Contacts of the strand formed by residues 272 - 277 (chain A) in PDB entry 3FFN
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 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A LEU* 6.3 2.2 - - + -
271A ALA* 1.3 80.1 - - - +
273A LEU* 1.3 60.0 + - - +
274A TYR* 3.9 30.3 - - + +
287A LEU* 4.1 14.1 - - + +
289A ALA 3.7 10.8 - - - +
290A ASP* 4.1 24.1 + - + +
294A PHE* 3.6 4.7 - - - -
306A ILE 3.9 0.3 - - - +
307A LEU* 3.6 3.8 - - - +
308A ASP* 2.8 38.1 + - + +
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Residues in contact with LEU 273 (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 LYS* 1.3 73.2 - - - +
274A TYR* 1.3 65.4 + - - +
287A LEU* 3.7 1.9 - - - +
288A VAL* 3.1 26.6 + - + -
289A ALA* 3.1 24.7 + - + +
294A PHE* 3.8 27.5 - - + -
298A ALA* 4.4 16.2 - - + -
299A LEU* 3.8 25.1 - - + -
305A PHE* 4.0 24.2 - - + -
306A ILE 3.5 21.8 - - - +
307A LEU* 3.9 16.6 - - + -
362A PHE* 5.6 1.8 - - + -
366A PHE* 4.2 8.7 - - + -
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Residues in contact with TYR 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 LYS* 3.9 34.5 - - + +
273A LEU* 1.3 75.6 - - - +
275A LYS* 1.3 64.8 + - - +
285A VAL* 4.3 24.5 - - + -
286A SER 3.2 22.4 - - - +
287A LEU* 3.6 23.7 - - + +
288A VAL* 4.0 0.4 - - - -
305A PHE* 3.0 14.5 - - - +
306A ILE* 2.8 46.5 + - + +
308A ASP* 4.0 9.2 + - + -
338A PHE* 3.9 29.6 - + - -
342A MET* 3.9 19.7 - - + +
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Residues in contact with LYS 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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274A TYR* 1.3 72.4 - - - +
276A VAL* 1.3 71.1 + - - +
277A SER* 4.6 13.5 + - - -
285A VAL* 3.3 7.5 - - - +
286A SER* 2.9 44.6 + - - +
288A VAL* 3.5 17.8 - - + +
300A LYS* 6.0 0.7 - - + -
303A ASP* 3.5 27.9 + - + +
304A CYS 3.8 4.5 - - - +
305A PHE* 3.7 23.3 - - + -
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Residues in contact with VAL 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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275A LYS* 1.3 82.4 - - - +
277A SER* 1.3 66.4 + - - +
278A ASN 4.9 1.3 - - - +
279A GLY 5.2 1.8 - - - +
283A MET* 5.2 1.6 - - - -
284A SER 3.8 3.6 - - - +
285A VAL* 4.2 8.7 - - + -
303A ASP* 5.1 3.8 - - - +
304A CYS* 2.9 38.4 + - + +
305A PHE 4.3 0.4 - - - -
306A ILE* 4.0 35.2 - - + +
317A VAL* 5.8 0.9 - - + -
327A GLU* 3.3 26.9 - - - +
334A THR* 4.1 22.4 - - + +
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Residues in contact with SER 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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275A LYS* 4.6 14.9 + - - -
276A VAL* 1.3 76.0 + - - +
278A ASN* 1.3 75.0 + - - +
283A MET* 4.1 0.3 - - - +
284A SER* 3.1 41.7 + - - +
285A VAL* 5.6 0.3 - - - -
286A SER* 4.9 6.2 + - - -
327A GLU* 4.5 0.9 - - - -
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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