Contacts of the strand formed by residues 150 - 157 (chain B) in PDB entry 5NET
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 PHE 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B VAL* 3.5 13.7 - - + -
115B LEU* 3.7 29.4 - - + -
139B LEU* 3.8 19.3 - - + -
140B SER* 3.6 42.8 + - - +
143B MET* 3.6 42.8 - - + +
144B SER* 6.0 0.4 - - - -
147B THR* 4.8 9.4 - - - +
148B SER 4.0 2.4 + - - -
149B ASN* 1.3 74.8 - - - +
151B ARG* 1.3 66.1 + - - +
152B LEU* 3.5 34.4 - - + +
197B THR 4.2 2.1 - - - +
198B ASN* 3.7 16.5 + - - +
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Residues in contact with ARG 151 (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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113B VAL 3.2 7.2 + - - +
114B ASP* 3.6 12.7 + - - +
115B LEU* 2.9 31.2 + - - +
149B ASN* 5.1 4.0 - - + +
150B PHE* 1.3 81.9 - - - +
152B LEU* 1.3 63.1 + - - +
196B LEU* 3.2 37.6 + - + +
197B THR* 3.2 16.5 - - - +
198B ASN* 3.5 22.4 - - - +
237B GLY* 2.4 33.5 + - - -
239B ARG* 3.1 55.9 - - - +
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Residues in contact with LEU 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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115B LEU* 3.4 7.6 - - + +
136B GLY* 4.0 18.8 - - - +
139B LEU* 3.8 27.4 - - + -
140B SER* 4.2 11.2 - - - +
150B PHE* 3.5 38.1 - - + +
151B ARG* 1.3 72.3 - - - +
153B GLY* 1.3 59.9 + - - +
194B LEU* 3.9 12.8 - - - +
196B LEU* 3.1 15.0 - - - -
197B THR* 3.1 18.2 + - - +
198B ASN 5.1 0.9 - - - +
199B ASP 5.6 0.4 - - - -
200B ALA* 4.2 17.7 - - + +
203B PHE* 3.6 32.8 - - + -
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Residues in contact with GLY 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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115B LEU 2.7 14.1 + - - +
116B TYR* 3.9 9.0 - - - -
117B TYR* 3.3 16.8 + - - +
152B LEU* 1.3 74.3 - - - +
154B PHE* 1.3 59.5 + - - -
194B LEU* 3.2 14.6 - - - -
196B LEU* 3.4 13.1 - - - +
203B PHE* 3.1 20.8 - - - -
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Residues in contact with PHE 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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116B TYR* 2.9 17.4 + - - -
117B TYR* 3.4 39.9 - + - -
119B MET* 3.5 28.0 - - + -
121B LEU* 5.5 0.7 - - + -
153B GLY* 1.3 74.8 - - - +
155B GLY* 1.3 80.5 + - - +
156B SER* 4.5 4.3 - - - -
192B HIS* 3.6 0.2 + - - -
193B ILE* 3.1 33.5 + - + -
194B LEU* 2.8 44.1 + - + +
203B PHE* 4.0 20.0 - + + -
206B ILE* 3.9 15.0 - - + -
207B VAL* 5.0 9.0 - - + -
210B GLN* 4.0 21.1 - - + -
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Residues in contact with GLY 155 (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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116B TYR* 3.2 20.2 + - - -
117B TYR 3.0 9.0 + - - +
118B LEU* 3.9 6.5 - - - -
119B MET 3.1 19.9 + - - -
154B PHE* 1.3 88.8 - - - +
156B SER* 1.3 63.3 + - - -
190B PHE* 4.1 2.0 - - - -
191B LYS 3.4 9.6 - - - -
193B ILE 4.2 0.2 - - - -
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Residues in contact with SER 156 (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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118B LEU* 4.1 1.2 - - - +
119B MET 3.3 8.7 - - - +
121B LEU* 3.6 30.1 - - - +
154B PHE* 4.5 7.6 - - - -
155B GLY* 1.3 76.2 - - - -
157B PHE* 1.3 64.7 + - - +
188B PHE* 3.4 15.7 - - - -
190B PHE* 3.0 9.2 - - - -
191B LYS* 3.0 37.8 + - - +
193B ILE* 3.7 12.0 - - - +
210B GLN* 4.5 0.5 + - - -
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.8 27.8 - - + -
119B MET 3.2 9.0 + - - -
120B ASP* 3.2 47.0 - - + -
121B LEU* 2.9 25.6 + - - -
156B SER* 1.3 76.9 - - - +
158B VAL* 1.3 72.4 + - - +
188B PHE* 4.0 2.7 - - - -
189B GLY 3.2 15.9 - - - +
220B GLU* 4.2 5.6 - - + -
221B GLY 4.2 2.2 - - - +
222B GLY* 3.5 24.9 - - - -
225B ALA* 3.8 17.9 - - + -
248B PHE* 3.5 35.2 - + - -
249B VAL 4.2 0.2 - - - -
250B SER* 4.1 4.7 - - - -
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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