Contacts of the strand formed by residues 250 - 255 (chain L) in PDB entry 6C23
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244L TYR* 3.9 8.5 - - - -
245L ASP* 3.4 40.5 + - - +
248L GLY 3.7 0.6 - - - -
249L GLU* 1.3 79.9 + - - +
251L ILE* 1.3 74.0 + - - +
262L LEU* 4.2 15.0 - - + -
263L TRP 3.7 13.7 - - - +
264L ARG* 4.2 17.9 - - + +
265L ILE* 4.2 7.6 - - - +
314L TRP* 3.5 33.5 - - + -
317L ASP* 4.0 14.6 + - - +
340L ILE* 3.5 40.6 - - + +
341L ASP* 4.9 6.0 + - - +
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Residues in contact with ILE 251 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207L LEU* 3.4 41.5 - - + -
215L LEU* 4.5 7.2 - - + -
217L LEU* 6.1 0.2 - - + -
229L PHE* 5.3 7.2 - - + -
243L ASP 3.1 19.3 - - - +
244L TYR* 4.4 13.7 - - + +
250L LYS* 1.3 78.9 - - - +
252L MET* 1.3 72.8 + - - +
262L LEU* 3.4 7.1 - - - +
263L TRP* 2.8 64.6 + - + +
265L ILE* 4.1 15.3 - - + -
314L TRP* 3.9 6.1 - - - -
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Residues in contact with MET 252 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242L ALA* 3.1 7.3 - - - +
243L ASP* 3.0 36.0 + - - +
251L ILE* 1.3 80.8 - - - +
253L SER* 1.3 66.6 + - - +
260L LEU* 3.5 20.4 - - + -
261L LYS* 3.0 42.6 - - - +
262L LEU* 3.5 22.4 - - + -
263L TRP* 5.4 0.2 - - - -
299L PHE* 5.5 0.9 - - + -
301L THR* 5.3 0.9 - - + -
312L VAL* 4.5 17.9 - - + -
313L ARG 6.4 0.4 - - - -
314L TRP* 4.0 13.9 - - + +
319L ILE* 3.8 21.1 - - + -
331L TRP* 4.0 20.4 - - + -
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Residues in contact with SER 253 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L LEU* 4.1 17.5 - - - -
235L HIS* 3.2 15.0 + - - -
239L VAL* 4.9 0.4 - - - -
241L SER 3.4 10.3 - - - -
252L MET* 1.3 80.1 - - - +
254L CYS* 1.3 62.4 + - - +
255L GLY 4.2 0.4 - - - -
260L LEU* 3.4 8.1 - - - +
261L LYS* 2.8 35.5 + - - +
263L TRP* 3.0 34.2 - - - -
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Residues in contact with CYS 254 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235L HIS* 4.2 1.4 + - - -
239L VAL* 3.5 2.8 - - - +
240L LEU* 2.8 25.1 + - - +
241L SER* 2.9 23.5 + - - +
253L SER* 1.3 77.8 + - - +
255L GLY* 1.3 59.3 + - - +
260L LEU* 4.1 6.7 - - + -
309L VAL* 3.0 41.3 - - - -
311L CYS* 3.8 12.1 - - - -
312L VAL* 3.4 33.0 - - + -
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Residues in contact with GLY 255 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235L HIS* 3.6 24.3 - - - -
238L GLU 3.8 6.7 - - - -
239L VAL* 4.2 2.7 - - - -
240L LEU* 4.4 5.4 - - - -
254L CYS* 1.3 75.3 - - - +
256L MET* 1.3 63.1 + - - -
257L ASP* 3.3 5.7 + - - -
258L HIS 4.0 1.9 + - - -
259L SER 3.7 10.6 + - - +
309L VAL* 3.2 27.7 + - - +
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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