Contacts of the strand formed by residues 237 - 243 (chain A) in PDB entry 1F0C
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 PHE 237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A SER* 3.8 1.7 - - - -
232A VAL* 2.9 67.9 + - + +
234A GLU* 4.2 3.6 - - + -
235A GLY* 3.7 13.5 - + - -
236A ASN* 1.3 76.9 - - - +
238A SER* 1.3 69.1 + - - +
239A ILE* 4.3 8.3 - - + -
253A ILE* 3.6 22.7 - - + -
254A LEU 3.3 16.6 - - - +
255A PRO* 3.7 1.8 - - + -
256A ASP* 3.6 8.9 + - - -
263A ILE* 3.4 35.0 - - + -
275A TRP* 3.5 43.1 - + - -
359B THR* 4.0 2.6 - - - +
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Residues in contact with SER 238 (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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229A HIS* 2.6 32.8 + - - -
230A ALA 3.5 4.9 - - - -
231A SER* 4.7 0.4 - - - +
237A PHE* 1.3 77.5 - - - +
239A ILE* 1.3 60.4 + - - +
252A VAL 3.6 0.7 - - - +
253A ILE* 3.5 2.9 - - - -
254A LEU* 2.8 36.7 + - - -
256A ASP* 4.0 2.9 + - - -
359B THR* 5.0 0.7 - - - -
360B VAL* 3.7 27.8 + - - +
364B PHE* 3.4 17.7 - - - -
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Residues in contact with ILE 239 (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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229A HIS* 3.1 7.3 - - - -
230A ALA* 2.9 54.1 + - + +
232A VAL* 4.1 10.3 - - + -
237A PHE* 4.3 7.6 - - + -
238A SER* 1.3 76.8 + - - +
240A ILE* 1.3 63.7 + - - +
251A VAL* 3.6 29.4 - - + -
252A VAL 3.3 6.5 - - - +
253A ILE* 3.7 21.1 - - + -
272A PHE* 4.5 4.5 - - + -
275A TRP* 3.9 30.3 - - + +
276A CYS* 4.8 2.2 - - - +
279A MET* 3.3 13.8 - - + +
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Residues in contact with ILE 240 (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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227A PHE* 4.0 11.0 - - + -
228A ASN 3.5 10.1 - - - +
229A HIS* 4.4 3.4 - - + -
239A ILE* 1.3 75.2 - - - +
241A GLU* 1.3 64.3 + - - +
242A LEU* 4.4 11.2 - - + -
250A MET 3.8 0.2 - - - +
251A VAL* 3.1 5.4 - - - +
252A VAL* 2.8 47.5 + - + -
279A MET* 3.3 7.9 - - - -
284A ILE* 4.0 22.0 - - + -
286A VAL* 3.7 30.7 - - + -
364B PHE* 3.5 43.5 - - + -
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Residues in contact with GLU 241 (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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227A PHE* 3.6 19.6 - - - +
228A ASN* 3.0 41.3 + - + +
240A ILE* 1.3 74.7 - - - +
242A LEU* 1.3 63.9 + - - +
243A PRO* 3.5 14.5 - - + +
249A SER* 2.7 35.8 + - - +
250A MET 3.6 2.7 - - - -
251A VAL* 4.3 11.3 - - + +
279A MET* 3.7 17.9 - - + +
375B ARG* 4.9 7.4 + - - -
377B VAL* 4.8 9.9 - - - +
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Residues in contact with LEU 242 (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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194A TRP* 3.5 25.5 - - + -
198A PHE* 4.6 12.3 - - + -
227A PHE* 3.7 28.5 - - + -
240A ILE* 4.4 12.8 - - + -
241A GLU* 1.3 74.3 - - - +
243A PRO* 1.3 67.1 - - + +
249A SER* 3.9 1.8 - - - -
250A MET* 2.7 66.9 + - + +
252A VAL* 4.4 7.2 - - + -
286A VAL* 4.3 22.4 - - + -
288A ILE* 4.6 17.3 - - + -
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Residues in contact with PRO 243 (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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194A TRP* 3.6 8.5 - - - +
195A LEU* 2.7 55.1 + - + -
196A MET 4.6 0.6 + - - +
227A PHE* 4.3 15.5 - - + -
241A GLU* 3.5 16.6 - - + +
242A LEU* 1.3 85.8 - - - +
244A TYR* 1.3 59.2 + - - +
248A THR 4.6 0.9 - - - +
249A SER* 3.7 11.9 - - - -
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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