Contacts of the strand formed by residues 64 - 69 (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 ASP 64 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H MET* 3.2 28.8 - - + +
49H PHE* 3.5 15.6 + - - +
50H ASP* 4.1 5.1 + - - +
62H GLU 2.8 12.0 + - - +
63H SER* 1.3 69.6 - - - +
65H MET* 1.3 61.0 + - - +
94H PRO* 3.3 22.5 - - - +
339I ARG* 2.7 23.2 + - - +
344I ARG* 3.5 21.3 + - - -
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Residues in contact with MET 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H MET* 3.4 5.2 - - - +
49H PHE* 2.9 51.3 + - + +
51H GLY* 4.7 3.1 - - - +
57H TRP* 4.7 8.1 - - + +
62H GLU 4.9 0.7 - - - +
63H SER* 3.4 41.9 + - - +
64H ASP* 1.3 74.6 - - - +
66H VAL* 1.3 62.5 + - - +
91H ILE* 3.8 21.1 - - + -
92H LEU 3.3 20.2 - - - +
93H GLU* 3.8 22.7 - - - +
94H PRO* 4.1 5.6 - - + -
100H TYR* 3.6 37.7 - - + +
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Residues in contact with VAL 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H GLU 3.4 25.4 - - - +
46H GLY* 4.2 0.9 - - - -
47H LYS 3.5 10.5 - - - +
48H MET* 4.1 12.1 - - - -
49H PHE* 4.3 2.2 - - - -
65H MET* 1.3 80.0 - - - +
67H LEU* 1.3 71.6 + - - +
68H MET* 3.5 10.0 + - + +
90H ASP 3.2 4.5 - - - +
91H ILE* 3.4 5.0 - - - +
92H LEU* 3.0 38.2 + - + +
94H PRO* 3.8 26.7 - - + -
95H GLY 5.0 0.2 - - - +
97H LEU* 4.2 14.4 - - + -
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Residues in contact with LEU 67 (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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19H LEU* 4.3 11.7 - - + -
21H PHE* 3.6 23.6 - - + -
31H VAL* 4.0 27.6 - - + -
42H PHE* 5.2 0.4 - - + -
46H GLY* 3.1 15.8 - - - -
47H LYS* 2.9 22.7 + - + +
49H PHE* 3.6 31.4 - - + -
66H VAL* 1.3 70.3 - - - +
68H MET* 1.3 60.9 + - - +
69H PRO* 3.0 12.1 - - - +
89H CYS* 3.7 22.7 - - + -
90H ASP 3.7 0.4 - - - -
91H ILE* 3.5 24.0 - - + -
180I PHE* 5.9 0.2 - - + -
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Residues in contact with MET 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H PHE 3.4 24.5 - - - +
44H GLU 3.6 11.2 - - - +
45H GLU* 3.4 11.7 - - - +
46H GLY* 3.4 22.9 - - - +
66H VAL* 4.3 4.7 - - + -
67H LEU* 1.3 72.5 - - - +
69H PRO* 1.3 78.4 - - - +
70H ASP 3.5 0.5 + - - -
89H CYS* 3.3 2.2 - - - +
90H ASP* 2.7 49.3 + - + +
92H LEU* 3.5 38.1 - - + -
97H LEU* 4.9 5.6 - - + -
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Residues in contact with PRO 69 (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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42H PHE* 3.6 45.1 - - + +
43H PHE* 4.0 27.8 - - + +
46H GLY* 3.8 6.1 - - - -
67H LEU 3.0 13.2 - - - +
68H MET* 1.3 101.9 - - - +
70H ASP* 1.3 59.0 + - - +
71H ALA 3.7 2.0 + - - -
87H ILE* 3.9 13.0 - - + -
88H ARG 3.9 0.7 - - - +
89H CYS* 3.8 15.9 - - - -
90H ASP* 5.2 0.3 - - - +
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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