Contacts of the strand formed by residues 250 - 255 (chain B) in PDB entry 1YAA
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 250 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B ALA* 3.8 7.9 - - + +
221B PHE* 4.1 22.4 - - + -
242B VAL* 4.0 29.2 - - + +
244B LEU* 3.9 30.5 - - + +
245B SER* 6.1 0.2 - - - -
248B SER 4.0 2.7 - - - +
249B PRO* 1.3 75.6 - - - +
251B PHE* 1.3 63.1 + - - +
252B VAL* 4.1 20.4 + - + -
269B ALA* 2.9 55.1 + - - +
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Residues in contact with PHE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 4.0 22.2 - + - -
115B SER* 4.0 9.2 - - - +
118B PHE* 4.3 11.4 - + - -
119B PHE* 3.8 33.0 - + - -
218B ILE* 3.7 25.1 - - + -
219B ALA 3.1 7.6 + - - +
220B LEU* 3.3 22.5 - - + -
221B PHE 2.8 26.0 + - - -
249B PRO* 3.6 24.2 - - + -
250B VAL* 1.3 74.1 - - - +
252B VAL* 1.3 63.6 + - - +
253B CYS* 4.2 0.7 - - - -
269B HIS* 3.6 49.1 - + - +
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 3.8 22.7 - - + -
88B PHE* 4.1 16.2 - - + -
221B PHE* 3.7 6.1 - - + +
223B THR* 3.8 18.2 - - - +
240B VAL* 3.6 24.5 - - + -
250B VAL* 4.1 13.7 - - + +
251B PHE* 1.3 77.7 - - - +
253B CYS* 1.3 64.7 + - - +
254B GLN* 3.7 6.9 + - + +
269B HIS* 2.8 61.2 - - - +
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Residues in contact with CYS 253 (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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108B GLY* 4.4 4.4 - - - +
111B ALA* 3.6 39.3 - - + -
112B LEU* 3.5 27.4 - - + -
115B SER* 3.7 11.0 - - - -
220B LEU* 3.5 24.0 - - + -
221B PHE 3.1 12.1 + - - +
222B ASP* 3.8 5.8 - - - +
223B THR* 2.9 28.0 + - - +
252B VAL* 1.3 73.2 - - - +
254B GLN* 1.3 59.5 + - - +
269B PHE* 4.4 2.5 - - - -
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Residues in contact with GLN 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ALA* 3.4 18.6 + - - +
86B ILE* 3.4 9.7 - - - +
87B ILE* 3.2 36.5 - - + +
107B SER 4.2 1.7 - - - +
108B GLY* 4.2 4.9 + - - -
223B THR* 3.4 7.6 - - + +
226B GLN* 4.5 0.8 + - - +
252B VAL* 3.7 2.6 + - + -
253B CYS* 1.3 73.0 - - - +
255B SER* 1.3 64.3 + - - +
256B PHE* 3.2 36.6 - - + -
259B ASN* 5.9 1.5 - - - +
268B GLY* 3.2 4.5 - - - -
269B CYS* 2.8 75.0 + - - +
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Residues in contact with SER 255 (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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108B GLY* 3.5 13.5 - - - +
223B THR 2.9 18.1 + - - +
224B ALA* 4.1 22.9 + - - +
254B GLN* 1.3 76.7 - - - +
256B PHE* 1.3 66.4 + - - +
257B ALA* 3.1 15.9 + - - +
258B LYS* 4.7 0.9 + - - +
259B ASN* 3.8 15.9 + - - +
267B VAL 4.2 1.1 - - - -
906B PLP 2.6 30.0 + - - -
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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