Contacts of the strand formed by residues 171 - 184 (chain B) in PDB entry 3U8M
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 PHE 171 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ILE* 3.6 38.1 - - + -
39B LEU 4.8 2.0 - - - -
41B VAL* 3.4 35.9 - - + -
128B VAL* 3.9 12.3 - - + -
165B PHE* 3.4 14.5 - - - -
166B SER 4.8 0.5 - - - +
169B SER* 2.9 11.5 + - - +
170B ARG* 1.3 118.1 - - + +
172B GLU* 1.3 62.8 + - - +
201B PHE* 3.9 20.9 - + + -
202B ARG 3.3 21.5 - - - +
203B LYS* 4.0 20.6 - - + -
204B LYS* 3.4 15.5 + - - +
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Residues in contact with GLU 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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165B PHE* 4.1 6.7 - - - -
171B PHE* 1.3 77.7 - - - +
173B ILE* 1.3 65.3 + - - +
174B LEU* 3.7 6.6 + - + +
201B PHE* 3.2 6.8 - - - +
202B ARG* 2.6 75.7 + - + +
203B LYS 4.1 4.0 - - - +
204B LYS* 3.8 26.5 - - + +
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Residues in contact with ILE 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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35B PHE* 3.7 21.5 - - + +
38B ILE* 4.7 3.8 - - + -
162B SER* 3.4 32.1 + - - +
165B PHE* 3.4 46.9 - - + -
172B GLU* 1.3 76.2 - - - +
174B LEU* 1.3 67.6 + - - +
175B ASP* 3.7 14.6 - - - +
176B VAL* 3.8 22.2 - - + -
199B LEU* 4.0 15.7 - - + -
200B ASN 3.7 4.5 - - - +
201B PHE* 4.4 0.4 - - + -
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Residues in contact with LEU 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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131B GLU 3.9 9.6 - - - +
132B SER* 3.4 33.9 - - - +
133B GLY* 4.2 2.7 - - - +
172B GLU* 4.5 7.0 - - + -
173B ILE* 1.3 79.2 - - - +
175B ASP* 1.3 62.8 + - + +
200B ASN* 2.6 33.2 + - - +
201B PHE* 4.3 4.9 - - - -
202B ARG* 3.7 42.0 - - + +
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Residues in contact with ASP 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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173B ILE* 3.6 4.1 - - - +
174B LEU* 1.3 83.1 - - + +
176B VAL* 1.3 78.4 + - - +
177B THR* 3.6 21.5 - - + +
198B SER 3.6 0.8 - - - +
200B ASN* 2.9 42.0 + - + +
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Residues in contact with VAL 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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33B LEU 5.2 3.1 - - - +
35B PHE* 4.1 15.5 - - + -
162B SER 6.0 2.5 - - - +
173B ILE* 3.8 19.3 - - + -
175B ASP* 1.3 87.6 + - - +
177B THR* 1.3 68.4 + - - +
178B GLN* 4.5 11.1 - - + +
197B VAL* 3.7 28.7 - - + -
198B SER 3.3 5.2 - - - +
199B LEU* 4.0 13.7 - - + -
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Residues in contact with THR 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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175B ASP* 3.6 20.8 - - - +
176B VAL* 1.3 76.9 - - - +
178B GLN* 1.3 65.7 + - - +
196B GLU 3.6 1.1 - - - +
197B VAL* 3.4 3.8 - - - +
198B SER* 2.7 54.6 + - - +
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Residues in contact with GLN 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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31B VAL 3.6 8.7 - - - +
32B SER* 4.1 8.7 + - - +
33B LEU 3.8 27.1 + - - +
154B PRO* 3.1 43.1 - - + +
155B THR 4.1 2.8 + - - -
176B VAL* 4.5 8.3 - - + +
177B THR* 1.3 82.9 - - - +
179B LYS* 1.3 60.7 + - - +
195B VAL* 4.5 4.3 - - + +
196B GLU 3.4 4.5 - - - +
197B VAL* 3.8 25.0 - - + +
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Residues in contact with LYS 179 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B PRO* 4.7 0.4 - - - -
178B GLN* 1.3 74.9 - - - +
180B LYS* 1.3 67.3 + - - +
181B ASN* 3.1 26.1 + - - +
195B VAL* 3.3 4.4 - - - -
196B GLU* 2.5 60.6 + - + +
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Residues in contact with LYS 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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151B SER* 4.5 0.4 - - - -
152B VAL 2.7 21.2 + - - +
153B ASP* 2.9 31.9 + - - +
154B PRO* 4.0 18.2 - - + +
179B LYS* 1.3 78.9 - - - +
181B ASN* 1.3 75.6 + - - +
182B SER* 6.4 0.7 - - - -
193B GLU* 2.3 44.3 + - - +
194B ASP 3.4 7.4 - - - +
195B VAL* 4.3 2.0 - - + +
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Residues in contact with ASN 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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179B LYS* 3.1 37.2 + - - +
180B LYS* 1.3 81.2 - - - +
182B SER* 1.3 61.7 + - - +
183B VAL* 4.2 8.3 - - + -
193B GLU* 3.1 8.2 - - - +
194B ASP* 2.6 64.1 + - - +
196B GLU* 3.3 30.6 + - - +
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Residues in contact with SER 182 (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 SER* 4.7 2.6 - - - -
180B LYS* 6.4 0.7 - - - -
181B ASN* 1.3 74.6 - - - +
183B VAL* 1.3 62.7 + - - +
184B THR 4.4 0.3 + - - -
191B ALA* 3.4 23.8 - - - +
192B TYR 3.6 4.3 + - - -
193B GLU* 4.0 18.4 + - - +
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Residues in contact with VAL 183 (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 LYS* 4.6 7.0 - - - +
181B ASN* 4.3 8.1 - - + -
182B SER* 1.3 79.6 + - - +
184B THR* 1.3 72.7 + - - +
185B TYR* 3.3 39.8 - - + +
191B ALA* 3.6 1.7 - - - -
192B TYR 2.8 31.9 + - - +
194B ASP* 3.4 22.4 - - - +
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Residues in contact with THR 184 (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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183B VAL* 1.3 81.6 - - - +
185B TYR* 1.3 65.8 + - - +
188B CYS 3.9 16.2 - - - +
189B PRO* 4.1 10.0 + - + +
190B GLU 4.0 9.8 - - - +
191B ALA* 4.2 12.1 - - - +
163C GLU* 5.1 3.1 - - - +
164C TYR* 5.7 0.7 - - - -
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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