Contacts of the strand formed by residues 174 - 180 (chain B) in PDB entry 5NJ8
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 GLY 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LYS 5.0 0.5 - - - +
168B ILE* 3.8 23.3 + - - +
169B LEU* 3.9 17.9 + - - +
172B ALA 3.3 1.8 - - - -
173B ASP* 1.3 79.8 - - - +
175B PHE* 1.3 60.7 + - - +
192B SER* 3.9 9.0 - - - -
196B VAL* 4.3 1.8 - - - -
340B ILE* 4.6 4.9 - - - -
341B GLY 3.2 9.0 - - - -
342B ARG* 3.7 11.0 - - - -
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Residues in contact with PHE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B GLY* 1.3 73.4 - - - -
176B LEU* 1.3 67.2 + - - +
177B PHE* 3.6 23.6 - + + -
190B SER* 3.9 0.4 - - - +
192B SER* 3.7 31.6 - - - +
193B VAL* 3.6 25.1 - - + -
196B VAL* 3.9 23.3 - - + -
197B LEU* 4.0 21.1 - - + -
204B TRP* 4.3 14.1 - + - -
267B MET* 3.9 28.5 - - + -
306B VAL* 4.8 3.1 - - + -
340B ILE* 3.1 6.1 - - - -
341B GLY* 2.9 57.4 + - - -
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Residues in contact with LEU 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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114A GLU* 3.5 29.4 - - + -
117A PHE* 3.9 26.5 - - + +
118A LEU* 3.7 20.1 - - + +
121A ALA* 4.6 0.2 - - + -
175B PHE* 1.3 79.3 - - - +
177B PHE* 1.3 68.7 + - - +
178B ILE* 3.6 24.0 - - + -
188B TYR* 4.1 7.4 - - + -
189B VAL* 3.5 2.3 - - - -
190B SER* 3.2 34.6 + - - +
338B VAL* 4.3 5.2 - - + -
339B ALA 3.3 20.4 - - - +
340B ILE* 3.5 16.8 - - + +
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Residues in contact with PHE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PHE* 3.6 26.5 - + + -
176B LEU* 1.3 77.9 - - - +
178B ILE* 1.3 64.2 + - - +
179B VAL* 3.7 24.2 - - + -
188B TYR 3.1 13.2 - - - +
189B VAL* 3.8 13.0 - - + -
204B TRP* 4.6 8.5 - + + -
209B LEU* 4.1 24.7 - - + -
263B PHE* 5.5 2.9 - + - -
267B MET* 4.6 6.1 - - + -
308B CYS* 4.1 20.2 - - + -
337B LEU* 3.7 5.6 - - + +
339B ALA* 2.7 58.9 + - + +
340B ILE 3.9 2.2 - - - -
341B GLY* 3.7 25.1 - - - -
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Residues in contact with ILE 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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110A LEU* 5.6 0.9 - - + -
117A PHE* 3.8 17.5 - - + -
176B LEU* 3.6 29.4 - - + -
177B PHE* 1.3 77.7 - - - +
179B VAL* 1.3 58.9 + - - +
186B VAL* 4.0 0.2 - - - -
187B VAL* 2.6 46.5 + - + -
188B TYR* 2.9 34.6 + - + +
315B TRP* 3.7 30.1 - - + +
336B CYS* 3.9 11.0 - - + -
337B LEU 3.3 3.6 - - - +
338B VAL* 3.6 26.7 - - + -
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Residues in contact with VAL 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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177B PHE* 3.7 23.6 - - + -
178B ILE* 1.3 80.8 - - - +
180B SER* 1.3 66.1 + - - +
184B GLY* 6.3 0.2 - - - -
185B ARG 3.3 9.9 - - - +
186B VAL* 3.9 19.3 - - + -
187B VAL* 3.9 4.7 - - - +
204B TRP* 5.6 0.2 - - + -
209B LEU* 3.8 38.4 - - + -
225B LEU* 5.4 6.3 - - + -
336B CYS* 3.1 4.9 - - - +
337B LEU* 2.8 48.9 + - + +
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Residues in contact with SER 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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179B VAL* 1.3 74.7 - - - +
181B CYS* 1.3 60.7 + - - +
182B GLU 2.9 10.5 + - - -
183B THR* 3.1 26.0 - - - +
184B GLY* 4.8 1.0 - - - -
185B ARG* 2.6 43.6 + - - -
187B VAL* 3.8 3.2 - - - +
225B LEU* 4.0 7.8 - - - +
334B LYS* 5.5 4.5 - - - +
335B PHE 4.0 2.4 + - - -
336B CYS* 3.7 17.5 - - - -
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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