Contacts of the strand formed by residues 232 - 239 (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 232 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223H PRO* 3.6 35.2 - - + -
226H VAL* 4.1 8.1 - - + -
231H SER* 1.3 72.3 - - - +
233H SER* 1.3 61.1 + - - +
234H ILE* 3.7 12.1 - - + -
294H LEU* 3.7 17.6 - - + +
295H LYS* 3.1 8.0 - - - +
296H MET* 2.8 39.6 + - + +
299H LEU* 3.5 29.8 - - + +
307H TYR* 3.7 43.1 - - + +
332H VAL* 3.8 10.8 - - + -
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Residues in contact with SER 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221H SER 4.3 0.7 - - - +
222H GLY* 4.2 1.6 - - - -
223H PRO* 3.5 19.8 - - - +
231H SER* 4.1 3.6 + - - -
232H LEU* 1.3 76.6 + - - +
234H ILE* 1.3 66.9 + - - +
294H LEU 3.4 5.6 - - - -
295H LYS* 4.0 22.9 - - - +
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Residues in contact with ILE 234 (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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220H GLU* 3.8 11.9 - - + -
221H SER 3.3 19.1 - - - +
222H GLY* 4.1 7.2 - - - -
232H LEU* 3.7 27.8 - - + -
233H SER* 1.3 79.7 - - - +
235H THR* 1.3 69.5 + - - +
236H CYS 4.0 0.2 + - - -
250H TRP* 3.5 29.1 - - + -
292H VAL 3.7 0.3 - - - +
293H PHE* 3.6 3.6 - - - +
294H LEU* 3.0 40.2 + - + +
307H TYR* 3.7 34.5 - - + -
330H THR* 3.8 8.7 - - + -
332H VAL* 4.4 0.9 - - + -
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Residues in contact with THR 235 (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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219H LYS 3.6 1.6 - - - +
220H GLU* 3.4 1.0 - - - -
221H SER* 2.8 48.6 + - - +
234H ILE* 1.3 76.2 - - - +
236H CYS* 1.3 66.3 + - - +
237H THR* 3.9 10.0 + - - +
291H GLN* 3.8 27.4 - - + +
292H VAL 3.6 2.7 - - - -
293H PHE* 3.5 28.7 - - + -
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Residues in contact with CYS 236 (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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218H LEU* 4.1 6.1 - - - -
219H LYS 3.3 4.9 - - - -
220H GLU* 4.4 0.2 - - - +
234H ILE 4.0 0.6 + - - -
235H THR* 1.3 74.2 - - - +
237H THR* 1.3 60.9 + - - +
238H VAL* 3.8 23.2 + - - +
248H VAL* 4.5 4.7 - - - -
250H TRP* 3.6 14.1 - - + -
290H SER 3.8 0.2 - - - +
291H GLN* 3.3 5.0 - - - +
292H VAL* 2.8 38.9 + - + +
309H CYS* 2.1 52.5 - - + -
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Residues in contact with THR 237 (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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217H GLN 4.2 0.7 - - - +
218H LEU* 3.5 1.2 - - - -
219H LYS* 2.8 38.1 + - - +
221H SER* 5.0 5.0 + - - -
235H THR* 4.0 6.1 + - - +
236H CYS* 1.3 74.6 - - - +
238H VAL* 1.3 69.1 + - - +
289H LYS 4.9 3.4 - - - +
290H SER* 3.5 8.7 - - - +
291H GLN* 3.7 23.4 + - + +
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Residues in contact with VAL 238 (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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217H GLN 3.3 9.0 - - - +
218H LEU* 3.7 28.5 - - + -
236H CYS* 3.8 15.5 - - - +
237H THR* 1.3 83.2 - - - +
239H SER* 1.3 63.8 + - - +
241H PHE* 3.5 32.5 - - + +
243H LEU* 3.9 26.0 - - + -
248H VAL* 4.6 2.5 - - + -
290H SER* 2.9 43.0 + - - +
292H VAL* 5.0 1.1 - - + -
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Residues in contact with SER 239 (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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215H GLN* 4.1 4.1 + - - -
216H VAL* 3.5 2.4 - - - -
217H GLN* 2.9 59.0 + - - +
238H VAL* 1.3 77.6 - - - +
240H GLY* 1.3 63.7 + - - +
241H PHE* 3.4 9.9 - - - +
290H SER* 5.5 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