Contacts of the strand formed by residues 209 - 215 (chain B) in PDB entry 2YEV
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 LEU 209 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A TYR* 3.5 27.6 - - + +
453A ASN* 4.0 9.9 - - - +
456A ILE* 6.2 0.2 - - + -
128B TRP* 3.5 7.8 - - - -
141B ASN* 4.1 1.0 - - - +
194B TYR* 4.0 16.8 - - + -
195B GLY 3.3 9.9 - - - +
196B PHE* 3.8 17.9 - - + -
206B ALA 3.7 17.9 - - - +
207B ARG* 4.2 3.6 - - - +
208B MET* 1.3 79.5 - - - +
210B PHE* 1.3 69.0 + - - +
211B ARG* 4.2 2.0 - - - +
277B ALA* 2.8 35.1 + - - +
278B GLY 3.5 21.3 - - - +
279B ILE* 4.0 16.4 - - + -
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Residues in contact with PHE 210 (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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128B TRP* 3.3 31.6 - + + -
130B PHE* 4.5 4.5 - + + -
141B ASN* 3.0 22.0 - - - +
164B PHE* 3.3 48.7 - + - -
165B TRP 3.6 5.4 - - - -
166B VAL* 3.4 23.1 - - + -
195B GLY* 2.8 39.7 + - - -
196B PHE 3.4 24.9 - - - -
209B LEU* 1.3 77.4 - - - +
211B ARG* 1.3 92.5 + - - +
212B VAL* 3.8 5.6 - - + -
278B GLY* 4.6 3.8 - - - -
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Residues in contact with ARG 211 (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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453A ASN* 4.8 0.8 - - - +
455A ASP* 4.8 4.0 + - - -
20B HIS* 4.4 13.3 + - - -
141B ASN 3.0 5.3 + - - +
142B GLU* 3.3 31.1 - - + +
143B LEU* 2.8 25.3 + - - -
192B LEU* 4.0 23.2 - - + +
193B TYR 3.2 13.7 - - - +
194B TYR* 3.3 39.4 + - - +
209B LEU* 4.2 0.2 - - - +
210B PHE* 1.3 99.0 + - - +
212B VAL* 1.3 63.8 + - - +
213B VAL* 4.8 0.2 - - + -
273B THR* 4.0 8.2 + - - +
274B SER* 3.9 13.7 + - - +
278B GLY* 2.9 41.5 + - - -
279B ILE 5.3 1.0 - - - -
280B VAL 5.4 1.2 - - - +
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Residues in contact with VAL 212 (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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143B LEU* 3.3 22.2 - - + +
145B LEU* 3.9 22.2 - - + -
164B PHE* 5.3 0.2 - - + -
166B VAL* 3.5 36.8 - - + -
169B LEU* 3.8 20.6 - - + -
185B PHE* 6.4 0.4 - - + -
191B GLY 3.5 3.3 - - - +
192B LEU* 3.7 1.0 - - - -
193B TYR* 2.8 46.8 + - + +
210B PHE* 3.8 8.7 - - + -
211B ARG* 1.3 76.9 - - - +
213B VAL* 1.3 60.9 + - - +
214B VAL* 3.7 9.1 + - + -
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Residues in contact with VAL 213 (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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142B GLU* 4.2 19.1 - - + +
143B LEU 2.7 8.8 + - - +
144B VAL* 3.3 18.6 - - + +
145B LEU 2.8 29.3 + - - +
191B GLY 3.8 2.2 - - - -
192B LEU* 3.7 20.9 - - + -
211B ARG* 4.8 0.9 - - + -
212B VAL* 1.3 70.9 - - - +
214B VAL* 1.3 58.9 + - - +
215B LEU* 4.0 9.6 - - + -
331B PHE* 3.6 44.2 - - + -
334B LEU* 3.7 20.4 - - + -
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Residues in contact with VAL 214 (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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145B LEU* 3.4 5.6 - - + +
147B ALA* 3.8 25.8 - - + +
169B LEU* 4.2 4.0 - - + -
187B PRO* 4.0 25.8 - - + -
189B GLU 3.7 15.7 - - - +
190B PRO* 3.2 11.6 - - + +
191B GLY* 2.9 36.5 + - - +
193B TYR* 3.8 22.2 - - + -
212B VAL* 4.0 15.7 - - + -
213B VAL* 1.3 73.9 - - - +
215B LEU* 1.3 65.9 + - - +
334B LEU* 4.1 3.1 - - - +
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Residues in contact with LEU 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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144B VAL* 3.6 25.8 - - + -
145B LEU 2.9 9.7 + - - +
146B PRO* 3.5 2.1 - - - +
147B ALA* 2.7 35.8 + - - -
190B PRO* 4.7 1.1 - - - -
213B VAL* 4.0 6.3 - - + -
214B VAL* 1.3 73.9 - - - +
216B PRO* 1.3 73.9 - - + +
219B GLU* 3.9 36.6 - - + +
220B PHE* 4.1 14.1 - - + +
223B PHE* 4.6 4.3 - - + -
329B PHE* 4.8 0.2 - - + -
331B PHE* 3.7 28.9 - - + -
334B LEU* 4.0 28.5 - - + -
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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