Contacts of the strand formed by residues 171 - 175 (chain B) in PDB entry 1N1M
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 ASP 171 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B VAL* 3.3 5.0 - - - -
168B TRP 2.9 30.9 + - - +
169B ASN* 3.0 15.0 + - - +
170B ASN* 1.3 77.9 - - - +
172B ILE* 1.3 61.7 + - - +
173B TYR* 3.4 16.8 + - + +
184B ARG* 3.2 17.2 + - - +
186B THR* 2.8 41.3 + - - +
187B TRP 3.2 0.7 + - - +
188B THR 3.4 0.5 + - - -
189B GLY* 2.9 32.6 + - - +
196B ASN* 3.5 0.7 + - - -
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ALA* 5.2 0.2 - - + -
166B TYR 3.6 5.8 - - - +
167B VAL* 4.2 3.4 - - + -
171B ASP* 1.3 71.9 - - - +
173B TYR* 1.3 74.9 + - - +
184B ARG* 3.8 2.6 - - - +
185B ILE* 3.0 49.4 + - + +
186B THR* 2.7 13.4 + - + +
196B ASN* 3.4 21.1 - - + +
197B GLY* 3.6 14.6 - - - +
214B LEU* 4.4 12.1 - - + -
223B LEU* 4.1 14.6 - - + -
225B TYR* 3.3 52.5 - - + -
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Residues in contact with TYR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ALA* 3.2 5.5 - - - +
166B TYR* 2.7 75.5 + + + +
168B TRP* 3.6 40.1 + + + -
169B ASN* 5.7 0.2 - - - +
171B ASP* 3.4 25.7 + - + +
172B ILE* 1.3 75.9 - - - +
174B VAL* 1.3 66.3 + - - +
182B SER* 4.5 6.3 - - - -
183B TYR 3.4 3.6 - - - +
184B ARG* 3.4 58.2 + - + -
185B ILE* 3.4 2.0 - - - -
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Residues in contact with VAL 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 LEU 3.2 11.0 - - - +
165B ALA* 4.3 2.7 - - + -
166B TYR* 5.4 0.4 - - - -
173B TYR* 1.3 77.3 - - - +
175B LYS* 1.3 69.4 + - - +
176B ILE* 4.3 7.4 - - + -
182B SER* 3.1 5.1 - - - -
183B TYR* 2.6 43.9 + - - +
185B ILE* 3.4 24.2 - - + -
216B TRP* 4.4 5.6 - - + -
223B LEU* 3.8 23.1 - - + -
273B THR* 4.3 13.5 - - + -
276B LEU* 3.4 29.8 - - + -
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Residues in contact with LYS 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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134B ILE* 4.2 6.9 - - - +
146B GLU* 3.3 24.3 + - - -
147B ARG 5.0 1.1 - - - -
148B ILE* 4.1 20.2 - - - +
162B HIS 4.7 0.2 - - - +
163B LYS* 3.6 4.2 - - - +
164B LEU* 2.8 52.2 + - + +
166B TYR* 4.2 13.2 - - + -
174B VAL* 1.3 73.8 - - - +
176B ILE* 1.3 64.4 + - - +
177B GLU 3.7 11.4 - - - +
178B PRO 3.2 20.0 + - - -
180B LEU 2.8 30.5 - - - +
181B PRO 5.1 0.2 - - - -
182B SER* 3.4 30.7 - - - +
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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