
229A GLN* 5.7 3.6 - - - +
230A HIS* 6.0 0.2 - - - -
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Residues in contact with GLU 187 (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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171A HIS* 5.7 4.0 - - - +
183A LYS* 2.6 51.0 + - + +
184A ALA* 3.4 21.3 - - - +
185A VAL 3.2 0.2 - - - -
186A LYS* 1.3 77.3 - - + +
188A ALA* 1.3 56.7 + - - +
190A GLU* 4.0 7.9 - - - +
191A ASN* 2.5 46.4 + - - +
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Residues in contact with ALA 188 (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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146A LEU* 3.7 21.9 - - + +
168A ILE* 4.4 6.8 - - + +
169A PRO 4.0 11.9 - - - +
170A ILE* 3.8 23.1 - - + -
184A ALA 3.4 5.9 + - - +
185A VAL 3.4 5.3 + - - +
186A LYS 3.3 0.4 - - - -
187A GLU* 1.3 78.2 - - - +
189A TYR* 1.3 63.3 + - - +
191A ASN* 3.7 6.4 - - - +
192A ALA* 3.0 26.0 + - - +
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Residues in contact with TYR 189 (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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146A LEU* 4.2 10.0 - - + +
185A VAL 3.1 7.9 + - - +
186A LYS 3.4 7.4 - - - +
188A ALA* 1.3 78.8 - - - +
190A GLU* 1.3 71.4 + - + +
192A ALA* 3.3 5.1 + - - +
193A GLN* 3.1 58.0 + - + +
199A VAL* 4.2 30.2 - - + +
226A PHE* 3.4 31.9 - + + -
230A HIS* 3.0 45.1 + + + +
232A ILE* 4.3 19.0 - - + +
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Residues in contact with GLU 190 (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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186A LYS* 2.9 31.8 + - + +
187A GLU* 4.2 6.2 - - - +
189A TYR* 1.3 82.7 - - + +
191A ASN* 1.3 67.7 + - - +
192A ALA 3.1 1.8 - - - -
193A GLN* 3.0 13.2 + - - +
194A LYS* 3.0 31.4 + - + +
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Residues in contact with ASN 191 (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 GLU* 2.5 41.6 + - - +
188A ALA* 3.7 7.2 - - - +
190A GLU* 1.3 74.9 - - - +
192A ALA* 1.3 54.8 + - - +
194A LYS* 3.7 7.8 + - - +
195A SER* 2.8 30.7 + - - -
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Residues in contact with ALA 192 (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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146A LEU* 5.4 0.2 - - + -
168A ILE* 3.4 32.1 - - + -
188A ALA 3.0 19.3 + - - +
189A TYR 3.4 5.4 - - - +
190A GLU 3.1 0.2 - - - -
191A ASN* 1.3 78.4 - - - +
193A GLN* 1.3 54.7 + - - +
195A SER* 3.3 6.8 + - - -
196A ASN 3.1 4.3 + - - -
197A ILE* 2.8 38.4 + - + +
199A VAL* 4.0 13.9 - - + -
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Residues in contact with GLN 193 (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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189A TYR* 3.1 53.0 + - + +
190A GLU* 3.0 15.7 + - - +
192A ALA* 1.3 72.8 - - + +
194A LYS* 1.3 67.1 + - - +
195A SER 3.0 1.6 - - - -
196A ASN* 2.6 30.9 + - - +
197A ILE 4.3 11.9 - - - +
199A VAL* 5.7 0.9 - - + +
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Residues in contact with LYS 194 (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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190A GLU* 3.0 22.0 + - + +
191A ASN* 4.0 7.0 - - - +
193A GLN* 1.3 83.4 - - - +
195A SER* 1.3 58.8 + - - +
196A ASN* 3.3 14.2 + - - -
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Residues in contact with SER 195 (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 ASN 2.8 16.7 + - - -
192A ALA* 3.3 8.8 + - - -
193A GLN 3.0 0.4 - - - -
194A LYS* 1.3 75.1 - - - +
196A ASN* 1.3 70.6 + - - +
197A ILE* 3.4 19.1 + - - +
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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