Contacts of the strand formed by residues 250 - 255 (chain B) in PDB entry 2AY6
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
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Residue Dist Surf HB Arom Phob DC
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218B LEU* 3.8 5.8 - - - -
219B PRO* 3.8 15.5 - - + +
221B ILE* 4.2 5.6 - - + -
240B THR 6.0 0.4 - - - +
243B ILE* 4.0 17.0 - - + -
244B ALA* 4.2 15.9 - - + +
247B ILE* 3.7 16.4 - - + +
249B GLU* 1.3 78.4 - - - +
251B LEU* 1.3 79.4 + - - +
252B ILE* 4.0 15.7 - - + -
273B LEU* 2.8 63.4 + - + +
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Residues in contact with LEU 251 (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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6A LEU* 3.9 28.9 - - + -
115B ALA* 4.0 16.4 - - + +
118B LEU* 4.8 10.8 - - + -
119B ALA* 4.6 3.6 - - + +
185B MET* 3.6 29.4 - - + -
218B LEU* 4.1 16.1 - - + +
219B PRO 3.1 10.4 + - - +
220B LEU* 3.3 17.6 - - + -
221B ILE 2.9 24.1 + - - -
250B VAL* 1.3 85.1 - - - +
252B ILE* 1.3 63.5 + - - +
270B LEU* 4.3 11.4 - - + -
271B LEU 3.3 3.1 - - - +
272B ALA* 4.1 11.2 - - + -
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Residues in contact with ILE 252 (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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87B ILE* 4.2 8.1 - - + -
88B LEU* 3.8 22.0 - - + -
221B ILE* 3.5 17.3 - - + +
223B LEU* 4.3 20.0 - - + -
240B THR* 3.5 28.7 - - + +
244B ALA* 5.4 0.9 - - + -
250B VAL* 4.0 13.0 - - + -
251B LEU* 1.3 78.4 - - - +
253B ALA* 1.3 62.9 + - - +
254B ALA 3.8 1.7 + - - +
269B CYS 3.7 1.0 - - - +
270B LEU* 3.4 6.4 - - - +
271B LEU* 2.8 63.9 + - + +
273B LEU* 4.1 14.1 - - + -
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Residues in contact with ALA 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* 4.5 2.5 - - - +
111B ALA* 3.9 25.6 - - + +
112B LEU* 3.7 31.2 - - + +
220B LEU* 4.7 4.6 - - + +
221B ILE 2.8 11.5 + - - +
222B ASP* 3.7 3.6 - - - +
223B LEU* 2.8 28.5 + - - +
251B LEU 4.2 0.6 - - - -
252B ILE* 1.3 70.8 - - - +
254B ALA* 1.3 61.0 + - - +
269B CYS 3.8 4.5 - - - -
270B LEU* 4.3 5.1 - - + +
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Residues in contact with ALA 254 (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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83B MET* 4.0 15.5 - - + -
87B ILE* 3.5 32.3 - - + -
108B GLY* 3.7 9.2 - - - -
111B ALA* 4.5 0.6 - - - +
223B LEU* 3.3 13.2 - - + +
252B ILE* 3.8 2.2 + - + +
253B ALA* 1.3 74.1 - - - +
255B SER* 1.3 60.6 + - - +
268B GLY* 3.1 5.2 - - - -
269B CYS* 2.9 38.3 + - - +
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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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83B MET* 5.6 0.6 - - - +
108B GLY* 3.8 8.3 - - - +
223B LEU 3.0 11.4 + - - +
224B ALA* 3.9 26.2 + - - +
254B ALA* 1.3 75.0 - - - +
256B CYS* 1.3 63.3 + - - +
257B SER* 3.3 11.4 + - - -
258B LYS 4.6 0.3 + - - -
259B ASN* 3.7 16.3 + - - +
267B THR 4.2 0.7 - - - -
413B PLP 2.6 45.0 + - - +
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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