Contacts of the helix formed by residues 169 - 179 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A PHE* 3.2 3.1 + - + +
168A ASP* 1.3 71.8 + - - +
170A LYS* 1.3 80.6 + - + +
172A LEU* 3.2 6.3 + - + +
173A LYS* 3.1 35.1 + - + +
205A ASN* 3.7 27.1 - - - +
208A GLU* 3.9 38.1 - - + +
209A VAL* 3.8 25.6 - - + +
212A ILE* 3.9 23.3 - - + -
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Residues in contact with LYS 170 (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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168A ASP* 3.1 12.6 + - - +
169A ILE* 1.3 104.1 - - + +
171A LYS* 1.3 63.9 + - + +
173A LYS* 3.3 10.6 + - + +
174A GLU* 2.9 36.6 + - - +
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Residues in contact with LYS 171 (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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148A ASN 5.6 0.4 - - - +
149A ILE* 3.8 29.3 - - + +
150A VAL 4.1 11.5 + - - -
152A GLU* 3.9 20.2 + - - +
155A PHE* 6.2 1.0 - - - -
168A ASP* 2.9 41.9 + - - +
170A LYS* 1.3 79.8 - - + +
172A LEU* 1.3 56.4 + - - +
174A GLU* 4.1 16.2 - - - +
175A ASN* 2.9 39.1 + - - +
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Residues in contact with LEU 172 (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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127A ILE* 4.0 26.7 - - + -
149A ILE* 3.6 15.2 - - + +
167A PHE* 5.1 3.1 - - + -
168A ASP 3.1 10.4 + - - +
169A ILE* 3.2 12.5 + - + +
171A LYS* 1.3 75.6 - - - +
173A LYS* 1.3 62.6 + - + +
175A ASN* 3.2 3.7 + - - +
176A ILE* 3.0 46.6 + - + +
187A ILE* 4.1 14.8 - - + -
209A VAL* 4.2 33.4 - - + +
212A ILE* 4.0 30.7 - - + -
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Residues in contact with LYS 173 (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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169A ILE* 3.1 26.9 + - + +
170A LYS* 3.7 12.9 - - + +
172A LEU* 1.3 77.2 - - - +
174A GLU* 1.3 63.6 + - + +
176A ILE* 3.2 9.7 + - - +
177A ALA* 3.0 23.3 + - - +
208A GLU* 4.7 6.3 + - - -
212A ILE* 4.1 32.0 - - + +
216A HIS* 6.4 1.8 - - + -
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Residues in contact with GLU 174 (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 LYS* 2.9 29.0 + - - +
171A LYS* 3.8 17.3 - - - +
173A LYS* 1.3 77.4 - - + +
175A ASN* 1.3 59.3 + - - +
177A ALA* 3.3 6.6 + - - +
178A GLN* 2.8 32.3 + - - +
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Residues in contact with ASN 175 (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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127A ILE* 3.8 20.4 - - + -
147A ILE* 3.7 22.4 - - - +
149A ILE* 3.9 17.5 - - + +
171A LYS* 2.9 32.6 + - - +
172A LEU* 3.7 4.9 - - - +
174A GLU* 1.3 75.9 + - - +
176A ILE* 1.3 61.1 + - - +
178A GLN* 4.3 8.5 + - - +
179A HIS* 2.9 56.1 + - + +
184A ILE* 4.5 0.3 - - - +
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Residues in contact with ILE 176 (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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127A ILE* 4.7 6.7 - - + -
172A LEU* 3.0 36.0 + - + +
173A LYS* 3.2 8.5 + - - +
175A ASN* 1.3 75.9 - - - +
177A ALA* 1.3 56.5 + - - +
180A GLY* 2.7 34.8 + - - +
181A ALA* 4.3 12.8 - - - +
184A ILE* 4.7 6.3 - - + -
187A ILE* 5.0 2.0 - - + -
212A ILE* 3.7 30.1 - - + -
216A HIS* 3.5 41.5 - - + +
218A ILE* 4.1 19.5 - - + -
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Residues in contact with ALA 177 (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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173A LYS 3.0 16.3 + - - +
174A GLU* 3.7 6.5 - - - +
176A ILE* 1.3 78.7 - - - +
178A GLN* 1.3 63.4 + - - +
180A GLY* 3.8 5.0 + - - -
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Residues in contact with GLN 178 (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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174A GLU* 2.8 19.1 + - - +
175A ASN* 3.9 12.5 + - - +
177A ALA* 1.3 80.5 - - - +
179A HIS* 1.3 87.5 + - + +
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Residues in contact with HIS 179 (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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123A ASN* 5.2 2.0 + - - +
125A VAL* 3.7 26.9 - - + +
145A LYS* 4.2 17.4 + - + -
147A ILE* 3.5 20.3 - - + +
175A ASN* 2.9 42.7 + - + +
178A GLN* 1.3 103.9 + - + +
180A GLY* 1.3 60.8 + - - +
183A ASN* 2.8 36.1 + - + +
184A ILE* 3.9 15.7 - - + -
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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