Contacts of the strand formed by residues 250 - 255 (chain B) in PDB entry 5LS6
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 LYS 250 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ARG* 5.5 1.6 - - - +
244B TYR* 3.6 2.9 - - - +
245B ASP* 2.9 53.6 + - - +
248B GLY 3.6 2.0 - - - -
249B GLU* 1.3 95.2 + - - +
251B ILE* 1.3 63.3 + - - +
262B LEU* 3.8 19.5 - - + -
263B TRP 3.6 9.0 - - - +
264B ARG* 4.0 20.4 - - + +
265B ILE* 3.7 4.4 - - - +
266B ASN* 5.5 1.5 - - - +
314B TRP* 3.5 27.4 + - + -
317B ASP* 4.4 12.5 + - - -
340B ILE* 4.0 22.4 - - + -
341B ASP* 3.5 23.3 + - - -
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Residues in contact with ILE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B LEU* 3.5 48.5 - - + -
215B LEU* 4.0 12.8 - - + -
217B LEU* 5.0 3.1 - - + -
229B PHE* 4.2 12.6 - - + -
242B ALA* 3.9 15.0 - - + -
243B ASP 3.5 5.4 - - - +
244B TYR* 4.1 23.8 - - + -
250B LYS* 1.3 77.4 - - - +
252B MET* 1.3 61.9 + - - +
262B LEU* 3.4 4.7 - - - +
263B TRP* 2.6 50.3 + - + +
265B ILE* 4.2 23.1 - - + -
314B TRP* 4.0 0.7 - - - -
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Residues in contact with MET 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B ALA* 3.2 1.7 - - - -
243B ASP* 3.0 30.6 + - - +
251B ILE* 1.3 72.4 - - - +
253B SER* 1.3 61.7 + - - +
260B LEU* 4.2 9.6 - - + -
261B LYS* 3.4 37.9 - - - +
262B LEU* 3.9 16.4 - - + -
299B PHE* 4.9 2.9 - - + -
312B VAL* 3.6 27.5 - - + +
313B ARG 6.2 0.2 - - - -
314B TRP* 3.4 29.5 - - + +
319B ILE* 3.3 32.1 - - + -
331B TRP* 3.8 17.3 - - + -
333B PRO* 4.5 9.9 - - + -
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Residues in contact with SER 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 3.4 30.1 - - - +
235B HIS* 3.1 14.3 + - - -
239B VAL* 4.3 2.0 - - - -
241B SER 3.3 11.9 - - - -
242B ALA* 3.5 3.1 - - - +
251B ILE* 4.1 0.6 - - - -
252B MET* 1.3 74.6 - - - +
254B CYS* 1.3 60.8 + - - +
260B LEU* 3.2 5.4 - - - +
261B LYS 2.6 40.8 + - - -
263B TRP* 2.9 26.6 + - - -
312B VAL* 4.2 2.0 - - - -
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Residues in contact with CYS 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B HIS* 3.8 7.2 - - - -
239B VAL* 3.1 11.3 - - - +
240B LEU 2.9 17.5 + - - -
241B SER* 2.9 24.7 + - - +
253B SER* 1.3 77.8 - - - +
255B GLY* 1.3 59.3 + - - +
259B SER 3.4 13.7 - - - +
260B LEU* 3.8 17.9 - - + -
309B VAL* 3.3 34.1 - - + -
311B CYS 4.3 0.2 - - - -
312B VAL* 3.5 23.3 - - - -
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Residues in contact with GLY 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B HIS* 4.6 1.1 - - - -
238B GLU 3.0 12.8 - - - -
239B VAL* 3.9 0.9 - - - -
240B LEU* 3.5 8.5 - - - -
254B CYS* 1.3 80.2 - - - +
256B MET* 1.3 66.2 + - - -
257B ASP* 3.4 7.4 - - - +
258B HIS* 3.4 7.4 + - - -
259B SER 3.6 5.3 + - - -
309B VAL* 3.1 31.0 + - - +
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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
------------------------------------------------------------
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