Contacts of the strand formed by residues 214 - 219 (chain B) in PDB entry 2WNU
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 ILE 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B SER* 3.9 6.7 - - - -
99B ALA 3.4 14.6 - - - +
100B THR* 3.8 12.1 - - + -
115B PHE* 3.8 5.2 - - - -
119B ILE* 4.3 9.2 - - + -
145B TYR* 3.1 8.3 - - - +
146B HIS* 2.9 47.3 + - + +
212B ASN 4.2 0.6 - - - -
213B SER* 1.3 74.2 - - - +
215B PHE* 1.3 62.4 + - - +
216B SER* 3.7 18.8 - - - +
162C VAL* 4.5 4.3 - - + -
164C PHE* 3.7 20.0 - - + -
178C GLY 3.4 28.3 - - - +
179C VAL* 3.9 21.8 - - + -
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Residues in contact with PHE 215 (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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97B PHE* 3.7 30.8 - + + -
98B SER* 3.4 1.0 - - - -
99B ALA* 2.9 31.4 + - + +
115B PHE* 3.6 40.4 - + + -
126B TYR* 4.2 4.3 - + - -
131B GLY 3.9 19.3 - - - -
143B PHE* 4.1 17.7 - + + -
144B THR 3.3 23.1 - - - -
145B TYR* 4.2 0.2 - - + -
157B LEU* 5.0 0.9 - - + -
195B VAL* 4.2 11.0 - - + -
196B PHE* 4.1 18.8 - - - -
197B LEU* 4.1 29.2 - - + -
214B ILE* 1.3 73.2 - - - +
216B SER* 1.3 73.1 + - - +
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Residues in contact with SER 216 (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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97B PHE* 2.9 17.0 - - - -
98B SER* 2.7 22.5 + - - -
143B PHE* 3.7 1.6 - - - -
144B THR* 2.9 50.0 + - - +
145B TYR* 4.8 0.2 - - - +
214B ILE* 3.7 13.9 - - - +
215B PHE* 1.3 80.9 + - - +
217B GLY* 1.3 58.8 + - - +
218B PHE* 5.8 0.2 - - - -
139C TYR* 5.2 2.7 - - - -
178C GLY 4.7 1.6 + - - -
179C VAL* 4.5 4.7 + - - -
180C LEU* 3.8 10.5 - - - -
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Residues in contact with GLY 217 (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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95B ILE* 6.4 0.2 - - - -
96B ALA* 3.2 2.4 - - - -
97B PHE* 2.8 51.9 + - - -
133B PHE* 6.2 0.4 - - - -
141B TYR* 5.4 0.9 - - - -
142B TYR 3.1 12.3 - - - -
143B PHE* 3.9 6.5 - - - -
216B SER* 1.3 76.3 - - - +
218B PHE* 1.3 66.0 + - - +
180C LEU* 3.4 1.6 - - - +
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Residues in contact with PHE 218 (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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217A PHE* 3.9 14.1 - + - -
95B ILE* 3.4 6.1 - - - +
96B ALA* 3.7 18.4 - - + -
141B TYR* 3.2 11.7 - - - +
142B TYR* 2.9 67.0 + + + -
144B THR* 5.3 1.6 - - + -
216B SER 5.6 0.2 - - - -
217B GLY* 1.3 77.5 - - - +
219B LEU* 1.3 69.1 + - - +
220B LEU* 3.5 22.9 - - + -
139C TYR* 4.0 28.9 - + - -
180C LEU* 3.6 17.5 - - + -
212C PHE* 4.4 0.9 - + - -
214C LEU* 3.3 37.5 - - + -
215C PHE* 4.8 1.6 - - + -
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Residues in contact with LEU 219 (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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93B GLN* 3.3 32.1 - - + +
95B ILE* 3.0 24.5 + - + +
137B VAL* 4.7 2.7 - - + +
139B GLY* 4.6 0.9 - - - -
140B LEU 3.5 8.1 - - - +
141B TYR* 3.6 36.4 - - + +
218B PHE* 1.3 78.3 - - - +
220B LEU* 1.3 61.4 + - - +
221B PHE 3.5 31.0 - - - +
222B PRO* 3.7 27.8 - - + -
214C LEU* 4.5 3.1 - - - +
215C PHE* 3.3 26.1 - - + -
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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