Contacts of the strand formed by residues 250 - 255 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G ARG* 4.9 4.2 - - - +
244H TYR* 3.6 5.0 - - - +
245H ASP* 3.1 50.1 + - - +
247H LEU* 5.9 0.4 - - - +
248H GLY 3.5 1.2 - - - -
249H GLU* 1.3 94.7 + - + +
251H ILE* 1.3 68.6 + - - +
262H LEU* 3.8 17.7 - - + -
263H TRP 3.7 8.3 - - - +
264H ARG* 4.1 16.4 - - + +
265H ILE* 3.9 3.7 - - - +
266H ASN* 5.5 2.4 - - - +
314H TRP* 3.6 38.6 - - + -
317H ASP* 4.5 8.5 + - - -
340H ILE* 4.2 9.2 - - + -
341H ASP* 3.5 27.2 + - - +
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Residues in contact with ILE 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207H LEU* 3.7 41.3 - - + -
215H LEU* 4.6 3.6 - - + -
217H LEU* 5.3 1.8 - - + -
229H PHE* 4.3 15.3 - - + -
242H ALA* 4.2 3.1 - - + -
243H ASP 3.5 9.2 - - - +
244H TYR* 4.2 13.9 - - + -
250H LYS* 1.3 80.6 - - - +
252H MET* 1.3 73.7 + - - +
262H LEU* 3.4 5.6 - - - +
263H TRP* 2.7 52.6 + - + +
265H ILE* 3.9 35.4 - - + -
314H TRP* 3.8 2.5 - - - +
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Residues in contact with MET 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242H ALA* 3.3 5.2 - - - +
243H ASP* 3.1 32.1 + - + +
251H ILE* 1.3 75.2 - - - +
253H SER* 1.3 62.3 - - - +
260H LEU* 4.3 11.7 - - + -
261H LYS 3.5 11.9 - - - -
262H LEU* 3.4 40.2 - - + -
299H PHE* 4.9 2.7 - - + -
312H VAL* 3.8 25.6 - - + +
314H TRP* 3.3 26.5 - - + +
319H ILE* 3.7 31.2 - - + -
331H TRP* 4.4 9.2 - - + -
333H PRO* 4.6 11.4 - - + -
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Residues in contact with SER 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H LEU* 4.0 19.7 - - - -
235H HIS* 2.8 26.6 + - - -
239H VAL* 4.1 2.9 - - - -
241H SER 3.6 12.8 - - - -
242H ALA* 4.1 1.3 - - - +
252H MET* 1.3 74.0 - - - +
254H CYS* 1.3 63.5 + - - +
260H LEU* 3.3 9.7 - - - +
261H LYS* 3.0 31.0 + - - +
263H TRP* 2.8 26.4 + - - -
312H VAL* 4.0 2.7 - - - -
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Residues in contact with CYS 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235H HIS* 3.8 7.2 - - - -
239H VAL* 3.6 4.9 - - - +
240H LEU 3.0 17.8 + - - -
241H SER* 3.1 29.7 + - - +
253H SER* 1.3 78.0 - - - +
255H GLY* 1.3 58.9 + - - +
259H SER 3.4 9.2 - - - +
260H LEU* 3.8 11.0 - - + -
309H VAL* 3.1 44.0 - - + -
311H CYS 3.8 4.0 - - - -
312H VAL* 3.4 22.4 - - + -
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Residues in contact with GLY 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235H HIS* 4.0 3.4 - - - -
238H GLU 3.3 12.3 - - - -
239H VAL* 4.3 1.1 - - - -
240H LEU* 3.7 5.8 - - - -
254H CYS* 1.3 78.3 - - - +
256H MET* 1.3 65.0 + - - -
257H ASP* 3.3 8.1 + - - -
258H HIS 3.4 7.1 + - - -
259H SER 3.6 6.9 + - - -
309H VAL* 2.9 33.3 + - - +
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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
------------------------------------------------------------
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