Contacts of the helix formed by residues 161 - 176 (chain B) in PDB entry 2H5X
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 ALA 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B GLY 4.0 0.8 + - - -
160B PHE* 1.3 75.6 - - - +
162B ALA* 1.3 67.4 + - - +
163B LYS* 3.3 7.1 + - + +
164B GLN* 3.5 12.1 + - + +
165B ALA* 2.9 24.2 + - - +
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Residues in contact with ALA 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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152B VAL* 4.9 3.1 - - + -
156B VAL* 4.2 19.3 - - + +
160B PHE 3.9 1.4 + - - -
161B ALA* 1.3 72.1 - - - +
163B LYS* 1.3 65.8 + - - +
165B ALA* 3.3 1.9 + - - +
166B GLU* 3.0 35.2 + - + +
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Residues in contact with LYS 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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161B ALA* 3.3 4.8 - - + +
162B ALA* 1.3 81.2 - - - +
164B GLN* 1.3 65.7 + - - +
165B ALA 3.0 0.2 + - - -
166B GLU* 3.1 18.7 + - - +
167B GLU* 3.1 20.1 + - - +
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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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160B PHE* 4.5 11.0 - - + -
161B ALA* 3.5 16.9 + - + +
163B LYS* 1.3 79.4 - - - +
165B ALA* 1.3 62.2 + - - +
167B GLU* 3.5 20.1 - - - +
168B ALA* 3.3 18.5 + - - +
192B LEU* 3.8 25.4 - - + +
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Residues in contact with ALA 165 (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 VAL* 3.7 20.4 - - + +
155B LEU* 3.8 30.9 - - + +
156B VAL* 4.5 2.9 - - + -
160B PHE* 4.5 5.8 - - + +
161B ALA 2.9 20.6 + - - +
162B ALA* 3.5 4.9 - - - +
164B GLN* 1.3 74.7 - - - +
166B GLU* 1.3 65.0 + - - +
168B ALA* 3.4 2.1 + - - -
169B THR* 2.8 29.0 + - - -
192B LEU* 5.3 1.8 - - - -
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Residues in contact with GLU 166 (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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148B ARG* 3.5 28.3 + - - +
152B VAL* 4.0 25.1 - - + +
162B ALA* 3.0 23.5 + - - +
163B LYS* 3.7 9.6 - - - +
165B ALA* 1.3 74.6 - - - +
167B GLU* 1.3 57.7 + - - +
169B THR* 3.0 2.5 + - - -
170B ASP* 2.8 47.6 + - - +
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Residues in contact with GLU 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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163B LYS* 3.1 15.9 + - - +
164B GLN* 3.5 22.8 - - - +
166B GLU* 1.3 80.5 - - - +
168B ALA* 1.3 52.1 + - - +
170B ASP* 4.1 7.0 - - - +
171B THR* 2.7 31.4 + - - -
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Residues in contact with ALA 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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164B GLN* 3.3 7.1 + - - +
165B ALA 4.0 2.9 - - - +
166B GLU 3.2 0.4 - - - -
167B GLU* 1.3 76.5 - - - +
169B THR* 1.3 64.9 + - - +
171B THR* 3.4 7.4 + - - -
172B VAL* 3.2 29.0 + - - +
188B ALA* 4.2 13.2 - - + +
191B LEU* 3.8 11.8 - - + +
192B LEU* 3.9 36.1 - - + -
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Residues in contact with THR 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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148B ARG* 4.1 27.8 - - + +
151B VAL* 3.8 29.9 - - + +
152B VAL* 3.8 11.7 - - - +
155B LEU* 3.5 15.9 - - - +
165B ALA 2.8 19.9 + - - -
166B GLU* 3.0 4.6 + - - -
168B ALA* 1.3 73.3 - - - +
170B ASP* 1.3 66.3 + - - +
172B VAL* 3.4 4.2 + - - +
173B LEU* 3.1 30.6 + - + +
184B ALA* 5.4 2.5 - - + -
188B ALA* 4.5 6.5 - - - +
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Residues in contact with ASP 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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148B ARG* 2.8 48.1 + - - +
166B GLU* 2.8 23.9 + - - +
167B GLU* 4.1 6.4 + - - +
169B THR* 1.3 76.5 - - - +
171B THR* 1.3 63.6 + - - +
173B LEU* 3.1 7.4 + - - +
174B ALA* 2.9 26.8 + - - +
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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 GLU 2.7 22.4 + - - -
168B ALA* 3.4 9.5 + - - -
169B THR 3.3 0.2 - - - -
170B ASP* 1.3 79.8 - - - +
172B VAL* 1.3 64.1 + - - +
174B ALA* 3.1 6.6 + - - +
175B ALA* 3.0 25.4 + - + +
191B LEU* 3.9 19.8 - - + +
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Residues in contact with VAL 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 ALA 3.2 14.7 + - - +
169B THR* 3.7 6.3 - - - +
170B ASP 3.3 0.2 - - - -
171B THR* 1.3 79.9 - - - +
173B LEU* 1.3 54.4 + - + +
175B ALA* 3.2 5.6 + - - +
176B ASN* 2.7 43.3 + - + +
183B SER 5.2 0.2 - - - -
184B ALA* 3.9 23.3 - - + +
187B SER* 3.5 37.0 - - - +
188B ALA* 3.6 22.4 - - + +
191B LEU* 3.9 10.1 - - + -
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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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147B VAL* 3.8 35.0 - - + -
148B ARG* 4.2 25.1 - - + +
169B THR* 3.1 24.0 + - + +
170B ASP* 3.7 5.4 - - - +
172B VAL* 1.3 77.7 - - + +
174B ALA* 1.3 67.0 + - - +
176B ASN* 3.0 13.3 - - + +
177B HIS 2.6 28.4 - - - +
178B ASP* 4.9 2.2 - - - -
179B ALA* 4.7 16.2 - - + +
180B THR 5.9 0.2 - - - +
184B ALA* 4.1 16.8 - - + -
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Residues in contact with ALA 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 ASP 2.9 16.8 + - - +
171B THR* 3.5 6.3 - - - +
173B LEU* 1.3 78.2 - - - +
175B ALA* 1.3 63.0 + - - +
177B HIS* 3.9 6.3 + - - +
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B THR* 3.0 15.1 + - + +
172B VAL* 3.6 9.4 - - - +
174B ALA* 1.3 78.9 - - - +
176B ASN* 1.3 57.9 + - - +
177B HIS* 3.3 11.3 + - - -
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Residues in contact with ASN 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 VAL* 2.7 27.5 + - + +
173B LEU* 3.0 8.4 - - + +
175B ALA* 1.3 70.6 - - + +
177B HIS* 1.3 77.8 + - - +
178B ASP* 2.5 12.8 + - - +
179B ALA* 3.0 30.1 + - - +
183B SER* 4.8 7.2 + - - -
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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