Contacts of the strand formed by residues 273 - 279 (chain A) in PDB entry 5LG1
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 VAL 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A VAL* 4.7 4.5 - - + -
266A VAL* 4.2 32.5 - - + -
271A PRO 3.0 10.5 + - - +
272A GLU* 1.3 73.8 - - - +
274A GLN* 1.3 64.6 + - - +
275A PHE* 4.0 24.5 - - + -
289A THR* 5.5 2.6 - - - +
292A ARG* 4.1 5.6 - - - +
302A VAL* 4.5 14.4 - - + +
323A VAL* 3.6 31.0 - - + -
324A SER 3.8 6.3 - - - +
325A ASN* 4.3 11.7 - - - +
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Residues in contact with GLN 274 (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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272A GLU* 3.9 9.2 - - + +
273A VAL* 1.3 79.5 - - - +
275A PHE* 1.3 66.1 + - - +
276A ASN* 4.9 5.0 - - - +
322A LYS 3.6 0.7 - - - +
323A VAL* 3.6 4.5 - - - -
324A SER* 2.7 48.2 + - - +
325A ASN 4.7 0.7 - - - +
326A LYS* 4.2 23.8 - - - +
327A GLY 5.3 0.5 + - - -
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Residues in contact with PHE 275 (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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261A CYS* 4.1 10.3 - - - -
263A VAL* 3.6 33.7 - - + -
273A VAL* 4.0 15.9 - - + -
274A GLN* 1.3 78.7 - - - +
276A ASN* 1.3 69.4 + - - +
277A TRP* 4.3 9.3 - - + +
289A THR* 3.7 28.0 - - + +
302A VAL* 3.5 30.7 - - + -
304A SER* 3.6 33.0 - - - +
321A CYS* 3.8 18.4 - - - -
322A LYS 3.5 1.6 - - - -
323A VAL* 3.9 11.4 - - + -
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Residues in contact with ASN 276 (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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274A GLN* 4.9 5.0 - - - +
275A PHE* 1.3 81.7 + - - +
277A TRP* 1.3 63.5 + - - +
278A TYR* 3.8 22.1 + - + +
283A GLU* 3.1 28.0 + - - +
320A LYS 3.6 2.3 - - - +
321A CYS* 3.7 1.2 - - - -
322A LYS* 2.8 58.4 + - + +
324A SER* 4.7 9.0 + - - -
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Residues in contact with TRP 277 (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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242A LEU* 3.8 13.0 - - + -
259A VAL* 3.7 32.5 - - + -
261A CYS* 3.5 33.7 - - + -
275A PHE* 4.4 10.8 - - + +
276A ASN* 1.3 78.2 - - - +
278A TYR* 1.3 64.2 + - - +
283A GLU* 3.2 10.3 - - - +
284A VAL* 3.1 49.1 + - + +
287A ALA* 3.3 22.7 - - + +
304A SER* 3.1 35.5 + - - -
306A LEU* 3.5 29.6 - - + -
319A TYR* 4.9 5.2 - - + -
320A LYS 3.4 21.8 - - - -
321A CYS* 4.2 8.3 - - + -
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Residues in contact with TYR 278 (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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276A ASN* 3.8 33.7 + - + +
277A TRP* 1.3 73.9 - - - +
279A VAL* 1.3 64.0 + - - +
280A ASP 4.0 0.9 - - - -
281A GLY* 3.6 27.6 - - - +
282A VAL 3.2 5.6 - - - +
283A GLU* 3.5 43.9 + - + -
318A GLU 3.5 0.9 - - - +
319A TYR* 3.4 5.2 - - - -
320A LYS* 2.9 64.2 + - + +
322A LYS* 3.8 30.8 + - + +
333A GLU* 6.0 0.2 - - - -
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Residues in contact with VAL 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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278A TYR* 1.3 75.1 - - - +
280A ASP* 1.3 70.8 + - - +
282A VAL* 2.7 27.9 + - + +
284A VAL* 4.2 28.5 - - + -
306A LEU* 4.4 3.6 - - + -
312A ASP* 4.8 6.3 - - - +
317A LYS* 3.9 28.7 + - + +
318A GLU 3.4 6.3 - - - +
319A TYR* 3.5 39.5 - - + +
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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
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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