Contacts of the strand formed by residues 204 - 211 (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 SER 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A PHE 3.4 6.0 + - - -
203A THR* 1.3 79.2 - - - +
205A ASP* 1.3 65.1 + - - +
206A TYR* 3.0 23.9 + - - -
219A SER* 4.3 2.0 - - - -
220A MET* 2.8 39.1 + - - +
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Residues in contact with ASP 205 (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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204A SER* 1.3 76.2 + - - +
206A TYR* 1.3 67.9 + - - +
217A ASP* 3.0 29.8 - - - +
218A VAL 3.3 4.5 - - - +
219A SER* 3.8 19.4 + - - -
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Residues in contact with TYR 206 (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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202A PHE 4.9 2.3 + - - -
204A SER* 3.0 31.9 + - - -
205A ASP* 1.3 95.9 - - - +
207A PRO* 1.3 79.3 - - + +
217A ASP* 3.7 5.1 - - - -
218A VAL* 2.8 32.9 + - - +
220A MET* 3.7 33.7 - - + -
222A SER* 3.4 18.8 + - - -
224A TYR* 3.9 11.8 + - - -
287A HIS* 4.0 16.3 + + + -
365B CYS* 5.3 10.1 - - - -
367B ASP* 5.9 2.5 - - + -
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Residues in contact with PRO 207 (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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206A TYR* 1.3 95.8 - - + +
208A PHE* 1.3 59.6 + - - +
209A TYR* 4.2 7.5 - - + +
215A MET* 4.2 31.9 - - + -
216A VAL 3.5 8.7 - - - +
217A ASP* 4.7 4.0 - - - +
218A VAL* 4.8 0.9 - - - +
220A MET* 5.1 0.2 - - - +
367B ASP* 3.6 18.7 - - - +
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Residues in contact with PHE 208 (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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207A PRO* 1.3 75.2 - - - +
209A TYR* 1.3 76.2 + - - +
210A VAL* 3.3 15.5 + - + -
215A MET* 3.6 2.8 - - - -
216A VAL* 2.7 31.3 + - + +
218A VAL* 3.5 28.9 - - + -
289A PRO* 4.3 7.2 - - + -
366B ALA 3.6 11.4 - - - -
367B ASP* 3.4 14.8 - - - -
368B HIS 3.2 36.1 - - - -
369B PRO* 3.4 4.7 - - + -
370B PHE* 4.2 2.7 - + - -
388B TYR* 3.4 37.9 - + - -
389B CYS 3.4 22.4 - - - -
391B PRO* 4.4 4.0 - - + -
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Residues in contact with TYR 209 (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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207A PRO* 5.1 7.1 - - + +
208A PHE* 1.3 73.0 - - - +
210A VAL* 1.3 64.8 + - - +
211A SER* 3.1 11.9 + - - +
212A PRO 3.3 28.0 - - - -
213A THR* 5.2 0.2 - - - -
214A GLU 3.7 1.8 - - - -
215A MET* 3.6 37.6 - - + -
257A ILE* 3.5 34.6 - - - +
367B ASP* 2.7 40.8 + - + +
368B HIS* 4.1 4.5 - - + -
369B PRO* 3.2 24.1 - - - +
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Residues in contact with VAL 210 (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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208A PHE* 3.3 9.0 + - + -
209A TYR* 1.3 72.0 - - - +
211A SER* 1.3 61.8 + - - +
214A GLU* 3.1 32.8 + - + +
216A VAL* 3.6 28.3 - - + -
360A DTT 3.8 24.5 + - - -
369B PRO* 4.4 3.3 - - - +
389B CYS 4.1 13.7 - - - +
390B SER* 3.5 28.7 - - - -
391B PRO* 4.5 0.2 - - + -
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Residues in contact with SER 211 (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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209A TYR* 3.1 19.7 - - - +
210A VAL* 1.3 79.7 - - - +
212A PRO* 1.3 77.6 - - - +
213A THR* 3.1 4.3 + - - -
214A GLU* 3.1 35.7 + - - +
257A ILE* 4.7 2.9 - - - -
360A DTT 4.9 13.2 - - - -
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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