Contacts of the strand formed by residues 297 - 301 (chain B) in PDB entry 2AG1
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 GLN 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B LEU* 3.5 33.1 + - + +
203B LYS* 6.3 0.4 - - - +
204B ALA* 6.3 0.4 - - - +
271B ASP* 3.1 13.0 + - - +
272B LEU* 3.1 20.5 - - + +
273B VAL 2.8 25.5 + - - -
295B SER 4.0 1.7 + - - +
296B ALA* 1.3 72.6 - - - +
298B VAL* 1.3 60.5 + - - +
299B ILE* 6.1 0.7 - - + -
315B ALA* 4.2 20.2 - - + +
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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
----------------------------------------------------------
273B VAL* 3.4 13.5 - - + +
275B MSE 3.7 26.9 - - + -
280B PHE* 4.4 1.8 - - + -
292B ILE* 3.9 25.6 - - + -
296B ALA* 3.6 10.7 + - + +
297B GLN* 1.3 79.3 - - - +
299B ILE* 1.3 69.6 + - - +
300B GLN* 4.2 1.6 - - + +
312B GLN* 4.7 6.3 - - - +
313B GLY 4.6 7.4 - - - +
314B ILE* 3.7 30.9 - - + +
315B ALA* 2.9 30.0 + - - +
316B LEU 3.2 7.3 + - - -
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Residues in contact with ILE 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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197B ALA* 3.7 37.0 - - + +
200B LEU* 4.2 11.4 - - + -
201B LEU* 5.4 1.8 - - + -
272B LEU* 4.2 29.4 - - + -
273B VAL 2.9 9.2 + - - +
274B LEU* 3.5 25.9 - - + +
275B MSE 2.9 27.2 + - - +
297B GLN 5.5 0.4 - - - -
298B VAL* 1.3 75.9 - - - +
300B GLN* 1.3 60.8 + - - +
301B VAL* 4.7 3.1 - - + -
315B ALA* 5.5 0.7 - - + -
316B LEU* 3.5 34.8 - - + +
318B ILE* 4.4 9.9 - - + -
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Residues in contact with GLN 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B MSE 3.7 17.7 - - + +
277B GLY 6.0 0.2 - - - +
278B ALA 4.1 12.6 + - - +
279B ARG* 4.4 4.0 - - - +
280B PHE* 3.3 24.2 - - - -
298B VAL* 3.9 6.8 - - + -
299B ILE* 1.3 73.5 - - - +
301B VAL* 1.3 68.1 + - - +
302B ASP* 4.1 3.6 - - + +
307B GLU* 2.8 33.7 + - - +
308B LEU* 3.7 12.2 - - + +
309B GLY* 2.7 26.4 + - - -
314B ILE* 3.8 13.1 - - + +
316B LEU 3.0 8.6 + - - +
317B GLY* 3.7 0.5 - - - -
318B ILE* 2.9 28.6 + - - +
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 4.6 9.0 - - + -
275B MSE 2.9 13.1 + - - +
276B LEU* 4.1 15.5 - - + -
277B GLY* 2.9 29.1 + - - -
299B ILE* 4.7 1.1 - - + -
300B GLN* 1.3 78.0 - - - +
302B ASP* 1.3 63.4 + - - +
318B ILE* 3.3 31.2 - - + +
320B ALA* 4.1 16.2 - - + +
322B VAL* 3.9 9.6 - - + +
325B THR* 3.5 41.5 - - + +
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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
------------------------------------------------------------
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