Contacts of the strand formed by residues 28 - 34 (chain F) 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 GLU 28 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181E PRO* 4.0 0.5 - - - +
182E VAL* 3.3 49.2 + - + +
20F ARG* 3.4 22.1 + - + -
21F PHE 3.5 8.5 - - - +
22F THR* 4.3 0.7 - - - +
26F GLY 3.4 3.8 + - - -
27F LYS* 1.3 72.7 - - - +
29F GLN* 1.3 73.1 + - - +
88F ARG* 2.6 37.4 + - - +
236F GLN* 3.6 39.8 - - - +
237F ILE* 5.1 1.6 + - - +
240F TYR* 4.1 10.4 - - - +
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Residues in contact with GLN 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179E TYR 3.0 24.1 - - - +
180E PHE* 3.0 16.8 - - + +
181E PRO* 3.5 7.4 - - - +
182E VAL* 4.3 1.3 - - - -
20F ARG* 3.0 8.5 - - - +
21F PHE* 2.6 71.3 + - + +
23F ASP* 4.1 15.0 + - + +
27F LYS* 2.6 44.1 + - - +
28F GLU* 1.3 87.2 + - - +
30F HIS* 1.3 62.2 + - - +
54F ILE* 5.0 6.8 - - + +
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Residues in contact with HIS 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E PHE* 3.0 32.8 + - - +
181E PRO 3.3 23.4 + - - -
182E VAL* 3.6 8.5 - - + -
183E PRO* 3.5 13.2 - - + +
186E ASP* 3.1 25.4 + - - -
189E GLN* 3.3 25.7 + - + +
192E ARG* 3.7 3.8 + - - -
210E HIS* 4.9 1.8 - - - +
211E HIS 5.8 2.2 + - - -
18F ASP* 2.9 42.6 - - - +
19F LEU 2.9 9.6 - - - +
20F ARG* 3.6 10.8 - - + -
21F PHE* 5.2 1.3 - - - -
29F GLN* 1.3 77.4 - - - +
31F VAL* 1.3 65.4 + - - +
32F THR* 3.9 1.3 - - - -
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Residues in contact with VAL 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E PHE* 4.0 19.3 - - + -
208E ALA* 5.2 2.0 - - + -
209E HIS 3.9 11.2 - - - +
210E HIS* 3.9 17.0 - - + +
17F VAL 3.5 0.9 - - - +
18F ASP* 3.3 1.7 - - - +
19F LEU* 2.7 70.1 + - + +
21F PHE* 5.5 1.3 - - + -
30F HIS* 1.3 80.2 - - - +
32F THR* 1.3 71.7 + - - +
33F ILE* 3.9 8.5 + - + -
49F PHE* 6.4 0.2 - - + -
67F LEU* 4.0 16.6 - - + -
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Residues in contact with THR 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E GLN* 2.6 31.0 + - - +
192E ARG* 4.3 0.2 + - - -
208E ALA* 3.2 0.9 - - - +
209E HIS* 2.9 62.5 + - + +
16F PHE* 3.6 28.0 - - + -
17F VAL 3.3 11.9 - - - +
18F ASP* 2.7 13.6 + - + +
30F HIS* 3.9 1.0 - - - -
31F VAL* 1.3 73.2 - - - +
33F ILE* 1.3 73.9 + - - +
34F PRO* 4.4 0.4 - - - +
84F THR* 5.6 1.1 - - - -
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Residues in contact with ILE 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E GLU 3.4 12.1 - - - +
208E ALA* 3.1 25.1 - - + -
16F PHE* 3.4 4.5 - - - -
17F VAL* 2.6 46.9 + - + +
19F LEU* 4.6 20.9 - - + -
31F VAL* 4.5 11.2 - - + -
32F THR* 1.3 80.0 - - - +
34F PRO* 1.3 73.2 - - - +
37F GLN* 3.6 15.0 - - + +
38F VAL* 4.0 18.2 - - + -
42F PHE* 5.5 3.8 - - + -
47F LYS* 5.0 17.3 - - + +
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Residues in contact with PRO 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E GLU* 4.8 2.2 - - - +
206E VAL* 3.0 36.3 - - + +
207E GLU 3.0 22.9 - - - +
208E ALA* 3.9 2.9 - - - +
15F LYS 3.7 8.5 - - - +
16F PHE* 3.9 15.5 - - + -
32F THR 4.4 0.2 - - - +
33F ILE* 1.3 94.3 - - - +
35F ALA* 1.3 66.9 + - - +
36F HIS* 3.5 26.2 - - + +
37F GLN* 2.9 16.9 + - + -
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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