Contacts of the strand formed by residues 150 - 154 (chain B) in PDB entry 1N8T
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 150 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B ILE* 3.7 4.3 - - - +
149B THR* 1.3 103.6 + - - +
151B VAL* 1.3 62.3 + - - +
152B ILE* 3.8 2.9 - - + +
179B ARG* 2.6 39.8 + - - -
181B TRP* 2.9 32.1 + - + +
197B CYS 5.1 1.1 - - - +
198B LEU* 4.0 12.1 - - + +
199B ASN* 5.5 2.8 + - - +
202B SER* 3.4 2.8 + - - +
203B SER* 3.5 15.8 + - - +
204B LEU 2.9 26.7 + - - +
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Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 4.8 0.7 - - + -
148B ILE* 4.3 10.5 - - + -
150B ASP* 1.3 76.5 - - - +
152B ILE* 1.3 63.0 + - - +
178B PRO* 3.7 23.1 - - + +
179B ARG 2.8 11.0 + - - +
180B VAL* 3.2 21.6 - - + +
181B TRP* 2.8 25.5 + - - +
204B LEU* 3.3 12.6 - - + +
206B ILE* 3.5 31.9 - - + -
282B SER* 4.3 5.6 - - - -
285B LEU* 4.0 24.2 - - + -
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Residues in contact with ILE 152 (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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150B ASP* 3.8 7.0 - - + +
151B VAL* 1.3 77.8 - - - +
153B ASN* 1.3 60.3 - - - +
154B ILE* 3.6 5.7 + - + -
181B TRP* 3.5 24.9 - - + +
183B VAL* 4.1 22.9 - - + -
191B ILE* 5.5 0.4 - - + -
194B THR* 4.4 3.6 - - + -
198B LEU* 3.8 24.9 - - + -
203B SER* 3.7 29.4 - - - +
204B LEU 2.9 19.4 + - - +
205B PHE* 3.4 32.0 - - + -
206B ILE* 2.9 26.4 + - - +
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Residues in contact with ASN 153 (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 VAL* 4.1 2.6 - - - +
152B ILE* 1.3 71.7 - - - +
154B ILE* 1.3 69.2 + - - +
155B GLY 4.1 1.0 - - - +
159B SER 2.9 28.2 + - - +
160B ASP* 4.2 4.1 + - - +
163B PRO* 5.0 2.1 - - - +
181B TRP 2.9 6.1 + - - +
182B PHE* 3.6 32.5 - - + -
183B VAL* 3.0 26.3 + - - +
206B ILE* 3.6 24.5 - - - +
208B ALA* 4.3 6.3 - - - +
245B LEU* 4.4 4.5 - - - +
279B ILE 4.8 3.3 - - - +
282B SER* 3.8 22.3 + - - +
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Residues in contact with ILE 154 (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 ILE* 4.2 12.6 - - + +
153B ASN* 1.3 79.5 - - - +
155B GLY* 1.3 60.8 + - - +
183B VAL* 3.5 17.9 - - + +
191B ILE* 4.6 7.0 - - + -
205B PHE* 4.1 8.1 - - + -
206B ILE 2.8 15.1 + - - +
207B ILE* 4.0 12.8 - - + -
208B ALA* 2.9 29.3 + - - +
217B THR* 3.7 21.9 - - + +
220B ASN* 3.5 46.2 - - + +
221B ALA* 4.0 10.8 - - - -
224B ALA* 4.1 14.8 - - + -
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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