Contacts of the helix formed by residues 166 - 176 (chain B) in PDB entry 5A0Q
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 TYR 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B VAL* 6.4 2.9 - - + -
29B ALA* 5.4 13.0 - - + -
161B ALA* 3.6 30.5 - - - +
162B MET* 3.9 6.3 - - - +
163B GLY 3.3 20.6 - - - +
164B LYS 3.3 3.0 - - - -
165B ASN* 1.3 77.1 - - - +
167B VAL* 1.4 83.7 + - + +
168B ASN 3.3 0.7 - - - -
169B GLY 3.5 1.3 - - - +
170B LYS* 2.9 59.7 + - + +
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Residues in contact with VAL 167 (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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165B ASN* 3.1 9.4 - - - +
166B TYR* 1.4 114.4 - - + +
168B ASN* 1.4 65.1 + - - +
170B LYS* 4.7 3.0 - - - +
171B THR* 2.9 18.2 + - - -
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Residues in contact with ASN 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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165B ASN* 2.7 34.7 + - - +
167B VAL* 1.4 83.7 + - - +
169B GLY* 1.4 62.8 + - - +
170B LYS 3.3 0.7 - - - -
171B THR* 3.1 18.9 + - - -
172B PHE* 3.0 25.3 + - + -
196B GLU* 4.0 18.1 - - + +
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Residues in contact with GLY 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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161B ALA* 4.1 11.0 - - - -
165B ASN 3.3 13.5 + - - -
166B TYR 3.1 6.3 + - - -
168B ASN* 1.4 76.6 - - - +
170B LYS* 1.3 59.6 + - - +
172B PHE* 3.5 2.7 + - - -
173B LEU* 3.1 14.9 + - - +
193B THR* 3.1 38.1 - - - +
196B GLU* 5.1 0.6 - - - +
197B SER* 5.3 1.8 - - - -
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Residues in contact with LYS 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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147B GLN* 4.8 7.3 + - - +
157B TRP* 3.6 38.3 - - + +
160B THR* 3.6 17.7 + - - -
161B ALA* 3.2 36.6 + - + +
166B TYR* 2.9 36.9 + - + +
167B VAL* 4.7 3.4 - - - +
169B GLY* 1.3 72.5 - - - +
171B THR* 1.4 64.4 + - - +
173B LEU* 3.3 9.2 + - - +
174B GLU* 3.2 23.5 + - - +
53C HIS* 5.3 8.2 - - + -
55C LEU* 4.5 2.9 - - - +
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Residues in contact with THR 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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167B VAL 2.9 20.8 + - - -
168B ASN* 3.1 15.2 + - - -
170B LYS* 1.4 72.9 - - - +
172B PHE* 1.3 67.0 + - - +
174B GLU* 3.2 35.1 + - + +
175B LYS* 3.3 30.5 + - + +
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Residues in contact with PHE 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 ASN* 3.0 30.4 + - + -
169B GLY* 3.7 5.2 - - - +
171B THR* 1.3 76.8 - - - +
173B LEU* 1.3 57.1 + - - +
175B LYS* 3.8 15.5 - - - +
176B ARG* 2.7 75.8 + - + +
192B LEU 5.4 3.6 - - - +
193B THR* 3.5 22.0 - - + +
196B GLU* 2.4 63.3 - - + -
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Residues in contact with LEU 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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35B VAL* 3.9 13.2 - - + -
36B GLY 4.6 0.2 - - - +
37B ILE* 3.7 28.3 - - + -
159B ALA* 4.0 16.4 - - + +
160B THR* 3.3 40.4 - - - +
161B ALA* 4.0 3.8 - - + -
169B GLY 3.1 17.9 + - - +
170B LYS* 3.6 7.6 - - - +
171B THR 3.2 0.8 - - - -
172B PHE* 1.3 77.2 - - - +
174B GLU* 1.4 56.5 + - - +
177B TYR* 3.1 23.6 - - + +
189B THR* 3.7 25.6 - - + +
193B THR* 4.0 9.0 - - + +
55C LEU* 3.7 11.3 - - + +
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Residues in contact with GLU 174 (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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170B LYS 3.2 9.4 + - - +
171B THR* 3.2 29.6 - - + +
172B PHE 3.2 0.2 - - - -
173B LEU* 1.4 74.9 - - - +
175B LYS* 1.4 59.8 + - + +
177B TYR 3.1 13.8 - - - +
178B ASN* 4.6 6.2 + - - +
53C HIS* 4.4 15.9 + - + -
54C LYS* 3.6 44.3 + - - +
55C LEU* 3.6 25.5 - - + +
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Residues in contact with LYS 175 (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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171B THR* 3.3 45.4 + - + +
172B PHE* 3.6 16.3 - - - +
174B GLU* 1.4 78.8 - - + +
176B ARG* 1.4 103.1 + - - +
177B TYR* 3.1 3.9 + - - +
178B ASN* 5.6 2.9 + - - -
54C LYS* 5.5 0.9 - - - +
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Residues in contact with ARG 176 (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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172B PHE* 2.7 54.7 + - + +
175B LYS* 1.4 111.8 - - - +
177B TYR* 1.3 58.8 + - - +
181B LEU* 6.1 0.3 - - - +
189B THR* 4.0 17.4 + - - +
192B LEU* 6.4 2.7 - - + -
193B THR* 5.1 0.9 - - - +
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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