Contacts of the helix formed by residues 167 - 181 (chain B) in PDB entry 3SI5
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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164A ALA 4.9 1.1 + - - +
165A ARG* 3.6 35.3 - - + +
162B TYR* 3.0 32.5 + - + +
165B ARG* 3.2 3.9 - - + +
166B GLU* 1.3 75.4 - - - +
168B PHE* 1.3 61.3 + - - +
169B ARG* 3.4 9.2 + - - +
170B LYS* 2.9 53.8 + - - +
171B ALA* 3.2 15.9 + - - +
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Residues in contact with PHE 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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165A ARG 3.1 7.3 + - - +
166A GLU* 3.6 28.5 - - + +
167A ASN* 3.8 29.8 - - + -
163B GLU* 3.7 35.0 - - + -
166B GLU* 3.8 26.2 - - + -
167B ASN* 1.3 72.7 - - - +
169B ARG* 1.3 59.7 + - - +
171B ALA* 3.3 5.0 + - - -
172B ASP* 2.9 31.0 + - - +
196B PHE* 3.5 7.1 - + + -
200B VAL* 3.6 32.5 - - + -
203B GLN* 4.2 18.2 - - + -
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Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA* 3.3 32.2 + - - +
165A ARG 3.2 12.9 + - - +
166A GLU* 3.5 36.6 + - + +
167B ASN* 3.3 6.5 - - - +
168B PHE* 1.3 77.5 - - - +
170B LYS* 1.3 61.5 + - - +
172B ASP* 3.4 4.5 + - - +
173B ALA* 3.0 27.0 + - + +
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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
----------------------------------------------------------
162B TYR* 3.6 44.3 + - + +
167B ASN* 2.9 36.8 + - - +
169B ARG* 1.3 76.7 - - + +
171B ALA* 1.3 65.9 + - - +
173B ALA* 3.3 7.4 + - - +
174B ILE* 2.9 31.0 + - + +
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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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159B ALA* 3.3 31.5 - - + +
162B TYR* 3.8 8.9 - - + +
163B GLU* 3.9 4.5 - - + +
167B ASN 3.2 19.1 + - - +
168B PHE 3.6 5.4 - - - +
169B ARG 3.3 0.2 - - - -
170B LYS* 1.3 75.1 - - - +
172B ASP* 1.3 62.7 + - - +
174B ILE* 3.2 4.3 + - - +
175B PHE* 3.0 27.8 + - - -
196B PHE* 3.9 20.6 - - + -
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Residues in contact with ASP 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLU* 5.3 3.8 - - - +
168B PHE 2.9 18.9 + - - +
169B ARG* 3.6 6.1 - - - +
171B ALA* 1.3 76.5 - - - +
173B ALA* 1.3 57.5 + - - +
175B PHE* 3.3 4.9 + - - +
176B GLN* 2.8 58.3 + - - +
193B HIS* 2.9 25.1 + - - -
196B PHE* 3.6 19.2 - - + -
197B GLN* 4.3 6.1 - - - +
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Residues in contact with ALA 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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169B ARG* 3.0 17.2 + - + +
170B LYS* 3.3 8.5 + - - +
172B ASP* 1.3 76.2 + - - +
174B ILE* 1.3 58.9 + - + +
176B GLN* 3.3 10.9 + - - +
177B GLU* 2.9 30.9 + - - +
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Residues in contact with ILE 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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155B TYR* 3.5 37.1 - - + +
158B TRP* 3.7 44.0 - - + -
159B ALA* 3.7 11.2 - - + +
162B TYR* 3.0 44.2 - - + -
170B LYS* 2.9 14.3 + - + +
171B ALA 3.2 6.3 + - - +
173B ALA* 1.3 74.5 - - + +
175B PHE* 1.3 66.9 + - - +
177B GLU* 3.3 5.7 + - + +
178B GLY 3.0 18.9 + - - -
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Residues in contact with PHE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B TYR* 5.2 1.8 - - - -
156B ILE* 4.4 14.1 - - + -
159B ALA* 3.4 24.2 - - + -
160B GLU* 5.4 4.5 - - - -
163B GLU* 5.3 2.0 - - - -
171B ALA 3.0 23.0 + - - -
172B ASP 3.5 3.8 - - - +
174B ILE* 1.3 75.6 - - - +
176B GLN* 1.3 62.7 + - - +
178B GLY* 3.2 2.9 + - - -
179B ILE* 3.0 29.0 + - - +
189B LEU* 3.9 22.9 - - + +
192B GLN* 3.7 25.8 - - + -
193B HIS* 3.2 46.2 - + + -
196B PHE* 3.6 40.2 - + + -
199B ARG* 5.4 3.8 - - - -
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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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172B ASP* 2.8 43.6 + - - +
173B ALA* 3.8 8.7 - - - +
175B PHE* 1.3 75.4 - - - +
177B GLU* 1.3 57.3 + - - +
179B ILE* 3.4 8.9 + - + +
180B GLN* 2.9 31.2 + - - +
193B HIS* 3.9 20.5 - - + -
197B GLN* 5.3 1.4 + - - -
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Residues in contact with GLU 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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143B HIS* 3.1 28.7 + - + +
155B TYR* 3.8 19.1 + - + -
158B TRP* 5.8 2.5 - - + -
173B ALA 2.9 16.7 + - - +
174B ILE* 3.6 6.1 - - + +
176B GLN* 1.3 77.8 - - - +
178B GLY* 1.3 57.4 + - - +
180B GLN* 3.4 18.1 + - - +
181B GLN* 3.0 50.9 + - - +
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Residues in contact with GLY 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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155B TYR* 3.6 35.7 - - - -
174B ILE 3.0 11.5 + - - -
175B PHE 3.7 2.9 - - - -
177B GLU* 1.3 73.8 - - - +
179B ILE* 1.3 65.2 + - - +
181B GLN* 3.1 10.0 + - - -
182B LYS 3.2 8.8 + - - -
183B ALA* 3.2 12.5 + - - +
189B LEU* 3.4 9.3 - - - +
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Residues in contact with ILE 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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175B PHE 3.0 22.8 + - - +
176B GLN* 3.7 6.7 - - + +
178B GLY* 1.3 74.8 - - - +
180B GLN* 1.3 58.3 + - - +
182B LYS* 3.1 22.9 + - - +
186B LEU* 3.9 8.4 - - + +
189B LEU* 3.6 16.4 - - + +
190B GLN* 3.8 42.6 - - + +
193B HIS* 3.4 42.8 - - + +
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Residues in contact with GLN 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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176B GLN 2.9 18.2 + - - +
177B GLU* 3.7 16.9 + - - +
179B ILE* 1.3 78.5 - - - +
181B GLN* 1.3 80.5 + - - +
182B LYS* 3.2 9.7 + - - +
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Residues in contact with GLN 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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149B VAL* 3.9 28.5 - - - +
150B SER* 5.3 3.5 - - - -
155B TYR* 3.8 13.7 - - + +
177B GLU* 3.0 34.5 + - - +
178B GLY 3.1 5.3 + - - +
180B GLN* 1.3 96.5 + - - +
182B LYS* 1.3 71.2 + - - +
183B ALA* 3.4 1.3 + - - +
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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