Contacts of the strand formed by residues 250 - 255 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ARG* 5.0 1.2 - - - +
244E TYR* 3.5 5.6 - - - +
245E ASP* 3.0 55.7 + - - -
247E LEU* 6.3 0.2 - - - +
248E GLY 3.7 0.6 - - - -
249E GLU* 1.3 87.8 + - + +
251E ILE* 1.3 63.2 + - - +
262E LEU* 4.0 16.6 - - + -
263E TRP 3.6 6.5 - - - -
264E ARG* 4.1 25.6 - - + +
265E ILE* 4.2 2.9 - - - +
266E ASN* 5.8 0.9 - - - +
314E TRP* 3.3 40.3 + - + -
317E ASP* 3.6 14.4 + - - -
340E ILE* 3.8 15.0 - - + -
341E ASP* 3.6 17.2 + - - +
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Residues in contact with ILE 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E LEU* 3.8 40.2 - - + -
215E LEU* 4.4 7.9 - - + -
217E LEU* 5.3 2.2 - - + -
229E PHE* 4.4 23.6 - - + -
242E ALA* 3.9 5.6 - - + -
243E ASP 3.4 9.9 - - - +
244E TYR* 4.1 26.0 - - + -
250E LYS* 1.3 79.2 - - - +
252E MET* 1.3 78.5 + - - +
262E LEU* 3.4 8.0 - - - +
263E TRP* 2.8 46.9 + - + +
265E ILE* 4.6 9.6 - - + -
314E TRP* 3.9 2.2 - - - -
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Residues in contact with MET 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E ALA* 3.3 0.9 - - - -
243E ASP* 3.1 31.4 + - + +
251E ILE* 1.3 80.2 - - - +
253E SER* 1.3 61.3 - - - +
260E LEU* 4.3 12.8 - - + +
261E LYS 3.6 29.6 - - - +
262E LEU* 3.8 22.9 - - + -
299E PHE* 5.1 2.5 - - + +
312E VAL* 3.6 26.4 - - + +
313E ARG 6.1 0.2 - - - -
314E TRP* 3.3 21.0 - - + +
319E ILE* 3.3 38.1 - - + -
331E TRP* 4.0 9.9 - - + -
333E PRO* 4.6 11.0 - - + -
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Residues in contact with SER 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E LEU* 3.9 10.2 - - - +
235E HIS* 2.8 22.8 + - - -
239E VAL* 4.5 2.9 - - - -
241E SER 3.5 12.8 - - - -
242E ALA* 3.8 9.2 - - - -
252E MET* 1.3 79.1 - - - +
254E CYS* 1.3 60.9 + - - +
259E SER 3.8 0.3 - - - +
260E LEU* 3.0 7.9 - - - +
261E LYS 2.8 36.3 + - - -
263E TRP* 3.0 24.3 + - - -
312E VAL* 3.9 4.0 - - - -
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Residues in contact with CYS 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235E HIS* 3.7 6.7 - - - -
239E VAL* 3.4 10.6 - - - +
240E LEU 2.8 18.9 + - - -
241E SER* 3.0 30.0 + - - +
253E SER* 1.3 74.4 - - - +
255E GLY* 1.3 58.3 + - - +
259E SER 3.3 6.7 - - - +
260E LEU* 3.6 10.3 - - + -
309E VAL* 3.2 42.8 - - + -
310E ASP 3.9 4.5 - - - -
312E VAL* 3.5 22.4 - - + -
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Residues in contact with GLY 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235E HIS* 3.9 2.6 - - - -
238E GLU 3.0 14.1 - - - -
239E VAL* 4.0 1.3 - - - -
240E LEU* 3.6 9.4 - - - -
254E CYS* 1.3 77.9 - - - +
256E MET* 1.3 63.6 + - - -
257E ASP* 3.4 9.0 - - - -
258E HIS 3.8 3.8 + - - -
259E SER 3.6 7.1 + - - -
309E VAL* 2.9 31.8 + - - +
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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