Contacts of the helix formed by residues 167 - 173 (chain B) in PDB entry 5AJI
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 ASN 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B ASN 3.4 14.6 - - - +
120B ALA* 3.4 14.6 - - + +
121B GLY* 3.2 22.7 - - - +
124B LEU* 3.8 8.7 - - + +
148B VAL* 4.1 1.5 - - - +
149B GLN 2.9 25.3 + - - -
150B ILE 3.3 3.8 + - - -
151B PHE 3.0 24.4 + - - +
152B SER 3.2 8.1 - - - -
153B THR* 2.8 26.2 + - - -
165B ILE 3.5 0.2 + - - -
166B PRO* 1.3 71.8 - - - +
168B GLY* 1.3 63.7 + - - +
170B ILE* 3.1 17.8 + - - +
171B ILE* 3.1 10.7 + - - +
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Residues in contact with GLY 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B SER* 4.4 13.7 - - - -
117B ASN* 2.9 16.9 + - - -
120B ALA* 3.5 14.6 - - - +
167B ASN* 1.3 76.9 - - - +
169B LYS* 1.3 61.1 + - - +
171B ILE* 3.4 5.7 - - - +
172B ALA* 3.2 24.3 + - - +
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Residues in contact with LYS 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ALA 3.5 23.3 - - - +
173A GLY* 4.5 6.5 - - - -
174A ASN* 2.7 40.5 + - - +
117B ASN* 4.5 0.6 + - - -
138B LEU 5.0 5.9 + - - -
139B GLY* 5.4 5.3 + - - -
165B ILE* 4.1 7.2 - - + +
166B PRO* 3.1 23.2 + - + +
168B GLY* 1.3 76.0 - - - +
170B ILE* 1.3 64.4 + - - +
172B ALA* 3.5 12.4 + - - +
173B GLY* 3.5 8.1 + - - -
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LEU* 4.1 10.5 - - + -
130B PHE* 4.0 13.2 - - + -
138B LEU* 3.8 28.0 - - + +
153B THR* 3.4 37.0 - - + +
165B ILE* 3.5 32.3 - - + +
166B PRO 3.5 3.1 - - - +
167B ASN* 3.1 12.5 + - - +
169B LYS* 1.3 77.4 - - - +
171B ILE* 1.3 58.9 + - - +
173B GLY* 3.3 23.7 + - - +
174B ASN 4.4 1.7 - - - +
175B ILE* 4.0 27.2 - - + +
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Residues in contact with ILE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ALA* 3.5 29.4 - - + +
123B LEU* 3.4 44.9 - - + -
124B LEU* 4.2 16.4 - - + -
167B ASN 3.1 5.8 + - - +
168B GLY* 3.4 12.6 - - - +
170B ILE* 1.3 77.9 - - - +
172B ALA* 1.3 64.5 + - + +
173B GLY 3.2 2.9 + - - +
175B ILE* 5.1 4.9 - - + -
117C ASN* 5.3 5.4 + - - +
166C PRO* 3.8 19.1 - - - +
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B GLY 3.2 16.5 + - - +
169B LYS* 3.8 7.6 - - - +
170B ILE 3.2 0.8 - - - -
171B ILE* 1.3 78.0 - - + +
173B GLY* 1.3 58.2 + - - +
166C PRO* 3.6 14.4 - - - +
169C LYS* 3.6 12.1 - - - +
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Residues in contact with GLY 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B GLY* 6.3 1.6 - - - -
169B LYS 3.5 6.1 + - - -
170B ILE 3.3 14.2 + - - +
171B ILE 3.2 2.1 - - - +
172B ALA* 1.3 82.2 - - - +
174B ASN* 1.3 69.6 + - - -
175B ILE* 3.8 2.6 + - - +
164C VAL 4.1 0.9 - - - +
166C PRO* 3.4 17.0 - - - +
169C LYS* 4.6 7.0 - - - -
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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