Contacts of the helix formed by residues 159 - 170 (chain B) in PDB entry 4BOS
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 159 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157B ASP* 3.0 19.7 + - - -
158B ASN* 1.3 77.6 - - - +
160B ALA* 1.3 60.0 + - - +
161B LEU 3.2 2.9 - - - -
162B PHE* 2.9 26.5 + - - +
163B THR* 3.1 14.5 + - - -
176B PRO 5.4 0.2 - - - -
179B ALA* 3.5 24.6 - - - +
183B ARG* 2.8 29.7 + - - +
216B ASP* 4.0 7.6 + - - +
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Residues in contact with ALA 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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154B VAL* 4.0 5.2 - - + -
155B PRO 3.6 9.2 - - - +
157B ASP* 3.8 1.2 + - - -
158B ASN 3.6 0.2 - - - -
159B SER* 1.3 74.2 - - - +
161B LEU* 1.3 65.2 + - - +
163B THR* 4.0 4.3 - - - -
164B SER* 2.8 31.5 + - - -
267B HIS* 3.3 22.9 - - + +
268B TYR* 3.4 12.1 - - + +
1310B NO3 3.3 31.0 + - - +
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Residues in contact with LEU 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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159B SER 3.2 0.2 - - - -
160B ALA* 1.3 80.3 - - - +
162B PHE* 1.3 67.7 + - + +
164B SER* 3.6 1.0 - - - -
165B VAL* 2.9 35.6 + - + +
220B GLY* 3.5 40.2 - - - +
221B GLY* 3.8 4.0 - - - +
224B GLU* 4.0 16.8 - - + -
225B ILE* 3.7 26.9 - - + -
228B LEU* 5.2 1.8 - - + -
261B LEU* 4.1 10.3 - - + -
268B TYR* 3.5 44.2 - - + -
1310B NO3 4.9 0.4 + - - -
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Residues in contact with PHE 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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159B SER* 2.9 23.5 + - - +
161B LEU* 1.3 78.6 - - + +
163B THR* 1.3 56.3 + - - +
165B VAL* 3.3 2.5 + - - -
166B TYR* 2.9 31.4 + - - +
178B CYS* 4.2 0.7 - - - -
179B ALA* 4.3 13.7 - - + -
182B MET* 3.4 38.3 - - + +
183B ARG* 3.5 48.9 - - + -
186B ILE* 3.5 28.5 - - + -
213B ILE* 4.2 4.9 - - + -
220B GLY* 4.2 19.5 - - - -
224B GLU* 4.0 23.1 - - + -
228B LEU* 4.4 4.7 - - + -
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Residues in contact with THR 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B VAL* 3.7 29.8 - - + -
155B PRO* 4.7 1.9 + - + +
157B ASP* 4.8 3.6 + - - -
159B SER* 3.1 20.4 + - - -
160B ALA* 4.0 4.8 - - - -
162B PHE* 1.3 75.4 - - - +
164B SER* 1.3 58.2 + - - +
166B TYR* 3.5 2.1 + - - +
167B TYR* 2.9 28.1 + - - +
173B VAL 5.0 0.3 - - - +
174B LEU* 4.0 15.0 - - + -
175B ASN 4.3 4.7 + - - +
176B PRO* 3.9 36.4 + - + +
178B CYS* 3.9 10.0 - - - -
179B ALA* 5.0 0.2 - - - +
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Residues in contact with SER 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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154B VAL* 3.6 2.1 - - - +
160B ALA 2.8 24.8 + - - -
161B LEU 3.6 3.1 - - - -
163B THR* 1.3 73.0 - - - +
165B VAL* 1.3 67.0 + - - +
167B TYR* 3.2 11.4 + - - +
168B VAL* 3.2 16.3 + - - +
261B LEU* 3.7 14.6 - - - -
268B TYR* 3.3 10.2 + - - -
269B ASP* 3.2 25.6 - - - -
270B PRO* 3.3 27.3 - - - +
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Residues in contact with VAL 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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161B LEU* 2.9 27.1 + - + +
162B PHE 3.8 2.7 - - - +
164B SER* 1.3 76.7 - - - +
166B TYR* 1.3 63.4 + - - +
168B VAL* 3.2 10.0 - - + +
169B VAL* 3.0 37.4 + - + +
182B MET* 4.2 9.0 - - + -
225B ILE* 5.3 2.0 - - + -
228B LEU* 4.2 21.3 - - + -
232B TYR* 4.1 22.0 - - + -
236B ILE* 4.5 15.5 - - + -
259B VAL* 6.1 0.2 - - + -
261B LEU* 3.9 21.8 - - + -
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Residues in contact with TYR 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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162B PHE 2.9 17.6 + - - +
163B THR 3.6 4.7 - - - +
165B VAL* 1.3 78.2 - - - +
167B TYR* 1.3 62.5 + - - +
169B VAL* 4.0 5.2 - - - -
170B GLU* 3.0 60.5 + - + +
173B VAL* 3.7 34.4 - - + +
175B ASN* 4.1 23.2 + - + -
178B CYS* 3.6 34.5 - - + -
182B MET* 4.0 13.6 - - + -
232B TYR* 4.4 9.2 - - - -
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Residues in contact with TYR 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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152B THR* 3.3 22.8 + - + +
154B VAL* 5.2 1.6 - - + -
163B THR 2.9 18.5 + - - +
164B SER 3.2 5.6 + - - +
166B TYR* 1.3 79.4 - - - +
168B VAL* 1.3 64.2 + - + +
171B GLY 3.5 0.9 + - - -
172B GLY* 2.8 60.1 + - - -
173B VAL 3.3 27.5 + - - +
174B LEU* 3.8 19.5 - - + -
270B PRO* 3.4 32.3 - - + -
271B LEU 5.3 0.2 - - - -
272B GLN* 2.4 34.6 + - + -
282B PRO* 5.3 2.8 - - - +
284B THR* 3.9 8.0 - - + +
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Residues in contact with VAL 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 SER 3.4 6.7 - - - +
165B VAL* 3.2 20.0 - - + +
167B TYR* 1.3 79.5 - - + +
169B VAL* 1.3 63.4 + - + +
171B GLY 3.1 2.8 + - - -
259B VAL* 3.7 32.5 - - + -
260B LEU 3.8 10.3 - - - +
261B LEU* 4.1 6.7 - - + -
270B PRO* 3.6 25.8 - - + -
271B LEU 3.7 19.5 - - - +
284B THR* 2.7 33.3 + - - +
285B ILE* 3.4 9.5 - - - +
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Residues in contact with VAL 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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165B VAL* 3.0 33.5 + - + +
166B TYR* 3.6 9.0 - - - +
168B VAL* 1.3 82.9 - - + +
170B GLU* 1.3 71.0 + - + +
171B GLY 3.2 1.0 + - - -
232B TYR* 3.7 59.0 - - + -
234B CYS* 4.2 15.9 - - - -
236B ILE* 5.6 0.9 - - + -
259B VAL* 4.3 6.5 - - + -
285B ILE* 3.8 15.7 - - - +
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Residues in contact with GLU 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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166B TYR* 3.0 53.4 + - + +
169B VAL* 1.3 81.8 - - + +
171B GLY* 1.3 60.3 + - - +
172B GLY 3.4 1.8 - - - -
173B VAL* 3.5 31.3 - - + +
232B TYR* 3.9 23.0 + - - -
285B ILE* 5.4 0.2 - - - -
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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