Contacts of the strand formed by residues 260 - 263 (chain B) in PDB entry 2B5L
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 CYS 260 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B MET* 5.4 2.2 - - - -
258B ILE* 3.7 7.5 - - - +
259B VAL* 1.3 80.9 - - - +
261B HIS* 1.3 64.1 + - - +
273B LEU* 3.3 3.8 - - - -
274B GLY* 2.9 36.5 + - - -
311B ALA* 3.8 26.2 - - - -
312B GLU 3.4 20.9 - - - +
313B CYS* 4.1 6.3 - - - -
314B LEU* 3.7 31.2 - - + -
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Residues in contact with HIS 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LYS* 5.2 12.1 + - - -
218B MET* 4.2 25.6 - - + -
219B VAL 5.3 0.6 + - - -
220B ILE* 3.4 49.0 - - + +
232B ILE* 5.5 0.4 - - + -
258B ILE* 5.6 0.4 - - + -
260B CYS* 1.3 75.1 - - - +
262B ASN* 1.3 77.6 + - - +
263B ARG* 4.8 2.5 - - + -
271B TYR* 4.3 1.9 - + + -
272B LEU 2.9 9.0 - - - -
273B LEU* 3.3 24.7 - - + -
314B LEU* 4.3 6.2 + - - +
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Residues in contact with ASN 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B THR* 5.7 3.1 - - - +
261B HIS* 1.3 86.4 + - - +
263B ARG* 1.3 78.7 + - - +
264B VAL* 3.6 0.5 + - - +
271B TYR* 3.2 7.3 - - - -
272B LEU* 2.7 38.6 + - + +
314B LEU* 3.1 27.6 - - + +
315B THR* 3.1 17.6 - - - +
316B TYR* 2.8 37.0 + - - +
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Residues in contact with ARG 263 (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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171B TYR* 2.8 35.6 + - - -
221B ALA 5.2 1.4 + - - -
223B PRO* 3.2 34.2 - - - +
261B HIS* 4.4 2.2 + - + -
262B ASN* 1.3 88.9 + - - +
264B VAL* 1.3 64.1 + - - +
265B ASP 3.5 19.7 - - - +
266B PRO* 3.7 18.1 + - - +
268B GLY* 3.7 1.1 - - - -
270B ARG 4.1 1.8 - - - +
271B TYR* 3.3 33.9 + - + -
316B TYR* 4.4 2.3 - - - +
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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
------------------------------------------------------------
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