Contacts of the strand formed by residues 217 - 222 (chain B) in PDB entry 4CY1
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 217 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B SER* 2.6 23.7 + - - -
189B SER* 3.5 24.7 - - - -
190B SER 3.0 21.3 + - - +
191B TYR* 4.0 3.0 + - - -
193B GLY 3.5 31.0 - - - +
194B LEU 3.9 7.2 - - - +
195B CYS* 3.8 15.5 - - - -
215B PRO 3.8 5.8 - - - +
216B PRO* 1.3 70.7 - - - +
218B SER* 1.3 53.6 + - - +
219B PHE 3.7 9.9 - - - +
231B ALA* 4.3 6.1 - - + -
232B ALA 3.3 16.6 - - - +
233B THR* 3.9 9.2 - - + -
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Residues in contact with SER 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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175B SER* 3.5 13.5 - - - +
191B TYR* 4.7 1.3 - - - -
216B PRO 3.7 1.0 + - - -
217B VAL* 1.3 72.3 - - - +
219B PHE* 1.3 62.4 + - - +
232B ALA* 2.8 24.6 + - - +
233B THR 4.0 0.7 + - - -
234B LEU* 3.5 36.1 - - - +
257B ASN* 3.8 5.7 + - - -
260B TYR 3.9 5.4 - - - -
261B CYS* 3.2 40.7 - - - +
262B ILE 4.9 0.5 + - - -
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Residues in contact with PHE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B SER* 3.9 0.6 + - - -
176B ALA* 4.0 11.9 - - + -
189B SER* 3.8 7.2 - - - -
217B VAL* 3.6 4.4 - - - +
218B SER* 1.3 81.6 + - - +
220B VAL* 1.3 92.7 + - - +
221B LYS* 3.8 24.5 - - + -
230B LEU* 4.5 4.9 - - + -
231B ALA* 3.3 1.7 - - - -
232B ALA* 2.8 33.8 + - + +
262B ILE 3.5 18.6 - - - +
263B PHE* 3.4 37.7 - + - -
264B ALA* 3.3 44.9 - - + -
592C ARG* 5.1 5.4 - - - -
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Residues in contact with VAL 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ALA* 3.5 17.2 - - + +
177B VAL 5.2 0.2 - - - +
178B HIS* 4.3 7.4 - - - +
187B VAL* 3.8 31.6 - - + +
188B SER 3.8 7.4 - - - -
189B SER* 3.4 35.0 - - - +
195B CYS* 4.0 9.6 - - - -
219B PHE* 1.3 85.7 - - - +
221B LYS* 1.3 68.3 + - - +
229B ILE* 3.8 21.5 - - + -
230B LEU 3.1 13.7 - - - +
231B ALA* 4.1 2.7 - - + -
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Residues in contact with LYS 221 (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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178B HIS* 3.8 34.3 - - + +
187B VAL* 4.2 2.0 - - - -
219B PHE* 3.8 16.5 - - + -
220B VAL* 1.3 77.3 - - - +
222B PHE* 1.3 71.4 + - - +
229B ILE* 3.2 6.2 - - - -
230B LEU* 2.8 37.0 + - + +
264B ALA 3.4 22.4 + - - +
265B ASN* 3.7 26.6 + - - +
266B PHE* 4.4 14.6 - - + +
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Residues in contact with PHE 222 (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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178B HIS* 3.1 41.8 + - + +
179B PHE 3.6 4.7 - - - -
180B ASN* 3.5 44.0 - - + -
185B LEU* 3.9 17.0 - - + -
187B VAL* 3.6 24.9 - - + -
197B ILE* 4.0 9.0 - - + -
221B LYS* 1.3 88.4 - - - +
223B SER* 1.3 69.8 + - - +
224B PRO* 3.9 1.2 - - - +
226B GLY* 4.8 4.3 - - - -
228B TYR 3.4 3.6 - - - -
229B ILE* 3.5 18.6 - - + -
243B TYR* 3.6 37.5 - + - -
266B PHE* 4.0 2.8 - - - -
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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