Contacts of the strand formed by residues 84 - 92 (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 THR 84 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H VAL* 4.1 1.3 - - - -
16H PHE* 3.3 29.6 - - + -
18H ASP* 4.1 7.6 - - - +
32H THR* 5.6 0.9 - - - -
76H ILE* 3.6 8.9 - - - +
77H ASP* 2.9 32.9 + - - +
80H PHE* 3.4 42.0 + - + -
82H ASP* 2.7 20.6 + - + +
83H SER* 1.3 73.1 + - - +
85H LEU* 1.4 67.1 + - - +
189I GLN* 5.1 3.1 - - - +
193I SER* 5.5 1.6 - - - +
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Residues in contact with LEU 85 (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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5H VAL* 4.1 22.9 - - + +
8H MET* 3.6 20.6 - - + -
9H LEU* 3.9 20.6 - - + -
14H VAL* 3.6 17.1 - - + +
16H PHE 2.8 9.3 + - - +
17H VAL* 3.0 12.8 - - + +
18H ASP 2.6 32.0 + - - -
74H ALA* 4.1 10.1 - - + -
75H VAL* 3.3 38.4 - - - +
76H ILE* 3.5 11.2 - - + +
84H THR* 1.4 72.9 + - - +
86H ILE* 1.3 61.4 + - - +
87H ILE* 4.4 7.9 - - + -
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Residues in contact with ILE 86 (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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18H ASP* 3.3 11.0 - - + +
20H ARG* 3.5 61.2 - - + +
73H THR 4.0 2.7 - - - +
74H ALA* 3.2 1.6 - - - -
75H VAL* 2.9 45.8 + - + +
77H ASP* 3.5 31.4 - - + +
85H LEU* 1.3 73.5 - - - +
87H ILE* 1.3 77.3 + - - +
88H ARG* 4.8 7.6 - - - +
202H MET* 3.8 18.8 - - + -
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Residues in contact with ILE 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H VAL* 4.5 15.3 - - + -
17H VAL* 3.8 22.4 - - + -
18H ASP 2.8 10.3 + - - +
19H LEU* 3.4 11.4 - - + -
20H ARG 2.9 21.8 + - - -
38H VAL* 5.8 0.9 - - + -
42H PHE* 4.9 8.5 - - + -
43H PHE* 4.6 11.9 - - + -
69H PRO* 3.9 13.0 - - + -
70H ASP 3.7 20.2 - - - +
71H ALA* 4.9 0.4 - - - +
73H THR* 3.8 8.3 - - - +
74H ALA* 4.1 12.6 - - + -
85H LEU* 4.4 13.9 - - + -
86H ILE* 1.3 84.8 - - - +
88H ARG* 1.3 73.5 + - - +
89H CYS* 3.6 3.0 + - - -
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Residues in contact with ARG 88 (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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20H ARG* 3.2 20.8 + - - +
21H PHE* 5.0 1.2 - - - +
22H THR* 4.4 5.9 + - - -
28H GLU* 2.6 45.9 + - - +
70H ASP* 3.1 26.1 + - - +
73H THR* 2.8 28.7 + - + +
86H ILE* 4.8 8.1 - - - +
87H ILE* 1.3 74.4 - - - +
89H CYS* 1.3 66.2 + - - +
105H ARG* 3.8 17.9 - - - +
233H ASP* 3.4 33.1 + - - +
236H GLN* 3.6 16.8 - - - +
237H ILE* 4.0 25.9 - - - +
368H TYR* 3.7 10.9 + - - -
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Residues in contact with CYS 89 (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* 3.6 35.9 - - - -
20H ARG 2.6 13.7 + - - +
21H PHE* 3.8 16.4 - - - +
22H THR 5.3 0.2 + - - -
67H LEU* 3.7 29.8 - - + -
68H MET 3.3 9.9 - - - +
69H PRO* 3.8 21.3 - - - -
87H ILE 3.7 9.6 - - - -
88H ARG* 1.3 76.7 - - - +
90H ASP* 1.3 62.5 + - - +
103H ASP* 5.5 0.3 - - - +
105H ARG* 4.0 15.5 - - - +
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Residues in contact with ASP 90 (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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66H VAL 3.2 2.8 - - - +
67H LEU* 3.6 1.6 - - - -
68H MET* 2.7 44.7 + - + +
69H PRO 5.2 0.2 - - - +
70H ASP* 4.3 6.2 - - - +
89H CYS* 1.3 73.2 - - - +
91H ILE* 1.3 65.0 + - - +
92H LEU* 3.6 18.6 + - + -
103H ASP* 3.8 7.9 - - - +
105H ARG* 3.1 30.7 + - - +
106H SER* 4.6 4.2 + - - +
109H LYS* 3.1 36.5 + - - +
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Residues in contact with ILE 91 (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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21H PHE* 4.1 17.3 - - + -
49H PHE* 3.8 17.0 - - + -
57H TRP* 3.8 26.0 - - + -
65H MET* 3.8 31.2 - - + -
66H VAL 3.4 1.8 - - - +
67H LEU* 3.5 32.1 - - + -
90H ASP* 1.3 71.6 - - - +
92H LEU* 1.3 62.9 + - - +
99H GLY* 3.8 2.6 - - - -
100H TYR* 2.9 38.0 + - + +
103H ASP* 2.9 29.7 + - + +
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Residues in contact with LEU 92 (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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65H MET* 3.3 10.3 - - - +
66H VAL* 3.0 37.1 + - + -
68H MET* 3.5 48.5 - - + -
90H ASP* 4.1 16.6 - - + -
91H ILE* 1.3 78.3 - - - +
93H GLU* 1.3 61.9 + - - +
97H LEU* 3.6 31.9 - - + +
98H GLN 4.3 3.6 - - - +
99H GLY* 3.8 21.8 - - - +
100H TYR* 4.0 3.1 - - - +
106H SER* 4.8 2.0 - - - +
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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