Contacts of the strand formed by residues 281 - 286 (chain H) in PDB entry 1FNS
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 LEU 281 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262H LEU* 3.5 34.3 - - + +
273H TYR* 3.5 46.8 - - + -
277H LEU* 3.6 25.9 + - + +
279H SER* 3.3 6.4 - - - +
280H ARG* 1.3 80.4 - - - +
282H SER* 1.3 68.8 + - - +
283H ILE* 4.3 9.2 - - + -
294H LEU* 3.6 39.3 - - + -
295H LYS 3.6 5.8 - - - +
296H MET* 4.4 11.9 - - + -
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Residues in contact with SER 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H TYR* 3.5 5.4 + - - -
280H ARG 5.5 0.2 - - - -
281H LEU* 1.3 76.8 - - - +
283H ILE* 1.3 66.5 + - - +
284H THR* 3.9 19.6 + - - +
293H PHE 3.4 2.9 + - - +
294H LEU* 3.5 2.3 - - - -
295H LYS* 2.9 47.2 + - - +
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Residues in contact with ILE 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250H TRP* 3.8 25.1 - - + +
263H GLY* 3.6 10.3 - - - +
264H MET* 3.4 34.3 - - - +
265H ILE* 3.5 34.1 - - + +
269H GLY 5.3 0.2 - - - +
271H THR* 3.5 19.4 - - + +
273H TYR* 3.0 27.1 + - + -
281H LEU* 4.3 12.1 - - + -
282H SER* 1.3 78.8 + - - +
284H THR* 1.3 67.0 + - - +
292H VAL* 3.7 17.3 - - + -
293H PHE 3.2 3.8 - - - +
294H LEU* 5.0 1.1 - - - -
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Residues in contact with THR 284 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265H ILE* 3.8 7.6 - - - -
282H SER* 3.9 14.5 + - - +
283H ILE* 1.3 79.1 - - - +
285H LYS* 1.3 62.2 + - - +
292H VAL* 3.5 4.9 - - - +
293H PHE* 2.6 50.5 + - - +
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Residues in contact with LYS 285 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243H LEU* 2.8 32.0 + - + -
246H TYR 4.9 0.4 + - - -
265H ILE* 3.8 22.4 + - + +
266H TRP 3.4 11.4 + - - -
267H GLY* 2.6 32.5 + - - -
268H ASP 4.8 0.7 - - - -
269H GLY* 3.9 13.7 - - - +
284H THR* 1.3 79.7 - - - +
286H ASP* 1.3 62.3 + - - +
287H ASN* 2.9 26.4 + - - +
291H GLN 3.3 14.4 - - - +
292H VAL* 4.0 10.1 - - + -
293H PHE* 3.8 9.6 - - - -
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Residues in contact with ASP 286 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243H LEU* 4.6 0.2 - - - -
285H LYS* 1.3 75.4 - - - +
287H ASN* 1.3 64.4 + - - +
288H SER* 2.8 28.4 + - - -
289H LYS* 2.9 51.2 + - + +
290H SER 3.1 9.5 + - - -
291H GLN* 2.9 15.8 + - + +
293H PHE* 3.8 13.0 - - + -
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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