Contacts of the strand formed by residues 278 - 286 (chain A) in PDB entry 2W77
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 278 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLU* 3.1 25.7 + - - +
143A ASP* 3.1 11.5 + - - -
274A THR* 4.3 20.2 - - - +
276A GLU* 3.2 28.4 + - - +
277A PHE* 1.3 90.9 - - - +
279A GLY* 1.3 60.0 + - - +
296A ASP* 4.8 0.3 - - - +
297A VAL* 3.8 0.6 - - - +
298A SER* 2.9 36.9 + - - -
310A ARG* 4.8 8.1 - - - +
815A PHE 5.5 4.5 - - - -
1822A PO4 3.1 40.7 + - - +
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A PHE* 4.6 0.4 - - - -
278A LYS* 1.3 79.6 - - - +
280A HIS* 1.3 68.3 + - - +
296A ASP* 3.0 15.5 - - - -
297A VAL* 4.5 0.7 - - - -
814A ASP* 3.4 3.8 - - - +
815A PHE* 2.9 44.3 + - - +
1822A PO4 4.9 6.0 + - - -
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Residues in contact with HIS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A GLY* 1.3 77.2 - - - +
281A VAL* 1.3 70.4 + - - +
282A GLU* 4.0 11.2 - - + -
294A GLU* 3.0 26.0 + - - -
295A LEU* 3.5 5.9 - - - +
296A ASP* 3.0 50.0 + - + +
812A ARG* 3.1 25.7 + - + +
813A TRP 3.0 16.2 - - - +
814A ASP* 3.8 13.2 - - - +
815A PHE* 3.7 4.1 - - - -
1820A PO4 3.1 23.2 + - - -
1822A PO4 4.0 3.6 + - - -
1823A PO4 3.0 15.4 + - - -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A HIS* 1.3 75.8 - - - +
282A GLU* 1.3 66.7 + - - +
283A LEU* 4.6 14.6 - - + -
293A SER* 6.1 0.2 - - - -
294A GLU 3.2 11.2 - - - +
295A LEU* 3.7 13.9 - - + -
811A THR 4.0 0.7 - - - +
812A ARG* 3.5 1.6 - - - +
813A TRP* 2.7 50.4 + - + +
815A PHE* 3.3 33.4 - - + -
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ASP* 5.8 4.2 - - - +
183A ASN* 6.4 0.2 - - - -
280A HIS* 4.0 4.6 + - + -
281A VAL* 1.3 75.0 - - - +
283A LEU* 1.3 73.6 + - - +
292A ARG 5.5 0.2 - - - -
293A SER* 3.3 1.7 - - - -
294A GLU* 2.9 48.6 + - + +
810A SER* 5.1 8.6 + - - -
811A THR 3.3 13.9 - - - +
812A ARG* 4.0 26.4 + - + +
1823A PO4 2.6 29.1 + - - -
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A VAL* 4.6 14.4 - - + -
282A GLU* 1.3 83.7 - - - +
284A GLY* 1.3 58.1 + - - +
292A ARG 3.6 4.0 - - - +
293A SER* 3.4 22.7 - - - -
810A SER* 3.1 5.7 - - - -
811A THR* 3.0 38.9 + - - +
283B LEU* 5.9 7.9 - - + -
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Residues in contact with GLY 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A LEU* 1.3 77.0 - - - +
285A ALA* 1.3 61.0 + - - +
291A TYR* 3.5 6.2 - - - +
292A ARG* 3.0 30.7 + - - +
808A MET* 3.5 17.7 - - - -
809A PHE 3.0 11.9 - - - -
810A SER* 3.8 3.8 - - - -
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A GLY* 1.3 74.5 - - - +
286A GLY* 1.3 56.0 + - - +
290A ASN 3.3 6.3 - - - -
291A TYR* 4.3 14.1 - - + +
808A MET* 3.4 4.8 - - - +
809A PHE* 2.7 37.1 + - + +
771B ILE* 3.2 22.6 - - + +
772B THR* 5.4 1.6 - - - +
775B LEU* 3.5 32.5 - - + -
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Residues in contact with GLY 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A ALA* 1.3 75.0 - - - +
287A SER* 1.3 72.5 + - - +
288A TRP 3.4 0.2 + - - -
289A ASP* 3.4 4.2 + - - -
290A ASN* 2.7 29.8 + - - -
807A LEU 3.1 15.0 - - - -
808A MET* 3.6 9.3 - - - -
771B ILE* 3.7 13.1 - - - +
772B THR* 4.8 2.7 + - - -
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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