Contacts of the strand formed by residues 171 - 181 (chain B) in PDB entry 2NUD
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 171 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167B TYR* 3.4 5.0 - - - -
168B LEU 3.0 31.8 + - - +
169B HIS* 3.6 18.2 + - - +
170B GLY* 1.3 83.4 - - - +
172B VAL* 1.3 70.1 + - - +
173B ILE* 3.7 5.6 + - + +
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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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165B THR* 4.0 21.1 - - + -
166B ALA 3.3 8.1 - - - +
167B TYR* 3.6 36.5 - - + +
170B GLY 4.4 0.2 + - - -
171B ASN* 1.3 80.0 - - - +
173B ILE* 1.3 65.9 + - - +
174B PRO* 4.2 9.1 - - + +
222B TYR* 5.3 2.3 + - - -
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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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166B ALA* 2.7 36.6 + - + +
168B LEU* 3.7 35.0 - - + +
171B ASN* 3.8 9.6 - - + +
172B VAL* 1.3 82.7 - - - +
174B PRO* 1.3 72.5 - - - +
175B LEU* 3.4 14.6 + - + +
222B TYR* 3.5 42.6 - - + -
225B ILE* 5.3 6.7 - - + -
226B ILE* 4.9 7.9 - - + -
257B TRP* 4.7 8.5 - - + -
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Residues in contact with PRO 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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164B GLN 3.9 5.4 - - - +
165B THR* 4.0 13.5 - - + -
172B VAL* 4.2 11.4 - - + +
173B ILE* 1.3 89.1 - - - +
175B LEU* 1.3 67.6 + - - +
177B THR* 6.1 0.7 - - - +
218B THR* 4.2 4.7 - - - +
219B ASN 4.9 0.7 + - - -
222B TYR* 3.6 32.0 - - + +
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Residues in contact with LEU 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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164B GLN* 2.8 36.3 + - - +
165B THR 4.2 2.2 - - - -
166B ALA* 3.6 11.4 - - + +
173B ILE* 3.7 22.2 - - + +
174B PRO* 1.3 80.3 - - - +
176B ASN* 1.3 63.6 + - - +
177B THR* 4.1 3.9 + - - -
216B ASP 4.1 0.9 - - - +
217B HIS 3.9 2.4 - - - +
218B THR* 3.3 48.1 + - + +
219B ASN 4.7 0.5 + - - -
226B ILE* 4.3 11.4 - - + -
256B TRP* 3.5 33.7 - - + -
257B TRP* 5.0 3.4 - - + -
260B SER* 3.9 13.2 - - - +
261B ALA* 5.3 0.2 - - - -
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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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162B TYR 3.9 0.7 - - - +
164B GLN* 2.8 58.3 + - - +
175B LEU* 1.3 81.6 - - - +
177B THR* 1.3 62.9 + - - +
178B PHE* 4.2 17.3 - - + -
215B ILE* 4.3 3.1 - - + -
216B ASP 3.5 3.8 - - - +
217B HIS* 2.8 37.4 + - - +
218B THR* 3.2 5.0 + - - -
260B SER 2.8 26.1 + - - +
262B MET* 5.3 0.2 - - - +
301B MET* 3.6 23.5 - - - +
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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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161B VAL* 3.8 16.8 - - + -
162B TYR 3.4 8.7 - - - +
163B ARG* 4.1 23.6 + - + +
174B PRO* 6.1 0.7 - - - +
175B LEU 4.5 3.6 + - - -
176B ASN* 1.3 76.3 + - - +
178B PHE* 1.3 65.6 + - - +
179B ARG* 3.0 33.3 + - - +
214B ARG 3.8 0.5 - - - +
215B ILE* 3.3 4.3 - - - -
216B ASP* 2.8 45.7 + - - +
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Residues in contact with PHE 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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127B LEU* 4.7 2.0 - - + -
134B VAL* 4.0 14.1 - - + -
138B VAL* 3.5 32.0 - - + +
160B LYS 3.6 1.2 - - - +
161B VAL* 3.3 11.3 - - - +
162B TYR* 2.9 48.5 + + + +
176B ASN* 4.2 12.8 - - + -
177B THR* 1.3 77.7 - - - +
179B ARG* 1.3 61.4 + - - +
214B ARG 3.7 3.4 - - - +
215B ILE* 3.5 37.2 - - + -
298B ILE* 4.9 5.4 - - + -
301B MET* 3.3 47.6 - - + -
302B LEU* 3.6 19.7 - - + -
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Residues in contact with ARG 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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127B LEU* 3.8 1.6 - - - +
147B GLU* 4.7 3.4 + - - -
149B MET* 4.1 29.6 - - - +
159B VAL* 4.1 9.4 - - + +
160B LYS 3.5 2.0 - - - -
161B VAL* 3.6 29.3 - - - +
163B ARG* 4.6 14.3 - - - +
177B THR* 3.0 28.2 - - + +
178B PHE* 1.3 77.2 - - - +
180B VAL* 1.3 66.5 + - - +
212B PRO 4.1 11.2 - - - +
213B ASP* 3.1 22.0 - - - +
214B ARG* 3.0 33.0 + - - +
216B ASP* 4.0 14.7 + - - +
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Residues in contact with VAL 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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127B LEU* 4.2 4.9 - - + -
135B LEU* 3.7 32.8 - - + +
138B VAL* 3.7 27.4 - - + -
139B VAL* 3.5 26.7 - - + -
159B VAL* 3.2 4.0 - - - +
160B LYS* 2.7 39.6 + - - +
179B ARG* 1.3 79.9 - - - +
181B ALA* 1.3 71.3 + - - +
182B THR* 3.8 0.5 + - - +
213B ASP* 3.3 9.9 - - - +
151D PHE* 4.1 13.5 - - + -
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Residues in contact with ALA 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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157B LEU* 4.7 9.9 - - + -
158B ASN 3.5 13.2 - - - +
159B VAL* 3.8 9.4 - - + -
180B VAL* 1.3 76.3 - - - +
182B THR* 1.3 62.5 + - - +
183B ASP 4.6 2.2 - - - +
184B THR* 4.3 3.3 + - - -
187B LEU* 3.9 28.0 - - + +
212B PRO* 3.9 14.5 + - + +
213B ASP* 2.8 11.1 + - - +
151D PHE* 3.8 19.9 - - - +
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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