Contacts of the strand formed by residues 206 - 211 (chain C) in PDB entry 1FPY
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 VAL 206 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C CYS* 3.6 43.1 - - + +
199C MET* 4.3 11.9 - - + -
200C GLU* 2.9 34.1 + - + +
205C VAL* 1.3 75.1 - - - +
207C GLU* 1.3 61.4 + - - +
208C ALA 3.6 14.4 - - - +
221C VAL* 3.9 7.2 - - + -
222C ALA 3.6 9.2 - - - +
223C THR* 4.3 7.0 - - + -
34D PRO* 3.2 14.2 - - + +
36D HIS* 3.1 26.2 - - - -
37D GLN* 4.3 0.2 - - - -
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Residues in contact with GLU 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C VAL* 3.7 1.3 + - + -
206C VAL* 1.3 76.5 - - - +
208C ALA* 1.3 65.9 + - + +
222C ALA* 2.8 15.9 + - + +
223C THR 4.1 1.0 - - - +
224C ARG* 3.5 45.6 - - + +
225C PHE* 5.1 0.9 - - - -
4473C ADP 3.5 37.6 + - - +
33D ILE* 3.4 9.7 - - - +
34D PRO* 3.2 14.6 - - - +
37D GLN* 3.5 28.4 + - - +
47D LYS* 5.7 1.0 - - - -
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Residues in contact with ALA 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206C VAL* 3.5 8.5 - - - -
207C GLU* 1.3 85.1 - - + +
209C HIS* 1.3 60.3 + - - +
210C HIS* 5.2 3.1 - - + -
221C VAL* 3.5 1.4 - - - +
222C ALA* 2.6 44.3 + - + +
31D VAL* 5.2 3.6 - - + -
32D THR 3.3 6.1 - - - +
33D ILE* 3.1 23.8 - - + -
34D PRO* 4.1 5.8 - - - -
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Residues in contact with HIS 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C GLN* 2.7 35.7 - - - -
192C ARG* 2.7 31.5 + - + +
193C SER* 3.0 30.6 + - - -
196C CYS* 3.6 29.6 - - - -
208C ALA* 1.3 76.6 - - - +
210C HIS* 1.3 68.3 + - - +
220C GLU 3.6 11.7 - - - +
221C VAL* 3.9 9.2 - - + -
16D PHE* 4.6 5.8 - + - -
31D VAL* 3.7 1.3 - - - +
32D THR* 2.9 47.1 + - + +
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Residues in contact with HIS 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C TYR* 4.2 10.8 - + - -
180C PHE* 3.4 28.1 - + + -
192C ARG* 3.5 18.2 - - - +
208C ALA* 5.2 4.9 - - + -
209C HIS* 1.3 85.8 + - - +
211C HIS* 1.3 86.9 + - - +
212C GLU* 3.4 24.7 - - - -
220C GLU* 3.2 56.3 + - + +
222C ALA* 5.7 3.6 - - + +
469C MN 4.1 5.5 + - - -
30D HIS 4.9 1.1 - - - +
31D VAL* 3.9 15.7 - - + +
32D THR 5.2 0.2 - - - +
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Residues in contact with HIS 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C GLU* 2.7 36.8 + - - -
173C PRO* 4.6 5.9 - - + +
178C GLY* 2.9 22.1 - - - +
179C TYR* 4.1 0.7 - - - -
180C PHE* 4.0 20.1 - - - +
181C PRO 5.8 0.2 - - - -
186C ASP* 3.3 30.9 + - + +
192C ARG* 3.6 11.3 - - - +
210C HIS* 1.3 106.2 + - - +
212C GLU* 1.3 86.4 + - - +
214C ALA 3.6 11.5 + - - -
217C GLY* 4.0 5.6 - - - -
218C GLN 3.1 14.0 + - - -
219C ASN* 3.7 15.5 + - - +
30D HIS* 5.8 1.4 + - + -
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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