Contacts of the strand formed by residues 240 - 245 (chain B) in PDB entry 6C9G
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 TYR 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A TRP* 3.8 15.0 - - + -
399A HIS 3.5 7.9 - - - +
400A LEU* 3.7 28.7 - - + -
401A GLY 4.6 0.2 - - - +
210B LEU* 2.8 39.8 + - - +
212B GLN 4.1 2.0 + - - -
213B VAL* 4.0 28.7 - - + -
214B ILE* 6.6 0.2 - - + -
215B LEU* 6.3 0.2 - - + -
235B MET* 3.3 35.2 - - + +
238B HIS* 3.6 28.7 - - + -
239B LEU* 1.3 78.2 - - - +
241B ALA* 1.3 61.9 + - - +
251B LEU* 3.6 1.9 - - - -
252B SER* 2.7 43.1 + - - +
253B ALA* 5.0 2.0 - - - -
254B THR 5.7 1.6 - - - -
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Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A TRP* 3.5 9.8 - - - -
399A HIS* 2.9 48.0 + - + +
401A GLY* 5.0 7.0 - - - +
545A ILE* 5.3 6.5 - - + -
239B LEU* 5.4 1.8 - - + -
240B TYR* 1.3 78.8 - - - +
242B LEU* 1.3 64.6 + - - +
249B MET* 5.7 1.3 - - + -
250B VAL 3.3 5.6 - - - +
251B LEU* 3.6 23.3 - - + -
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A ALA* 4.0 23.1 - - + -
397A LYS 3.6 30.7 - - - +
398A TRP* 3.8 30.7 - - + +
399A HIS* 3.7 4.7 - - - -
241B ALA* 1.3 78.6 - - - +
243B SER* 1.3 71.0 + - - +
244B ILE* 3.3 9.0 + - - +
249B MET* 5.1 1.7 - - - +
250B VAL* 3.0 50.4 + - + +
267B TYR* 5.3 4.0 - - + +
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Residues in contact with SER 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A LYS 5.3 0.8 + - - -
399A HIS* 3.4 20.7 + - - -
242B LEU* 1.3 77.0 - - - +
244B ILE* 1.3 69.1 + - - +
245B LYS* 3.3 9.4 + - - +
248B VAL 4.8 0.3 - - - +
250B VAL* 6.0 0.9 - - - +
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Residues in contact with ILE 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A ILE* 5.2 4.5 - - + -
546A LYS* 5.8 0.9 - - - -
549A ALA* 4.7 20.2 - - + -
242B LEU 3.3 4.6 + - - +
243B SER* 1.3 75.5 + - - +
245B LYS* 1.3 63.1 + - - +
247B GLY* 4.4 5.4 - - - -
248B VAL 3.5 25.8 - - - +
249B MET* 4.1 25.1 - - + +
270B ILE* 3.8 34.8 - - + -
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Residues in contact with LYS 245 (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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243B SER 3.3 8.6 + - - +
244B ILE* 1.3 75.2 - - - +
246B ASP* 1.3 91.4 + - - +
247B GLY 3.1 1.8 - - - +
248B VAL* 3.1 23.9 + - - +
58C LYS* 3.7 8.9 + - - +
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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