Contacts of the strand formed by residues 206 - 211 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J PRO* 3.0 16.6 - - + +
36J HIS* 3.0 27.0 - - - -
196K CYS* 3.6 43.3 - - + +
199K MET* 4.3 11.4 - - + -
200K GLU* 2.9 34.6 + - + +
205K VAL* 1.3 73.1 - - - +
207K GLU* 1.3 63.8 + - - +
208K ALA 3.6 13.9 - - - +
221K VAL* 3.9 7.4 - - + -
222K ALA 3.6 8.7 - - - +
223K THR* 4.3 7.6 - - + -
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Residues in contact with GLU 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33J ILE* 3.3 10.2 - - - +
34J PRO* 3.0 14.6 - - - +
37J GLN* 3.4 29.7 + - - +
47J LYS* 5.7 0.5 - - - -
205K VAL* 3.7 1.7 + - + -
206K VAL* 1.3 75.8 - - - +
208K ALA* 1.3 67.5 + - + +
222K ALA* 2.8 16.0 + - + +
223K THR 4.1 1.0 - - - +
224K ARG* 3.5 45.8 - - + +
225K PHE* 5.1 0.7 - - - -
4481K ADP 3.5 38.1 + - - +
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Residues in contact with ALA 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J VAL* 5.2 3.4 - - + -
32J THR 3.2 5.8 - - - +
33J ILE* 3.0 24.9 - - + -
34J PRO* 3.9 6.7 - - - -
206K VAL* 3.5 8.7 - - - +
207K GLU* 1.3 84.7 - - + +
209K HIS* 1.3 61.2 + - - +
210K HIS* 5.4 3.1 - - + -
221K VAL* 3.5 1.4 - - - +
222K ALA* 2.6 45.5 + - + +
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Residues in contact with HIS 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J PHE* 4.5 5.6 - + - -
31J VAL* 3.8 0.9 - - - +
32J THR* 2.8 51.1 + - + +
189K GLN* 2.7 36.1 + - - -
192K ARG* 2.7 31.4 + - + +
193K SER* 3.0 29.9 + - - -
196K CYS* 3.6 30.5 - - - -
208K ALA* 1.3 74.8 - - - +
210K HIS* 1.3 66.9 + - - +
220K GLU 3.6 12.8 - - - +
221K VAL* 3.9 7.4 - - + -
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Residues in contact with HIS 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J HIS* 4.9 1.3 - - - +
31J VAL* 3.9 17.3 - - + +
32J THR 5.1 0.2 - - - +
179K TYR* 4.2 10.1 - + - -
180K PHE* 3.4 27.7 - + + -
192K ARG* 3.5 18.8 - - - +
208K ALA* 5.2 4.5 - - + -
209K HIS* 1.3 84.6 + - - +
211K HIS* 1.3 87.9 + - - +
212K GLU* 3.4 25.4 - - - -
220K GLU* 3.2 56.4 + - + +
222K ALA* 5.7 3.8 - - + +
469K MN 4.1 5.5 + - - -
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Residues in contact with HIS 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J HIS* 5.8 2.0 + - + -
155K GLU* 2.7 36.3 + - - -
173K PRO* 4.6 5.3 - - + +
178K GLY* 2.9 22.4 - - - +
179K TYR* 4.1 0.6 - - - -
180K PHE* 4.0 19.3 - - - +
181K PRO 5.8 0.2 - - - -
186K ASP* 3.3 30.4 + - + +
192K ARG* 3.6 11.3 - - - +
210K HIS* 1.3 104.9 + - - +
212K GLU* 1.3 86.1 + - - +
214K ALA 3.6 12.5 + - - -
217K GLY* 4.0 5.4 - - - -
218K GLN 3.1 13.4 + - - -
219K ASN* 3.7 15.0 + - - +
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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