Contacts of the strand formed by residues 84 - 92 (chain F) in PDB entry 1F1H
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14F VAL* 4.1 0.4 - - - -
16F PHE* 3.0 13.6 + - - +
18F ASP* 4.0 16.8 + - - +
32F THR* 5.5 0.3 - - - +
76F ILE* 3.6 10.0 - - - +
77F ASP* 3.0 31.9 + - + +
80F PHE* 3.4 25.6 - - + -
82F ASP 2.6 30.5 + - - +
83F SER* 1.3 73.3 + - - +
85F LEU* 1.3 60.5 + - - +
1488F MPD 2.9 38.6 + - + +
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Residues in contact with LEU 85 (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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5F VAL* 4.0 22.4 - - + -
8F MET* 4.1 27.6 - - + -
9F LEU* 3.8 21.8 - - + -
14F VAL* 3.8 17.6 - - + +
16F PHE 2.8 8.2 + - - +
17F VAL* 3.1 11.0 - - + +
18F ASP 2.7 28.8 + - - -
74F ALA* 4.2 8.5 - - + -
75F VAL* 3.6 31.2 - - - +
76F ILE* 3.8 14.1 - - + +
84F THR* 1.3 73.2 + - - +
86F ILE* 1.3 62.5 + - - +
87F ILE* 4.3 8.1 - - + -
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Residues in contact with ILE 86 (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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18F ASP* 3.4 11.7 - - + +
20F ARG* 3.5 58.8 - - + +
73F THR 3.9 1.7 - - - +
74F ALA* 3.3 1.9 - - - -
75F VAL* 2.6 48.6 + - + +
77F ASP* 3.5 31.2 - - + +
85F LEU* 1.3 73.5 - - - +
87F ILE* 1.3 71.1 + - - +
88F ARG* 4.7 9.4 - - - +
202F MET* 3.6 25.8 - - + -
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Residues in contact with ILE 87 (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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5F VAL* 4.2 26.7 - - + -
17F VAL* 3.9 22.9 - - + -
18F ASP 2.9 8.3 + - - +
19F LEU* 3.5 11.9 - - + -
20F ARG 3.0 19.7 + - - -
38F VAL* 5.7 0.9 - - + -
42F PHE* 4.8 8.5 - - + -
43F PHE* 4.6 9.6 - - + -
69F PRO* 3.9 20.0 - - + -
70F ASP 3.7 17.5 - - - +
71F ALA* 4.7 2.7 - - - +
73F THR* 3.9 3.1 - - - +
74F ALA* 4.2 11.9 - - + +
85F LEU* 3.9 7.2 + - + -
86F ILE* 1.3 81.0 - - - +
88F ARG* 1.3 73.0 + - - +
89F CYS* 3.7 2.6 - - - -
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Residues in contact with ARG 88 (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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20F ARG* 3.3 21.4 + - - +
21F PHE* 5.1 3.5 - - - +
22F THR* 4.9 3.6 + - - -
28F GLU* 2.5 44.7 + - - +
70F ASP* 3.0 24.8 + - - +
73F THR* 2.9 30.4 + - + +
75F VAL* 6.2 1.2 - - - +
86F ILE* 4.2 10.9 - - - +
87F ILE* 1.3 76.4 - - - +
89F CYS* 1.3 64.8 + - - +
105F ARG* 3.8 17.9 - - - +
233F ASP* 3.4 34.3 + - - +
236F GLN* 3.7 15.1 - - - +
237F ILE* 3.8 29.1 - - - +
368F TYR* 3.8 10.1 + - - -
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Residues in contact with CYS 89 (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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19F LEU* 3.8 26.5 - - - -
20F ARG 2.7 15.4 + - - +
21F PHE* 4.0 10.8 - - + +
67F LEU* 3.6 31.2 - - + -
68F MET 3.3 10.5 - - - +
69F PRO* 3.8 19.3 - - - -
70F ASP* 4.4 0.4 - - - +
87F ILE 3.7 11.4 - - - -
88F ARG* 1.3 81.9 - - - +
90F ASP* 1.3 65.2 + - - +
103F ASP* 5.6 0.2 - - - +
105F ARG* 3.8 17.2 - - - +
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Residues in contact with ASP 90 (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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66F VAL 3.4 1.7 - - - +
67F LEU* 3.7 2.4 - - - -
68F MET* 2.8 45.8 + - + +
70F ASP* 4.3 5.2 - - - +
89F CYS* 1.3 74.0 - - - +
91F ILE* 1.3 63.6 + - - +
92F LEU* 3.9 17.9 - - + -
103F ASP* 3.7 7.7 - - - +
105F ARG* 3.0 39.0 + - - +
106F SER* 4.4 4.4 + - - +
109F LYS* 3.1 29.2 + - - +
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Residues in contact with ILE 91 (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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21F PHE* 3.9 23.3 - - + -
49F PHE* 4.0 15.9 - - + -
57F TRP* 3.7 24.7 - - + -
65F MET* 3.7 31.0 - - + -
66F VAL 3.4 2.7 - - - +
67F LEU* 3.6 29.2 - - + -
89F CYS 5.5 0.2 - - - +
90F ASP* 1.3 73.7 - - - +
92F LEU* 1.3 63.6 + - - +
99F GLY* 3.7 4.0 - - - -
100F TYR* 3.0 32.2 + - + +
103F ASP* 2.8 31.3 + - + +
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Residues in contact with LEU 92 (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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65F MET* 3.4 7.1 - - - +
66F VAL* 2.9 39.1 + - + +
68F MET* 3.3 50.3 - - + -
90F ASP* 4.1 15.9 - - + -
91F ILE* 1.3 79.0 - - - +
93F GLU* 1.3 62.1 + - - +
97F LEU* 3.8 31.4 - - + +
98F GLN 4.1 4.5 - - - +
99F GLY* 3.5 24.5 - - - +
100F TYR 4.4 0.4 - - - -
106F SER* 4.6 1.8 - - - +
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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