Contacts of the strand formed by residues 248 - 256 (chain A) in PDB entry 1FNH
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 GLU 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A GLU 4.3 0.5 - - - +
220A PRO* 3.4 31.4 - - + +
246A GLY 4.1 0.6 + - - -
247A THR* 1.3 72.2 - - - +
249A TYR* 1.3 67.1 + - - +
250A THR* 4.2 2.2 + - - +
268A ARG* 3.3 44.0 + - + +
269A LYS* 3.8 14.6 + - - +
270A LYS* 4.0 16.7 - - + +
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Residues in contact with TYR 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A LEU* 4.2 12.7 - - + +
217A TYR* 3.9 32.8 - + + -
218A GLU 3.9 14.4 - - - -
219A LYS* 3.4 26.0 - - + +
243A LEU* 3.6 21.1 - - + -
244A GLU* 2.8 47.5 + - - +
247A THR* 3.3 40.5 + - + -
248A GLU* 1.3 74.3 - - - +
250A THR* 1.3 61.2 + - - +
251A ILE* 4.2 9.1 + - + +
268A ARG* 3.2 6.5 - - - +
269A LYS 3.0 34.9 + - - +
271A THR* 4.2 9.6 - - + -
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Residues in contact with THR 250 (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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216A LYS 3.6 0.9 - - - +
217A TYR* 3.0 23.9 - - - -
218A GLU* 3.1 19.8 + - - -
248A GLU* 5.1 2.6 + - - +
249A TYR* 1.3 73.9 + - - +
251A ILE* 1.3 64.7 + - - +
252A TYR* 3.4 36.6 - - + +
266A ILE* 4.0 14.1 - - + -
267A GLY 3.3 9.9 - - - +
268A ARG* 4.0 25.3 + - - +
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Residues in contact with ILE 251 (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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189A LEU* 4.2 11.2 - - + -
191A PHE* 3.7 27.8 - - + -
199A LEU* 4.5 6.5 - - + -
201A VAL* 4.8 6.1 - - + -
215A ILE* 3.9 19.3 - - + -
216A LYS 3.2 5.8 - - - +
217A TYR* 3.7 19.7 - - + -
240A ILE* 3.7 21.5 - - + -
243A LEU* 6.0 0.2 - - + -
249A TYR* 4.3 15.3 - - + +
250A THR* 1.3 81.1 - - - +
252A TYR* 1.3 66.0 + - - +
253A VAL* 4.1 14.6 - - + -
265A LEU 3.5 0.4 - - - +
266A ILE* 3.4 11.8 - - - +
267A GLY 2.7 32.1 + - - +
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Residues in contact with TYR 252 (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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214A ILE 3.6 2.6 - - - +
215A ILE* 3.2 5.4 - - - +
216A LYS* 2.6 70.9 + - + +
218A GLU* 3.3 30.5 + - + -
224A PRO* 4.6 5.8 - - + -
250A THR* 3.4 35.6 - - + +
251A ILE* 1.3 75.0 - - - +
253A VAL* 1.3 63.3 + - - +
254A ILE* 3.9 13.1 - - + +
264A PRO* 4.3 9.9 - - + -
265A LEU 3.5 3.8 - - - -
266A ILE* 3.9 30.1 - - + -
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Residues in contact with VAL 253 (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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186A PRO* 4.0 9.9 - - + +
189A LEU* 4.0 16.2 - - + -
201A VAL* 5.2 1.3 - - + -
203A TRP* 3.9 50.0 - - + +
213A TYR* 4.1 16.6 - - + -
214A ILE 4.0 1.1 - - - -
215A ILE* 4.4 13.7 - - + +
251A ILE* 4.2 11.7 - - + -
252A TYR* 1.3 75.3 - - - +
254A ILE* 1.3 62.0 + - - +
264A PRO* 3.7 0.5 - - - +
265A LEU* 2.8 47.9 + - + +
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Residues in contact with ILE 254 (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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186A PRO* 4.7 0.4 - - - -
213A TYR* 3.0 12.3 - - - +
214A ILE* 2.9 59.4 + - + +
216A LYS* 4.2 19.3 - - + +
252A TYR* 4.4 6.5 - - + -
253A VAL* 1.3 82.5 - - - +
255A ALA* 1.3 75.1 + - - +
256A LEU* 4.1 3.6 - - + -
261A LYS* 3.8 21.3 - - + +
262A SER* 3.2 26.5 - - - +
264A PRO* 3.6 25.8 - - + -
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Residues in contact with ALA 255 (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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183A ILE* 4.1 1.3 - - + -
186A PRO* 4.2 4.1 - - + +
206A PRO* 4.0 19.3 - - + -
210A ILE* 3.5 21.1 - - + -
212A GLY 3.9 2.9 - - - -
213A TYR* 4.3 4.7 - - + -
254A ILE* 1.3 71.6 - - - +
256A LEU* 1.3 77.6 + - - +
260A GLN 3.0 12.4 - - - +
261A LYS* 3.2 0.7 - - - -
262A SER* 2.7 39.8 + - - +
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Residues in contact with LEU 256 (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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210A ILE* 2.9 11.5 - - - +
211A THR* 2.3 45.4 + - + +
212A GLY* 2.9 20.5 + - - +
213A TYR 4.1 4.9 - - - +
214A ILE* 3.0 38.4 - - + -
230A ARG* 4.3 14.6 - - - +
254A ILE* 3.8 13.9 - - + +
255A ALA* 1.3 103.0 - - - +
257A LYS* 1.3 54.4 + - - +
258A ASN* 4.5 2.2 - - - +
259A ASN 5.6 4.0 - - - +
260A GLN 3.4 8.3 - - - +
261A LYS* 4.5 8.7 - - + -
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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