Contacts of the strand formed by residues 294 - 299 (chain B) in PDB entry 4K9N
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 ARG 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ALA* 3.8 25.1 - - - +
268B ASP 2.8 15.5 + - - +
269B VAL* 3.4 12.6 - - + +
270B VAL* 2.8 27.0 + - - +
289B LEU* 4.9 0.4 - - - -
292B GLY 4.1 0.2 + - - -
293B THR* 1.3 74.9 - - - +
295B LEU* 1.3 69.0 + - - +
296B ILE* 3.6 26.7 - - + +
312B ASP* 2.9 28.7 + - - -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 5.1 0.4 - - + -
270B VAL* 3.3 18.8 - - + +
272B VAL* 3.9 22.7 - - + -
277B VAL* 4.1 10.5 - - + -
278B PHE* 3.9 24.0 - - + -
289B LEU* 4.0 33.0 - - + +
293B THR 4.2 0.4 - - - -
294B ARG* 1.3 79.5 + - - +
296B ILE* 1.3 78.4 + - - +
297B SER* 3.9 12.3 - - - +
310B MET* 4.1 10.3 - - + +
311B GLY* 3.2 18.4 - - - +
312B ASP* 3.0 22.3 + - - +
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 3.8 34.5 - - + -
196B ALA* 4.7 5.4 - - + -
197B LEU* 5.2 2.0 - - + -
269B VAL* 4.2 19.5 - - + -
270B VAL 2.9 7.9 + - - +
271B LEU* 3.4 14.9 - - + +
272B VAL* 2.8 25.5 + - - +
294B ARG* 3.6 42.2 - - + +
295B LEU* 1.3 81.1 - - - +
297B SER* 1.3 63.1 + - - +
298B VAL* 5.3 0.2 - - + -
312B ASP* 3.6 12.6 - - + +
314B ILE* 4.3 18.4 - - + -
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Residues in contact with SER 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ARG* 6.0 0.7 - - - -
272B VAL* 3.4 7.5 + - - +
275B ALA 4.4 4.0 + - - -
277B VAL* 3.8 29.0 - - - +
295B LEU* 4.1 4.5 - - - -
296B ILE* 1.3 74.9 - - - +
298B VAL* 1.3 64.3 + - - +
299B THR* 4.0 13.5 - - - +
305B ALA* 5.7 0.5 - - - -
312B ASP 2.9 16.6 + - - -
313B ALA* 3.1 7.6 - - - +
314B ILE* 2.7 34.1 + - - +
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 5.0 0.7 - - + -
271B LEU* 4.3 17.0 - - + -
272B VAL 2.8 15.7 + - - +
273B ILE* 3.5 11.3 - - + -
274B GLY 2.8 31.5 + - - -
275B ALA 4.5 0.7 + - - -
296B ILE* 5.3 0.2 - - + -
297B SER* 1.3 77.7 + - - +
299B THR* 1.3 59.4 + - - +
314B ILE* 3.4 19.3 - - + +
316B ALA* 4.9 2.9 - - + +
318B ILE* 4.0 13.2 - - + -
321B MET* 3.8 48.9 - - + -
325B LEU* 4.8 9.2 - - + -
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Residues in contact with THR 299 (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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274B GLY* 4.7 2.5 - - - +
275B ALA 4.5 5.2 - - - -
297B SER* 4.0 14.1 - - - +
298B VAL* 1.3 75.2 - - - +
300B CYS* 1.3 57.8 + - - +
301B ASP 3.0 18.2 + - - +
304B GLU* 2.7 30.2 + - - +
305B ALA* 3.8 32.8 - - + +
313B ALA* 4.8 1.3 - - + -
314B ILE 2.9 10.8 + - - +
315B VAL* 3.1 11.7 - - + -
316B ALA 3.0 25.3 + - - -
318B ILE* 4.0 4.0 - - - -
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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
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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