Contacts of the strand formed by residues 239 - 245 (chain B) in PDB entry 2YVL
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 239 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A TYR* 3.5 44.0 + + - -
227A PHE* 4.2 10.7 - + - -
188B PHE 3.7 1.7 - - - +
189B LEU* 3.8 0.2 - - - -
190B LEU* 2.8 44.9 + - - +
191B PRO 3.7 12.8 - - - -
192B THR* 3.9 8.7 - - - -
193B ALA* 3.6 32.1 - - + +
196B VAL* 3.6 19.1 - - + -
212B VAL* 4.3 9.6 - - + -
213B VAL 4.0 3.6 - - - -
214B GLU* 4.1 11.2 - - + -
236B HIS* 3.8 11.2 - + - -
238B ALA* 1.3 72.9 - - - +
240B LEU* 1.3 63.0 + - - +
241B VAL* 4.7 0.4 - - - +
239C TYR* 4.9 2.6 + - - -
220D TYR* 4.0 10.2 + - - -
227D PHE* 5.5 0.3 - - - -
228D ARG* 4.5 1.1 - - + -
229D PRO* 3.5 21.1 - - + +
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Residues in contact with LEU 240 (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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79B ASP* 4.0 21.8 - - + +
82B TYR* 4.6 1.3 - - + -
83B ILE* 4.0 25.6 - - + -
163B PHE* 4.7 0.7 - - + -
188B PHE 3.5 6.1 - - - +
189B LEU* 3.7 31.0 - - + -
211B GLU 3.7 0.9 - - - +
212B VAL* 3.3 6.1 - - - +
213B VAL* 2.9 42.7 + - + +
214B GLU* 5.6 0.2 - - - -
215B ILE* 3.8 32.8 - - + +
238B ALA 4.3 6.3 - - - +
239B TYR* 1.3 78.1 - - - +
241B VAL* 1.3 61.5 + - - +
242B PHE* 3.7 21.0 + - + -
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Residues in contact with VAL 241 (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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187B GLY* 3.1 4.7 - - - -
188B PHE* 2.7 54.8 + - + +
190B LEU* 4.4 10.1 - - + -
196B VAL* 4.3 19.3 - - + -
199B LEU* 4.0 25.6 - - + -
200B LEU* 4.9 10.5 - - + -
203B ILE* 5.1 6.1 - - + -
210B LEU* 5.3 3.8 - - + -
211B GLU 3.5 8.3 - - - +
212B VAL* 4.2 19.7 - - + -
239B TYR 4.7 1.8 - - - +
240B LEU* 1.3 78.5 - - - +
242B PHE* 1.3 70.5 + - - +
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Residues in contact with PHE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 3.9 19.3 - + - -
83B ILE* 3.8 29.4 - - + -
86B LYS* 3.7 43.5 - - + -
87B LEU* 4.2 14.8 - - + -
163B PHE* 4.3 8.1 - + - -
186B VAL* 3.2 7.2 - - - +
187B GLY* 3.7 22.7 - - - -
188B PHE* 5.7 0.7 - - - -
203B ILE* 6.4 0.2 - - - -
209B ASN 3.7 1.5 - - - +
210B LEU* 3.4 7.4 - - - +
211B GLU* 2.9 44.0 + - + +
213B VAL* 4.2 8.3 - - + -
240B LEU* 3.7 28.3 - - + -
241B VAL* 1.3 78.8 - - - +
243B GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 243 (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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185B PRO* 3.4 6.4 - - - +
186B VAL* 2.9 40.7 + - - +
203B ILE* 5.9 0.2 - - - -
207B PHE* 4.5 1.6 - - - -
208B GLY 3.3 12.3 - - - -
209B ASN 3.9 3.1 - - - -
210B LEU* 4.2 8.5 - - - -
242B PHE* 1.3 76.6 - - - +
244B ARG* 1.3 67.7 + - - +
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Residues in contact with ARG 244 (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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11A LEU* 5.2 0.2 - - - +
46A GLU* 2.9 15.4 + - - -
56A TYR* 3.3 36.8 + - + +
57A ARG* 2.8 29.1 + - - +
58A PRO 5.2 0.2 - - - -
59A THR* 3.6 15.8 - - - +
62A GLU* 3.5 21.8 + - - -
183B GLY 2.7 26.4 + - - -
184B ALA 3.4 4.0 - - - -
185B PRO* 3.8 23.1 - - - +
207B PHE* 3.2 5.6 - - - +
208B GLY* 2.8 30.7 + - - +
209B ASN* 4.0 23.4 - - + +
243B GLY* 1.3 82.2 - - - -
245B LYS* 1.3 64.1 + - - +
246B LEU 3.2 0.3 + - - -
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Residues in contact with LYS 245 (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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47A GLY* 3.6 4.3 - - - -
56A TYR* 3.6 8.9 - - - -
177B HIS* 2.8 55.7 + - + +
178B LYS* 4.4 6.9 + - - +
180B LEU* 2.7 26.8 + - + +
181B MET 3.4 17.3 - - - +
182B GLU* 3.3 29.7 + - - +
183B GLY* 3.6 17.0 + - - +
184B ALA 2.8 27.9 + - - +
207B PHE* 3.5 16.2 - - + -
244B ARG* 1.3 71.6 - - - +
246B LEU* 1.3 65.4 + - - +
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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