Contacts of the helix formed by residues 169 - 181 (chain B) in PDB entry 2R3B
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 THR 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166B GLU 4.6 7.4 - - - +
167B GLN* 2.8 22.6 + - - +
168B GLN* 1.3 75.1 - - - +
170B LEU* 1.3 56.7 + - - +
171B ALA* 3.6 7.1 + - - +
172B ASN* 3.0 33.1 + - - +
173B ASN* 2.7 35.5 + - - -
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Residues in contact with LEU 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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-2B PHE* 4.3 28.3 - - + -
-1B GLN 5.6 2.7 - - - +
0B GLY 5.7 2.0 - - - +
1B MSE 3.8 32.1 - - + -
169B THR* 1.3 72.6 - - - +
171B ALA* 1.3 59.6 + - - +
173B ASN* 3.8 5.9 - - - +
174B GLN* 2.9 36.8 + - + +
194B PHE* 3.8 21.0 - - + -
199B PRO* 4.6 11.7 - - + -
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Residues in contact with ALA 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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169B THR* 3.2 7.0 + - - +
170B LEU* 1.3 82.1 - - - +
172B ASN* 1.3 61.3 + - - +
174B GLN* 3.5 6.0 + - - +
175B ARG* 3.0 45.0 + - - +
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Residues in contact with ASN 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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163B LEU* 3.7 16.7 - - + +
167B GLN* 2.8 52.9 + - - +
169B THR* 3.0 23.5 + - - +
171B ALA* 1.3 75.3 - - - +
173B ASN* 1.3 67.1 + - - +
175B ARG* 2.9 28.4 + - - +
176B GLN* 3.0 27.9 + - - +
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Residues in contact with ASN 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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157B TRP* 2.9 32.9 + - - +
163B LEU* 3.6 6.4 - - - +
168B GLN* 3.3 34.3 + - - +
169B THR 2.7 24.7 + - - +
170B LEU 3.8 0.6 - - - +
172B ASN* 1.3 72.5 - - - +
174B GLN* 1.3 55.8 + - - +
176B GLN* 3.2 1.6 + - - -
177B GLN* 2.9 28.8 + - - +
186B LEU* 3.4 21.7 - - - +
194B PHE* 3.5 31.7 - - + -
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Residues in contact with GLN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 2.9 24.1 + - + +
171B ALA* 3.7 5.6 - - - +
173B ASN* 1.3 77.5 - - - +
175B ARG* 1.3 58.0 + - - +
177B GLN* 2.9 31.3 + - - +
178B ALA* 2.9 29.0 + - + +
194B PHE* 3.7 22.4 - - + +
195B HIS 3.0 18.5 + - - +
197B GLY 4.1 3.8 + - - -
199B PRO* 3.9 24.2 - - - +
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Residues in contact with ARG 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 ALA* 3.0 31.9 + - - +
172B ASN* 2.9 35.1 + - - +
174B GLN* 1.3 76.9 - - - +
176B GLN* 1.3 70.9 + - - +
178B ALA* 3.2 8.9 + - + +
179B LYS* 3.0 26.0 + - - +
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Residues in contact with GLN 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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157B TRP* 3.9 18.4 - - + -
161B SER* 3.4 25.8 - - - +
162B HIS* 5.7 0.3 + - - -
163B LEU* 3.6 25.5 - - + +
172B ASN 3.0 18.6 + - - +
173B ASN 3.9 3.1 - - - +
175B ARG* 1.3 91.1 + - - +
177B GLN* 1.3 65.8 + - - +
179B LYS* 3.4 32.0 + - - +
180B LEU* 3.3 26.6 + - + +
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Residues in contact with GLN 177 (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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157B TRP* 4.1 1.8 - - - -
173B ASN 2.9 13.9 + - - +
174B GLN* 2.9 23.0 - - - +
176B GLN* 1.3 77.0 - - - +
178B ALA* 1.3 71.2 + - - +
180B LEU* 3.2 4.7 + - - +
181B GLY* 2.9 27.5 + - - -
182B SER 2.8 32.5 + - - +
184B ILE* 4.0 17.7 - - + -
194B PHE* 3.7 31.0 - - + +
195B HIS* 3.4 24.1 - - - +
196B ALA* 3.9 4.4 - - - +
299B EDO 3.8 8.3 - - - -
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Residues in contact with ALA 178 (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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174B GLN* 2.9 15.6 + - + +
175B ARG* 3.2 13.0 + - + +
177B GLN* 1.3 86.6 + - - +
179B LYS* 1.3 62.6 + - - +
181B GLY* 3.3 11.6 + - - +
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Residues in contact with LYS 179 (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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162B HIS* 5.8 4.0 + - - -
175B ARG* 3.0 13.9 + - + +
176B GLN* 3.6 35.4 + - - +
177B GLN 3.2 0.2 - - - -
178B ALA* 1.3 78.5 - - - +
180B LEU* 1.3 62.3 + - + +
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Residues in contact with LEU 180 (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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135B PHE* 4.6 17.3 - - + -
142B LEU* 4.6 8.0 - - + +
145B PRO* 3.3 19.6 - - - +
150B PHE* 4.5 13.0 - - + -
157B TRP* 4.2 5.8 - - + -
160B LEU* 4.0 31.9 - - + +
161B SER* 5.8 1.3 - - - -
176B GLN 3.3 13.6 + - - +
177B GLN* 3.2 7.4 + - - +
179B LYS* 1.3 82.2 - - + +
181B GLY* 1.3 60.5 + - - +
182B SER* 3.7 12.6 + - - +
184B ILE* 4.0 20.4 - - + -
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Residues in contact with GLY 181 (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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145B PRO* 3.2 23.0 - - - +
146B GLU* 3.5 3.8 + - - +
177B GLN* 2.9 14.9 + - - -
178B ALA* 3.3 10.9 + - - -
180B LEU* 1.3 77.3 - - - +
182B SER* 1.3 58.4 + - - +
299B EDO 3.3 16.4 - - - -
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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