Contacts of the strand formed by residues 16 - 22 (chain I) 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 PHE 16 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I VAL* 2.9 9.5 - - - +
15I LYS* 1.3 95.6 - - + +
17I VAL* 1.3 60.4 - - - +
32I THR* 3.6 23.8 - - + -
33I ILE 3.4 3.1 - - - -
34I PRO* 3.9 23.6 - - + -
35I ALA 3.9 0.7 - - - +
82I ASP* 4.0 13.7 - - + -
83I SER 3.3 3.0 + - - -
84I THR* 3.3 15.0 - - + -
85I LEU 2.8 28.7 + - - -
189J GLN* 6.0 0.2 - - - +
193J SER* 3.6 44.2 - - - -
196J CYS* 4.0 18.6 - - + -
197J LEU* 3.7 25.8 - - + -
209J HIS* 4.6 5.8 - + - -
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Residues in contact with VAL 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I VAL* 6.4 0.2 - - + -
9I LEU* 4.3 18.8 - - + -
16I PHE* 1.3 80.3 - - - +
18I ASP* 1.3 61.5 + - - +
19I LEU* 3.6 24.4 + - + -
31I VAL 3.5 1.6 - - - +
32I THR* 3.3 5.0 - - - +
33I ILE* 2.6 49.2 + - + +
35I ALA* 4.3 10.3 - - - -
38I VAL* 3.9 24.2 - - + -
42I PHE* 5.2 0.4 - - + -
85I LEU* 3.0 13.9 - - + +
87I ILE* 3.8 21.1 - - + -
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Residues in contact with ASP 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I PHE 4.2 0.4 - - - -
17I VAL* 1.3 71.7 - - - +
19I LEU* 1.3 65.9 + - - +
20I ARG* 2.8 33.0 + - - +
30I HIS* 2.9 29.7 - - - +
31I VAL 3.3 4.0 - - - +
32I THR* 2.7 29.6 + - + -
80I PHE* 4.0 9.5 - - + -
84I THR* 4.1 13.2 + - - +
85I LEU 2.6 12.9 + - - +
86I ILE* 3.3 9.2 - - + +
87I ILE 2.8 27.6 + - - -
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Residues in contact with LEU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I VAL* 3.6 28.0 - - + +
18I ASP* 1.3 71.6 - - - +
20I ARG* 1.3 60.7 + - - +
21I PHE* 4.8 2.7 - - - -
30I HIS* 2.9 5.2 - - - -
31I VAL* 2.7 63.4 + - + +
33I ILE* 4.6 19.5 - - + -
42I PHE* 4.1 27.4 - - + -
47I LYS* 5.1 6.5 - - + -
67I LEU* 4.3 15.9 - - + -
87I ILE* 3.4 9.9 - - + +
89I CYS* 3.6 23.6 - - - -
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Residues in contact with ARG 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ASP* 2.8 22.8 + - - +
19I LEU* 1.3 80.2 - - - +
21I PHE* 1.3 59.7 + - - +
28I GLU* 3.4 30.7 + - + +
29I GLN 3.0 8.1 - - - +
30I HIS* 3.6 13.9 - - + +
77I ASP* 2.6 27.7 + - - -
80I PHE* 3.6 8.7 - - - -
86I ILE* 3.5 40.1 - - + +
87I ILE 2.9 9.1 + - - +
88I ARG* 3.2 14.8 - - - +
89I CYS* 2.6 34.6 + - - -
202I MET* 5.2 0.6 - - - +
240I TYR* 3.4 39.8 + - - +
182J VAL* 4.2 4.7 - - - +
183J PRO* 6.0 0.2 - - - -
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Residues in contact with PHE 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I LEU 4.8 2.5 - - - -
20I ARG* 1.3 78.6 - - - +
22I THR* 1.3 65.8 + - - +
23I ASP* 4.6 0.4 - - - -
28I GLU* 3.5 4.1 - - - +
29I GLN* 2.6 69.4 + - + +
30I HIS* 4.7 1.6 - - - -
31I VAL* 5.5 0.7 - - + -
49I PHE* 4.3 8.5 - + - -
54I ILE* 3.7 20.4 - - + -
57I TRP* 3.6 35.0 - + - -
67I LEU* 3.6 28.0 - - + -
88I ARG* 5.0 4.3 - - - +
89I CYS 3.8 17.3 - - - +
91I ILE* 4.1 14.1 - - + -
103I ASP* 6.1 0.7 - - - +
180J PHE* 3.9 20.2 - + - -
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Residues in contact with THR 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I PHE* 1.3 85.3 + - - +
23I ASP* 1.3 74.4 + - - +
26I GLY* 3.4 15.9 - - - +
27I LYS 3.8 2.2 - - - +
28I GLU* 4.3 0.6 - - - +
57I TRP* 3.6 8.1 - - - -
88I ARG* 4.4 5.5 + - - -
103I ASP* 4.5 4.0 + - - +
104I PRO* 3.5 19.2 - - + +
105I ARG* 5.9 3.6 - - - +
236I GLN* 3.1 34.2 + - - +
366I ASN* 4.4 1.8 - - - +
368I TYR* 3.4 36.0 + - + -
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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