Contacts of the helix formed by residues 169 - 179 (chain D) in PDB entry 1AX4
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 ILE 169 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167D PHE* 3.1 3.5 + - + +
168D ASP* 1.3 72.7 + - - +
170D LYS* 1.3 80.8 + - + +
172D LEU* 3.3 7.0 + - + +
173D LYS* 3.1 33.3 + - + +
205D ASN* 3.8 20.6 - - - +
208D GLU* 3.9 38.1 - - + +
209D VAL* 3.7 30.7 - - + +
212D ILE* 3.9 22.7 - - + -
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Residues in contact with LYS 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ASP* 3.0 13.0 + - - +
169D ILE* 1.3 97.5 - - + +
171D LYS* 1.3 68.6 + - + +
172D LEU 3.3 0.2 + - - -
173D LYS* 3.3 12.1 + - + +
174D GLU* 3.0 36.7 + - - +
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Residues in contact with LYS 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ASN 5.6 0.4 - - - +
149D ILE* 3.7 28.9 - - + +
150D VAL 4.1 14.6 + - - -
152D GLU* 3.9 21.1 + - - +
155D PHE* 6.1 1.4 - - - -
168D ASP* 2.9 36.2 + - - +
170D LYS* 1.3 81.2 - - + +
172D LEU* 1.3 55.1 + - - +
174D GLU* 4.1 15.0 - - - +
175D ASN* 2.8 39.7 + - - +
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Residues in contact with LEU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ILE* 4.0 19.3 - - + -
149D ILE* 3.6 25.7 - - + +
167D PHE* 5.1 2.5 - - + -
168D ASP 3.1 9.3 + - - +
169D ILE* 3.4 12.6 - - + +
170D LYS 3.2 0.4 - - - -
171D LYS* 1.3 76.4 - - - +
173D LYS* 1.3 64.1 + - - +
175D ASN* 3.2 3.1 + - - -
176D ILE* 3.0 45.8 + - + +
187D ILE* 4.2 14.6 - - + -
209D VAL* 4.2 34.1 - - + +
212D ILE* 4.0 29.8 - - + -
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Residues in contact with LYS 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D ILE* 3.1 26.4 + - + +
170D LYS* 3.3 13.1 + - + +
172D LEU* 1.3 77.2 - - - +
174D GLU* 1.3 62.7 + - + +
176D ILE* 3.2 9.9 + - + +
177D ALA* 3.0 23.3 + - - +
208D GLU* 4.7 6.1 + - - -
212D ILE* 4.1 30.4 - - + +
216D HIS* 6.3 1.6 - - + -
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Residues in contact with GLU 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D LYS* 3.0 29.7 + - - +
171D LYS* 3.7 17.2 - - - +
173D LYS* 1.3 75.1 - - + +
175D ASN* 1.3 61.3 + - - +
177D ALA* 3.3 6.7 + - - +
178D GLN* 2.8 33.7 + - - +
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Residues in contact with ASN 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ILE* 3.8 20.2 - - + -
147D ILE* 3.7 21.7 - - - +
149D ILE* 3.8 18.1 - - + +
171D LYS* 2.8 32.3 + - - +
172D LEU* 3.2 4.7 + - - +
174D GLU* 1.3 79.2 - - - +
176D ILE* 1.3 59.3 + - - +
178D GLN* 4.4 9.2 + - - +
179D HIS* 2.8 58.1 + - + +
184D ILE* 4.5 0.2 - - - +
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Residues in contact with ILE 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ILE* 4.8 6.5 - - + -
172D LEU* 3.0 30.2 + - + +
173D LYS* 3.2 8.7 + - - +
175D ASN* 1.3 77.9 - - - +
177D ALA* 1.3 55.1 + - - +
180D GLY* 2.7 35.1 + - - +
181D ALA* 4.4 13.7 - - + +
184D ILE* 4.8 6.3 - - + -
187D ILE* 5.2 2.0 - - + -
212D ILE* 3.7 30.5 - - + -
216D HIS* 3.9 36.1 - - + +
218D ILE* 4.1 19.5 - - + -
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Residues in contact with ALA 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D LYS 3.0 15.4 + - - +
174D GLU* 3.7 6.1 - - - +
176D ILE* 1.3 79.7 - - - +
178D GLN* 1.3 61.1 + - - +
180D GLY* 3.9 4.9 + - - -
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Residues in contact with GLN 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D GLU* 2.8 23.1 + - - +
175D ASN* 3.9 10.3 - - - +
177D ALA* 1.3 77.1 - - - +
179D HIS* 1.3 86.5 + - + +
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Residues in contact with HIS 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ASN* 5.1 2.2 + - - +
125D VAL* 3.6 27.5 - - + +
145D LYS* 4.1 16.8 + - + -
147D ILE* 3.4 20.9 - - + +
175D ASN* 2.8 44.6 + - + +
178D GLN* 1.3 100.6 + - - +
180D GLY* 1.3 58.5 + - - +
183D ASN* 2.7 35.6 + - + +
184D ILE* 3.8 17.0 - - + -
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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