Contacts of the strand formed by residues 244 - 248 (chain B) in PDB entry 5AYZ
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 ALA 244 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B ASP 3.2 7.7 + - - +
218B LEU* 3.4 28.8 - - + +
219B VAL 3.0 25.1 + - - -
237B LYS* 3.7 1.8 - - - +
242B SER 3.8 3.0 + - - -
243B VAL* 1.3 76.7 - - - +
245B VAL* 1.3 61.2 + - - +
265B ASP* 3.3 21.5 - - + +
266B VAL* 5.8 0.9 - - + -
194C PHE* 6.2 2.0 - - + -
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 5.7 0.2 - - - -
219B VAL* 3.4 9.9 - - + +
221B LEU* 3.8 29.4 - - + -
233B ALA* 4.1 2.9 - - + -
236B LEU* 4.3 26.7 - - + -
237B LYS* 4.4 8.1 - - + -
243B VAL* 4.2 11.4 - - + +
244B ALA* 1.3 78.5 - - - +
246B GLU* 1.3 65.2 - - - +
263B HIS 3.6 24.7 - - - +
264B ILE* 3.8 11.0 - - + -
265B ASP* 2.8 37.7 + - - +
266B VAL* 3.2 5.9 + - - -
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Residues in contact with GLU 246 (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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160B HIS* 2.9 25.1 + - - -
199B GLU* 2.6 33.5 - - - +
218B LEU* 4.6 2.8 - - + +
219B VAL 2.9 6.1 + - - +
220B LEU* 3.8 13.8 - - + +
221B LEU* 2.7 34.8 + - - +
244B ALA 4.2 0.2 - - - -
245B VAL* 1.3 79.7 - - - +
247B ALA* 1.3 67.1 + - - +
264B ILE* 4.6 0.2 - - - -
266B VAL* 3.2 33.5 - - + +
268B SER* 2.9 30.0 + - - +
401B NCN 3.6 4.3 - - - -
194C PHE* 3.9 4.7 - - - -
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B LEU 3.6 4.7 - - - +
229B LEU* 3.8 35.7 - - + -
246B GLU* 1.3 75.1 - - - +
248B SER* 1.3 61.4 + - - +
251B ILE* 3.8 14.0 - - + +
259B PHE* 4.8 1.6 - - + -
264B ILE* 4.0 15.2 - - + +
266B VAL 2.9 7.8 + - - +
267B ILE* 3.4 7.7 - - + -
268B SER 3.1 24.8 + - - -
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Residues in contact with SER 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 3.5 19.1 - - - -
221B LEU 3.2 8.7 + - - +
222B ASP* 3.4 4.1 - - - -
223B ASN* 2.8 30.3 + - - -
224B PHE 4.8 0.5 + - - -
246B GLU* 4.6 0.2 - - - -
247B ALA* 1.3 74.0 - - - +
249B GLY* 1.3 52.2 + - - +
251B ILE* 3.8 7.3 - - - +
259B PHE* 6.0 0.3 - - - -
268B SER* 2.6 36.6 + - - -
401B NCN 3.0 35.5 - - - -
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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