Contacts of the strand formed by residues 254 - 258 (chain B) in PDB entry 1YFL
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 GLU 254 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 5.0 11.2 - - + -
174B TYR* 6.6 0.2 - - + -
210B SER* 6.2 0.7 - - - +
211B ASN 3.8 4.7 - - - -
212B VAL* 4.0 8.7 - - + -
234B HIS* 3.4 0.7 - - - -
235B LEU* 2.5 48.7 + - + +
236B ASN* 3.9 16.2 - - - +
252B THR 3.4 5.1 + - - +
253B ASP* 1.3 71.8 + - - +
255B VAL* 1.3 56.2 + - - +
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B SER* 3.3 19.6 + - - -
211B ASN* 3.0 32.3 + - + +
213B LEU* 4.0 21.3 - - + -
232B VAL* 4.8 5.8 - - + -
234B HIS* 3.1 46.0 - - + +
235B LEU* 3.7 6.5 - - - +
253B ASP* 3.5 11.0 - - - +
254B GLU* 1.3 79.6 - - - +
256B TYR* 1.3 60.8 + - - +
257B ILE* 3.9 26.0 - - + -
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Residues in contact with TYR 256 (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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18B LEU* 3.5 36.8 - - + -
21B HIS* 3.3 41.5 + + + +
22B PHE* 3.9 11.5 - + - -
167B PHE* 3.4 16.5 - - - -
169B TYR* 4.3 5.4 - + - -
208B GLY* 3.3 38.5 - - - -
209B LEU 3.3 15.9 - - - -
210B SER* 4.1 2.7 - - - +
232B VAL* 3.3 1.1 - - - -
233B LYS* 3.2 29.5 + - + +
235B LEU* 4.0 10.0 - - + +
255B VAL* 1.3 76.8 - - - +
257B ILE* 1.3 59.6 + - - +
258B PHE* 3.3 34.2 - + + +
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Residues in contact with ILE 257 (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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207B PHE* 4.3 3.3 - - + -
209B LEU* 2.8 58.6 + - + +
211B ASN* 5.2 2.9 - - + -
213B LEU* 4.4 9.2 - - + -
223B LEU* 4.9 8.3 - - + +
226B TRP* 4.0 24.2 - - + -
227B SER* 3.8 30.5 - - - +
230B TYR* 4.2 7.9 - - + -
231B ASN 3.6 16.8 - - - +
232B VAL* 4.0 10.8 - - + -
255B VAL* 3.9 24.5 - - + -
256B TYR* 1.3 72.0 - - - +
258B PHE* 1.3 63.5 + - - +
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Residues in contact with PHE 258 (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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21B HIS* 4.0 32.8 - + + -
207B PHE* 3.4 22.4 - - - +
230B TYR* 3.4 6.2 - - - +
231B ASN* 2.9 67.3 + - + +
232B VAL 3.9 10.8 - - - -
233B LYS* 4.4 3.8 - - + -
256B TYR* 3.3 47.1 - + + +
257B ILE* 1.3 78.3 - - - +
259B ASN* 1.3 85.6 - - - +
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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