Contacts of the strand formed by residues 158 - 164 (chain P) 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 VAL 158 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126P PRO* 4.5 2.0 - - + -
150P ALA* 5.5 0.2 - - + -
153P PHE* 3.6 40.4 - - + -
156P ASP* 2.8 18.8 + - + +
157P HIS* 1.3 78.9 - - - +
159P GLU* 1.3 70.3 + - - +
160P LEU 4.2 0.4 - - - -
179P PRO* 5.6 3.6 - - + -
193P LEU* 3.8 27.8 - - + -
215P VAL* 3.8 24.5 - - + -
216P GLN 3.1 6.3 - - - +
217P PHE* 4.1 7.6 - - + -
218P TYR* 5.4 0.4 - - - -
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Residues in contact with GLU 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P ARG* 5.0 5.6 + - - -
10P HIS* 3.3 26.3 + - - +
158P VAL* 1.3 79.9 - - - +
160P LEU* 1.3 62.1 + - - +
161P SER* 4.0 2.9 + - - -
214P GLN 3.7 1.2 - - - +
215P VAL* 3.4 3.6 - - - -
216P GLN* 2.8 45.1 + - + +
218P TYR* 2.7 30.8 + - + -
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Residues in contact with LEU 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148P CYS* 4.4 4.9 - - - -
150P ALA* 4.6 2.9 - - + -
158P VAL* 4.2 0.8 - - - +
159P GLU* 1.3 72.3 - - - +
161P SER* 1.3 74.9 + - - +
162P TRP* 3.9 13.0 - - + +
175P THR* 4.2 22.3 + - + +
193P LEU* 4.2 34.4 - - + +
195P SER* 3.6 35.2 - - - +
213P CYS* 3.7 20.4 - - - -
214P GLN 3.4 2.5 - - - -
215P VAL* 3.7 26.2 - - + +
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Residues in contact with SER 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159P GLU 4.6 3.1 + - - -
160P LEU* 1.3 80.8 - - - +
162P TRP* 1.3 62.9 + - - +
163P TRP* 3.2 20.7 + - - -
168P GLU* 3.7 24.9 - - - -
173P VAL* 6.4 0.7 - - - -
214P GLN* 2.7 51.1 + - - +
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Residues in contact with TRP 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130P VAL* 4.4 11.7 - - + -
146P LEU* 3.7 40.8 - - + -
147P VAL 4.2 1.1 - - - -
148P CYS* 3.4 41.3 - - + -
160P LEU* 3.9 7.7 - - + +
161P SER* 1.3 74.8 - - - +
163P TRP* 1.3 68.2 + - - +
164P VAL 4.2 0.9 - - - -
168P GLU* 3.3 25.0 - - - +
169P VAL* 3.6 17.1 + - + +
173P VAL* 4.0 24.7 - - + -
195P SER* 3.1 24.8 + - - -
196P ARG 4.2 1.6 - - - -
197P LEU* 3.5 41.6 - - + +
211P PHE* 4.8 3.4 - - + -
212P ARG 3.3 21.5 - - - -
213P CYS* 4.0 15.5 - - + -
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Residues in contact with TRP 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161P SER* 3.2 25.2 + - - -
162P TRP* 1.3 91.9 + - - +
164P VAL* 1.3 62.8 + - - +
166P GLY* 3.4 32.9 + - - -
167P LYS* 3.8 5.2 - - - +
168P GLU* 3.9 26.2 - - + -
210P HIS* 2.9 15.6 + - - +
212P ARG* 2.8 60.1 + - + +
214P GLN* 3.1 41.7 - - + +
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Residues in contact with VAL 164 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162P TRP 4.2 0.2 - - - -
163P TRP* 1.3 73.4 - - - +
165P ASN* 1.3 73.8 + - - +
166P GLY 2.9 9.3 + - - -
167P LYS* 3.1 24.0 + - - +
169P VAL* 4.1 24.9 - - + +
197P LEU* 4.0 18.6 - - + -
199P VAL* 5.4 1.3 - - + -
203P PHE* 3.4 38.1 - - + -
209P ASN* 4.6 2.2 - - + +
210P HIS 3.5 3.8 - - - +
211P PHE* 3.9 26.0 - - + -
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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