Contacts of the strand formed by residues 279 - 286 (chain B) in PDB entry 2A1A
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 GLY 279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B GLY* 2.9 26.2 + - - -
277B GLY 3.8 0.8 - - - -
278B PHE* 1.3 78.0 - - - +
280B GLN* 1.3 73.9 + - - +
281B VAL* 5.5 2.9 - - - +
296B LYS* 5.4 4.5 - - - -
297B ARG 3.1 15.5 - - - -
298B VAL* 4.4 3.1 - - - -
334B PRO* 4.0 3.6 - - - -
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Residues in contact with GLN 280 (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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272B LEU* 4.5 9.2 - - + -
274B GLY 3.6 8.5 - - - +
275B SER* 3.5 24.2 + - - +
276B GLY 4.7 4.0 + - - -
279B GLY* 1.3 88.4 + - - +
281B VAL* 1.3 64.3 + - - +
282B PHE* 4.0 11.0 - - + -
296B LYS* 3.6 2.3 - - - +
297B ARG* 2.4 69.0 + - - +
334B PRO* 2.9 42.2 + - - +
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Residues in contact with VAL 281 (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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272B LEU* 3.7 3.0 - - - +
273B ILE* 3.1 35.5 + - + +
274B GLY* 2.8 27.8 + - - +
275B SER* 5.9 0.2 - - - -
279B GLY 5.5 1.6 - - - -
280B GLN* 1.3 77.9 - - - +
282B PHE* 1.3 66.2 + - - +
294B VAL* 3.7 28.7 - - + -
295B ILE 3.9 3.1 - - - +
296B LYS* 4.3 21.5 - - + +
366B MET* 5.7 1.8 - - + -
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Residues in contact with PHE 282 (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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255B GLY 5.0 1.1 - - - -
257B HIS* 4.1 18.6 - - + -
258B THR* 3.8 21.5 - - + -
263B PHE* 3.8 24.7 - + + -
270B ILE* 3.7 18.8 - - + -
271B GLU 3.2 15.7 - - - +
272B LEU* 4.2 7.9 - - + -
273B ILE* 3.8 3.4 - - - +
280B GLN* 4.0 14.6 - - + -
281B VAL* 1.3 78.3 - - - +
283B LYS* 1.3 62.1 + - - +
294B VAL* 3.2 13.9 - - - +
295B ILE* 2.7 43.5 + - + +
297B ARG* 3.4 57.0 - - + -
363B PHE* 5.0 1.1 - + - -
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Residues in contact with LYS 283 (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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269B GLU 3.3 3.7 - - - +
270B ILE* 3.5 0.3 - - - +
271B GLU* 2.7 62.6 + - + +
273B ILE* 3.7 25.4 - - + -
282B PHE* 1.3 73.6 - - - +
284B ALA* 1.3 64.2 + - - +
292B THR* 3.9 22.7 - - + -
293B TYR 3.7 5.2 - - - +
368B PHE* 3.9 39.7 - - + -
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Residues in contact with ALA 284 (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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263B PHE* 3.9 9.6 - - + -
267B PHE* 3.7 19.3 - - + -
268B LYS 3.7 11.9 - - - +
269B GLU* 3.8 5.2 - - - -
270B ILE* 3.8 19.1 - - + -
283B LYS* 1.3 79.0 - - - +
285B LYS* 1.3 62.1 + - - +
286B HIS 4.2 0.4 + - - -
291B LYS 4.1 0.2 - - - +
292B THR* 3.2 6.9 - - - +
293B TYR* 2.8 33.7 + - - +
295B ILE* 4.0 4.2 - - + +
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Residues in contact with LYS 285 (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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267B PHE* 3.6 2.6 - - - -
268B LYS* 2.9 63.5 + - + +
269B GLU* 3.7 30.4 + - + +
284B ALA* 1.3 75.5 - - - +
286B HIS* 1.3 71.2 + - - +
290B GLY* 3.9 26.5 - - - +
291B LYS 3.6 4.3 - - - +
292B THR* 4.2 14.6 - - - +
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Residues in contact with HIS 286 (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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266B ASP* 3.9 22.7 + - + -
267B PHE* 3.7 32.1 - + + -
268B LYS* 4.5 2.8 - - - -
285B LYS* 1.3 75.0 - - - +
287B ARG* 1.3 62.9 + - - +
288B ILE* 2.9 48.7 + - + +
289B ASP* 3.0 43.7 + - - +
290B GLY* 3.3 18.2 + - - -
291B LYS 3.1 11.7 + - - +
293B TYR* 4.1 3.4 - - + -
365B GLN* 4.8 5.6 + - - -
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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