Contacts of the helix formed by residues 169 - 179 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167C PHE* 3.2 3.8 + - + +
168C ASP* 1.3 68.5 + - - +
170C LYS* 1.3 84.7 + - + +
172C LEU* 3.2 7.5 + - + +
173C LYS* 3.1 34.9 + - + +
205C ASN* 3.7 21.1 - - - +
208C GLU* 3.9 36.8 - - + +
209C VAL* 3.6 33.0 - - + +
212C ILE* 3.9 22.9 - - + -
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Residues in contact with LYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ASP* 3.0 11.3 + - - +
169C ILE* 1.3 103.8 - - + +
171C LYS* 1.3 64.2 + - + +
173C LYS* 3.3 11.7 + - + +
174C GLU* 3.0 37.5 + - - +
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Residues in contact with LYS 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ASN 5.6 0.4 - - - +
149C ILE* 3.7 29.3 - - + +
150C VAL 4.2 11.1 + - - -
152C GLU* 3.9 20.4 + - - +
155C PHE* 6.2 1.2 - - - -
168C ASP* 2.9 45.5 + - - +
170C LYS* 1.3 79.1 - - + +
172C LEU* 1.3 55.8 + - - +
174C GLU* 3.8 14.8 - - - +
175C ASN* 2.8 39.3 + - - +
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Residues in contact with LEU 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ILE* 4.0 28.3 - - + -
149C ILE* 3.6 15.6 - - + +
167C PHE* 5.1 2.7 - - + -
168C ASP 3.1 9.7 + - - +
169C ILE* 3.5 12.1 - - + +
170C LYS 3.2 0.2 - - - -
171C LYS* 1.3 77.7 - - - +
173C LYS* 1.3 63.0 + - - +
175C ASN* 3.2 3.2 + - - +
176C ILE* 3.0 42.0 + - + +
187C ILE* 4.1 18.8 - - + -
209C VAL* 4.3 33.9 - - + +
212C ILE* 4.0 30.5 - - + -
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Residues in contact with LYS 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C ILE* 3.1 27.2 + - + +
170C LYS* 3.7 12.0 - - + +
172C LEU* 1.3 77.4 - - - +
174C GLU* 1.3 63.9 + - + +
176C ILE* 3.2 9.3 + - + +
177C ALA* 3.1 23.3 + - - +
208C GLU* 4.8 6.1 + - - -
212C ILE* 4.2 29.0 - - + +
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C LYS* 3.0 30.0 + - - +
171C LYS* 3.8 17.5 - - - +
172C LEU 3.3 0.2 - - - -
173C LYS* 1.3 76.2 - - + +
175C ASN* 1.3 60.4 + - - +
177C ALA* 3.3 6.1 + - - +
178C GLN* 2.9 33.2 + - - +
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Residues in contact with ASN 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ILE* 3.8 20.4 - - + -
147C ILE* 3.7 21.8 - - - +
149C ILE* 3.9 14.7 - - + +
171C LYS* 2.8 33.9 + - - +
172C LEU* 3.2 5.1 + - - +
174C GLU* 1.3 79.7 - - - +
176C ILE* 1.3 58.8 + - - +
178C GLN* 4.4 8.5 + - - +
179C HIS* 2.9 57.1 + - + +
184C ILE* 4.4 0.7 - - - +
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Residues in contact with ILE 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ILE* 4.9 2.2 - - + -
172C LEU* 3.0 36.9 + - + +
173C LYS* 3.6 7.2 - - - +
174C GLU 3.2 0.2 - - - -
175C ASN* 1.3 76.6 - - - +
177C ALA* 1.3 54.6 + - - +
180C GLY* 2.7 34.2 + - - +
181C ALA* 3.7 14.1 + - + +
184C ILE* 4.7 9.9 - - + -
187C ILE* 5.2 2.0 - - + -
212C ILE* 3.7 30.3 - - + -
216C HIS* 4.2 31.4 - - + +
218C ILE* 4.1 21.3 - - + -
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Residues in contact with ALA 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C LYS 3.1 15.4 + - - +
174C GLU* 3.8 5.8 - - - +
176C ILE* 1.3 79.4 - - - +
178C GLN* 1.3 61.0 + - - +
180C GLY* 3.8 4.9 + - - -
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Residues in contact with GLN 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C GLU* 2.9 18.1 + - - +
175C ASN* 4.0 11.0 - - - +
177C ALA* 1.3 79.7 - - - +
179C HIS* 1.3 85.4 + - + +
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Residues in contact with HIS 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C ASN* 5.0 2.2 + - - +
125C VAL* 3.6 27.1 - - + +
145C LYS* 4.1 17.3 + - + -
147C ILE* 3.4 21.2 - - + +
175C ASN* 2.9 44.8 + - + +
177C ALA 4.5 0.2 - - - -
178C GLN* 1.3 100.8 + - - +
180C GLY* 1.3 58.2 + - - +
183C ASN* 2.7 38.7 + - + +
184C ILE* 3.9 16.6 - - + -
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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