Contacts of the strand formed by residues 191 - 200 (chain J) in PDB entry 2NX5
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 TYR 191 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152J GLY 2.9 24.4 + - - -
153J PHE* 2.8 45.5 + - + -
154J PHE* 4.0 16.2 - + - -
155J PRO* 4.4 1.1 - - + -
156J ASP* 3.5 44.6 + - + -
179J PRO* 4.0 20.2 - - + -
180J LEU 3.4 18.2 - - - +
181J LYS* 3.7 34.7 - - + -
182J GLU* 4.1 2.0 - - - -
188J ASP* 5.9 1.4 - - - -
189J SER 3.6 17.7 - - - -
190J ARG* 1.3 74.4 - - - +
192J ALA* 1.3 59.6 + - - +
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Residues in contact with ALA 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181I TRP* 3.7 29.4 - - + -
150J ALA 3.2 9.9 - - - +
151J THR* 3.8 1.6 - - + -
153J PHE* 3.6 2.0 - - - -
179J PRO* 3.4 3.8 - - - +
180J LEU* 2.8 42.1 + - + +
182J GLU* 3.4 24.9 - - + +
191J TYR* 1.3 74.3 - - - +
193J LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148J CYS 3.5 1.9 - - - +
149J LEU* 3.5 5.8 - - - +
150J ALA* 2.7 40.2 + - + +
153J PHE* 4.1 12.1 - - + -
158J VAL* 3.8 24.0 - - + -
160J LEU* 4.2 27.5 - - + +
175J THR* 4.3 10.5 - - + -
176J ASP* 3.5 36.3 - - + +
179J PRO* 3.7 26.9 - - + -
180J LEU* 4.7 2.2 - - - -
192J ALA* 1.3 75.2 - - - +
194J SER* 1.3 66.0 + - - +
215J VAL* 6.0 0.4 - - + -
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Residues in contact with SER 194 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161I THR* 3.3 20.2 - - - +
179I VAL* 4.0 11.4 - - - +
147J VAL* 4.9 0.9 - - - -
148J CYS 3.2 5.4 - - - -
149J LEU* 3.8 16.6 - - - -
160J LEU* 4.9 0.9 - - - -
175J THR* 3.8 3.1 - - - +
176J ASP* 2.6 51.0 + - - +
193J LEU* 1.3 76.6 - - - +
195J SER* 1.3 62.5 + - - +
196J ARG* 3.1 17.3 + - - -
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Residues in contact with SER 195 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J VAL* 3.3 5.9 - - - +
148J CYS* 2.7 33.1 + - - -
160J LEU* 3.5 28.9 - - - +
162J TRP* 2.8 25.6 + - - -
174J CYS 2.9 20.8 + - - -
175J THR* 3.1 15.3 + - - -
194J SER* 1.3 76.7 - - - +
196J ARG* 1.3 64.6 + - - +
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Residues in contact with ARG 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I LEU* 4.3 5.2 - - + -
161I THR* 2.9 28.3 + - - -
162I ASP 3.7 7.5 + - - -
164I CYS* 4.5 2.1 - - - +
166I LEU* 4.4 5.4 - - + -
177I SER* 2.9 52.9 + - - -
178I ALA* 3.5 5.5 - - - +
179I VAL* 3.6 21.4 - - + +
145J THR* 3.8 13.2 - - + -
146J LEU 3.3 8.7 - - - +
147J VAL* 4.3 6.7 - - + -
162J TRP* 3.9 3.0 + - - -
172J GLY 3.5 2.8 - - - +
173J VAL* 3.7 1.9 - - - -
174J CYS* 2.7 64.8 + - - +
176J ASP* 4.3 7.3 + - - +
194J SER* 3.1 21.6 + - - -
195J SER* 1.3 82.0 + - - +
197J LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 197 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J THR* 3.3 2.3 - - - -
146J LEU* 2.7 43.8 + - + +
162J TRP* 3.6 47.4 - - + -
164J VAL* 3.9 26.0 - - + -
169J VAL* 4.1 6.7 - - + -
171J SER 3.8 21.5 - - - +
172J GLY 3.5 5.4 - - - +
173J VAL* 4.1 10.8 - - + -
196J ARG* 1.3 74.6 - - - +
198J ARG* 1.3 61.4 + - - +
199J VAL* 4.3 16.4 - - + -
211J PHE* 4.1 15.0 - - + -
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Residues in contact with ARG 198 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142I THR* 3.7 9.6 + - - -
143I ASP* 2.7 41.2 + - - -
166I LEU* 3.9 28.5 - - + +
168I MET* 3.3 27.1 - - - +
173I PHE* 3.7 5.2 - - - -
175I SER* 3.1 23.0 + - - -
137J GLU* 3.6 14.0 + - - -
141J THR* 3.9 11.1 + - - +
143J LYS* 3.4 40.1 - - + +
144J ALA 3.5 6.1 - - - +
145J THR* 3.4 27.4 + - + +
172J GLY* 3.2 16.0 + - - -
196J ARG 4.2 0.2 - - - -
197J LEU* 1.3 73.7 - - - +
199J VAL* 1.3 65.6 + - - +
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Residues in contact with VAL 199 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I MET* 3.9 8.7 - - + -
143J LYS* 3.7 2.7 - - - +
144J ALA* 2.8 42.1 + - - +
146J LEU* 4.5 6.3 - - + -
164J VAL* 5.7 2.5 - - + -
171J SER 6.0 0.4 - - - +
197J LEU* 4.0 19.5 + - + -
198J ARG* 1.3 78.2 - - - +
200J SER* 1.3 64.1 + - - +
203J PHE* 3.8 36.3 - - + -
204J TRP* 4.2 12.6 - - + -
211J PHE* 4.1 15.5 - - + -
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Residues in contact with SER 200 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168I MET* 3.9 8.2 - - - +
171I MET* 4.9 16.4 - - - -
142J GLN 3.7 8.1 - - - -
143J LYS* 4.5 2.9 - - - +
199J VAL* 1.3 74.5 - - - +
201J ALA* 1.3 67.1 + - - +
202J THR* 4.1 9.9 + - - -
203J PHE* 2.9 29.5 + - - +
204J TRP 3.1 8.8 + - - -
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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