Contacts of the helix formed by residues 153 - 164 (chain B) in PDB entry 3ASZ
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 SER 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B VAL* 4.4 3.6 - - - -
152B ARG* 1.3 75.1 - - - +
154B LEU* 1.3 65.2 + - - +
155B GLU* 3.6 9.6 + - - +
156B GLY* 3.0 21.5 + - - +
157B VAL* 2.9 25.3 + - - +
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Residues in contact with LEU 154 (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 PHE* 4.9 2.5 - - + -
143B LEU* 3.4 44.2 - - + -
147B VAL* 4.3 5.1 - - + +
153B SER* 1.3 73.2 - - - +
155B GLU* 1.3 57.4 + - - +
157B VAL* 3.3 1.0 + - - +
158B VAL* 3.0 51.3 + - + +
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Residues in contact with GLU 155 (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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153B SER* 3.2 8.3 + - - +
154B LEU* 1.3 81.0 - - - +
156B GLY* 1.3 59.5 + - - +
158B VAL* 3.9 5.8 - - - +
159B ALA* 3.1 24.9 + - + +
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Residues in contact with GLY 156 (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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152B ARG* 5.5 3.4 - - - -
153B SER* 3.0 20.6 + - - -
155B GLU* 1.3 75.5 - - - +
157B VAL* 1.3 64.8 + - - +
159B ALA* 3.3 5.6 + - - +
160B GLN* 2.9 26.9 + - - +
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B PHE* 3.9 20.9 - - + -
142B ARG* 4.5 7.2 - - + +
143B LEU* 4.0 33.7 - - + +
146B ASP* 3.5 39.7 - - + +
147B VAL* 4.6 1.6 - - + -
152B ARG* 3.8 8.7 - - + +
153B SER 2.9 20.7 + - - +
154B LEU 3.7 4.3 - - - +
156B GLY* 1.3 76.3 - - - +
158B VAL* 1.3 57.8 + - - +
160B GLN* 3.8 5.7 - - - +
161B TYR* 2.8 34.8 + - + +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B PHE* 4.1 16.2 - - + -
154B LEU* 3.0 40.5 + - + +
155B GLU* 3.9 6.1 - - - +
157B VAL* 1.3 75.7 - - - +
159B ALA* 1.3 58.2 + - - +
161B TYR* 3.6 4.2 - - - +
162B LEU* 2.9 52.8 + - + +
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Residues in contact with ALA 159 (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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155B GLU* 3.1 16.6 + - + +
156B GLY* 3.7 4.9 - - - +
158B VAL* 1.3 80.4 - - - +
160B GLN* 1.3 61.7 - - - +
162B LEU* 4.1 2.4 - - - -
163B GLU* 3.0 48.6 + - - +
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Residues in contact with GLN 160 (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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59B TYR* 4.7 7.9 - - - +
60B ASP* 4.4 2.0 + - - -
93B TYR* 5.1 5.1 + - - -
142B ARG* 3.0 20.7 + - - -
146B ASP* 4.3 3.6 - - - +
152B ARG* 3.4 16.9 + - - -
156B GLY 2.9 17.0 + - - +
157B VAL* 3.9 4.6 - - - +
159B ALA* 1.3 75.7 - - - +
161B TYR* 1.3 58.7 + - - +
163B GLU* 5.0 1.8 - - - -
164B GLN* 2.8 49.7 + - - +
165B VAL* 3.0 12.6 + - + +
212B C5P 3.2 39.2 + - - -
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Residues in contact with TYR 161 (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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15B THR* 5.4 1.6 - - + -
135B ALA* 3.9 28.6 + - - +
138B ARG* 4.7 12.7 + - - -
139B PHE* 3.7 45.8 - + + -
142B ARG* 5.2 7.6 - - + -
157B VAL* 2.8 20.8 + - + +
158B VAL* 3.6 3.4 - - - +
160B GLN* 1.3 78.6 - - - +
162B LEU* 1.3 77.8 + - + +
165B VAL* 3.4 34.6 + - + +
166B LYS* 2.8 65.3 + - + +
169B HIS* 6.5 0.2 - - + -
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Residues in contact with LEU 162 (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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158B VAL* 2.9 36.3 + - + +
159B ALA* 4.3 2.5 - - - +
161B TYR* 1.3 95.8 - - + +
163B GLU* 1.3 64.2 + - + +
166B LYS* 4.6 16.5 - - + +
167B PRO* 3.4 18.2 - - - +
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Residues in contact with GLU 163 (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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58B ASN* 5.2 1.0 + - - -
159B ALA* 3.0 36.4 + - - +
160B GLN* 5.0 0.6 - - - -
162B LEU* 1.3 81.4 - - + +
164B GLN* 1.3 68.5 + - + +
167B PRO* 3.8 11.2 - - - +
168B MET* 6.1 0.3 - - - +
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Residues in contact with GLN 164 (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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55B LEU 5.1 2.7 + - - +
56B ARG* 3.5 15.2 + - - +
57B VAL 3.5 23.6 + - - +
58B ASN* 3.7 35.7 - - - +
59B TYR 4.3 1.4 + - - -
60B ASP* 4.5 3.8 - - - +
160B GLN* 2.8 38.7 + - + +
162B LEU 3.6 0.8 - - - -
163B GLU* 1.3 88.1 + - + +
165B VAL* 1.3 65.4 + - - +
166B LYS 3.5 1.6 - - - -
167B PRO* 3.3 2.5 - - - +
168B MET* 3.1 31.7 + - - +
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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