Contacts of the strand formed by residues 206 - 211 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G PRO* 3.1 25.6 - - + +
36G HIS* 3.1 15.1 - - - -
37G GLN* 4.3 0.2 - - - -
196H CYS* 3.6 44.2 - - + +
199H MET* 4.3 11.4 - - + -
200H GLU* 2.9 34.5 + - + +
205H VAL* 1.3 74.3 - - - +
207H GLU* 1.3 63.8 + - - +
208H ALA 3.6 13.5 - - - +
221H VAL* 3.9 7.0 - - + -
222H ALA 3.6 9.4 - - - +
223H THR* 4.3 7.2 - - + -
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Residues in contact with GLU 207 (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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33G ILE* 3.4 10.2 - - - +
34G PRO* 3.1 14.1 - - - +
37G GLN* 3.5 27.8 + - - +
47G LYS* 5.8 0.3 - - - -
205H VAL* 3.7 2.4 + - + -
206H VAL* 1.3 75.9 - - - +
208H ALA* 1.3 66.1 + - + +
222H ALA* 2.8 16.4 + - + +
223H THR 4.1 1.2 - - - +
224H ARG* 3.5 44.8 - - + +
225H PHE* 5.1 0.7 - - - -
4478H ADP 3.5 37.7 + - - +
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Residues in contact with ALA 208 (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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31G VAL* 5.2 3.6 - - + -
32G THR 3.2 5.8 - - - +
33G ILE* 3.1 24.2 - - + -
34G PRO* 4.0 5.2 - - - -
206H VAL* 3.5 9.1 - - - +
207H GLU* 1.3 85.5 - - + +
209H HIS* 1.4 61.5 + - - +
210H HIS* 5.2 3.5 - - + -
221H VAL* 3.5 1.4 - - - +
222H ALA* 2.6 44.4 + - + +
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Residues in contact with HIS 209 (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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16G PHE* 4.6 5.4 - + - -
31G VAL* 3.8 1.5 - - - +
32G THR* 2.9 47.1 + - + +
189H GLN* 2.7 35.6 + - - -
192H ARG* 2.7 31.4 + - + +
193H SER* 3.0 30.6 + - - -
196H CYS* 3.6 30.7 - - - -
208H ALA* 1.4 76.2 - - - +
210H HIS* 1.3 66.9 + - - +
220H GLU 3.6 11.9 - - - +
221H VAL* 3.9 7.9 - - + -
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Residues in contact with HIS 210 (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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30G HIS* 4.9 1.3 - - - +
31G VAL* 3.9 16.2 - - + +
32G THR 5.2 0.4 - - - +
179H TYR* 4.2 11.0 - + - -
180H PHE* 3.4 26.1 - + + -
192H ARG* 3.5 17.5 - - - +
208H ALA* 5.2 4.7 - - + -
209H HIS* 1.3 86.0 + - - +
211H HIS* 1.3 88.4 + - - +
212H GLU* 3.4 25.1 - - - -
220H GLU* 3.2 57.1 + - + +
222H ALA* 5.7 4.0 - - + +
469H MN 4.1 5.3 + - - -
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Residues in contact with HIS 211 (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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30G HIS* 5.8 2.0 + - + -
155H GLU* 2.7 36.9 + - - -
173H PRO* 4.6 6.1 - - + +
178H GLY* 2.9 22.1 - - - +
179H TYR* 4.1 0.6 - - - -
180H PHE* 4.0 20.0 - - - +
181H PRO 5.8 0.4 - - - -
186H ASP* 3.3 30.6 + - + +
192H ARG* 3.6 11.7 - - - +
210H HIS* 1.3 105.6 + - - +
212H GLU* 1.3 87.3 + - - +
214H ALA 3.6 11.7 + - - -
217H GLY* 4.0 6.3 - - - -
218H GLN 3.1 13.5 + - - -
219H ASN* 3.7 14.2 + - - +
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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