Contacts of the helix formed by residues 103 - 118 (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 ASP 103 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F PHE* 6.1 0.5 - - - +
22F THR 4.5 4.7 + - - +
57F TRP* 4.6 3.1 - - - -
89F CYS 5.5 0.5 - - - +
90F ASP* 3.8 7.0 - - - +
91F ILE* 2.9 52.7 + - + +
100F TYR* 3.1 18.7 + - + +
102F ARG* 1.3 74.7 - - - +
104F PRO* 1.3 63.5 - - - +
105F ARG* 2.9 18.5 + - - +
106F SER* 2.8 47.8 + - - -
107F ILE* 3.0 12.5 + - - +
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Residues in contact with PRO 104 (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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22F THR 3.5 15.5 - - - +
23F ASP 3.7 20.2 - - - +
24F THR* 4.0 8.1 - - - +
57F TRP* 4.2 4.9 - - + -
102F ARG 2.9 12.7 - - - +
103F ASP* 1.3 90.2 - - - +
105F ARG* 1.3 56.4 + - - +
107F ILE* 3.4 5.8 + - + +
108F ALA 3.0 22.3 + - - -
366F ASN* 3.8 14.4 - - - +
368F TYR* 3.4 22.5 - - + +
369F LEU* 3.6 27.4 - - + +
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Residues in contact with ARG 105 (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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22F THR* 5.5 3.7 + - - +
70F ASP* 3.1 33.1 + - - +
73F THR* 3.5 12.3 - - - +
88F ARG* 3.8 13.8 - - - +
89F CYS 4.0 14.6 + - - +
90F ASP* 3.1 30.7 + - - +
103F ASP* 2.9 14.7 + - - +
104F PRO* 1.3 77.2 - - - +
106F SER* 1.3 65.9 + - - +
108F ALA* 3.3 2.4 + - - +
109F LYS* 3.1 36.3 + - + +
229F THR* 4.6 11.7 - - + +
233F ASP* 2.9 37.5 + - - -
368F TYR* 3.9 32.6 - - + -
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Residues in contact with SER 106 (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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90F ASP* 4.6 7.2 + - - +
91F ILE 3.9 1.9 + - - -
92F LEU* 4.8 1.4 - - - +
99F GLY* 3.8 22.1 - - - -
100F TYR 3.8 15.0 - - - -
103F ASP* 2.8 27.5 + - - -
105F ARG* 1.3 77.5 - - - +
107F ILE* 1.3 52.8 + - - +
109F LYS* 3.0 12.4 + - - +
110F ARG* 2.7 45.2 + - - +
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Residues in contact with ILE 107 (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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100F TYR 5.0 0.7 - - - +
101F ASP 3.6 25.1 - - - +
102F ARG* 4.4 5.2 - - - +
103F ASP 3.0 14.3 + - - +
104F PRO* 3.5 9.6 - - + +
106F SER* 1.3 77.7 - - - +
108F ALA* 1.3 62.1 + - - +
110F ARG* 3.4 13.3 + - - +
111F ALA* 3.1 18.7 + - - +
369F LEU* 4.1 18.8 - - + -
372F ALA* 4.7 2.9 - - + -
433F VAL* 3.6 20.5 - - + +
434F PHE* 3.5 46.0 - - + -
438F ALA* 4.7 5.4 - - + -
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Residues in contact with ALA 108 (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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104F PRO 3.0 14.0 + - - +
105F ARG 3.6 8.1 - - - +
106F SER 3.2 0.2 - - - -
107F ILE* 1.3 77.2 - - - +
109F LYS* 1.3 62.9 + - - +
111F ALA* 3.4 1.8 + - - -
112F GLU* 3.1 16.6 + - - +
228F MET* 3.5 26.9 - - + +
229F THR* 3.5 18.4 + - - +
232F ALA* 5.9 0.2 - - + -
368F TYR* 3.9 28.2 + - + +
372F ALA* 4.7 3.8 - - - -
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Residues in contact with LYS 109 (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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70F ASP* 4.3 6.7 + - - -
90F ASP* 3.1 38.4 + - - +
105F ARG* 3.1 34.1 + - + +
106F SER* 3.0 12.4 + - - +
108F ALA* 1.3 75.1 - - - +
110F ARG* 1.3 65.6 + - - +
112F GLU* 2.9 8.4 + - - +
113F ASP* 2.9 31.9 + - - +
229F THR* 4.0 20.6 - - + -
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Residues in contact with ARG 110 (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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99F GLY* 3.1 24.5 + - - -
100F TYR 3.9 3.7 + - - -
101F ASP* 3.0 34.0 + - - +
106F SER* 2.7 25.5 + - - +
107F ILE* 3.5 12.6 - - - +
109F LYS* 1.3 72.7 - - - +
111F ALA* 1.3 63.1 + - - +
113F ASP* 3.1 13.6 + - - +
114F TYR* 3.0 23.7 + - - +
431F GLY 5.5 1.9 - - - +
432F GLY 3.5 18.7 + - - -
433F VAL* 3.0 39.2 + - + +
435F THR* 3.5 20.0 - - - +
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Residues in contact with ALA 111 (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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107F ILE 3.1 11.1 + - - +
108F ALA 3.5 9.4 - - - +
109F LYS 3.2 0.2 - - - -
110F ARG* 1.3 81.6 - - - +
112F GLU* 1.3 60.8 + - - +
114F TYR* 3.6 3.6 + - - +
115F LEU* 3.2 15.6 + - - +
228F MET* 4.2 13.5 - - + -
372F ALA* 4.2 8.1 - - + -
375F LEU* 3.7 18.9 - - + +
376F MET* 4.0 13.2 - - - -
433F VAL* 3.7 22.8 - - + +
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Residues in contact with GLU 112 (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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108F ALA 3.1 16.6 + - - +
109F LYS* 2.9 11.4 + - - +
111F ALA* 1.3 73.1 - - - +
113F ASP* 1.3 66.8 + - - +
115F LEU* 3.3 19.1 + - - +
116F ARG* 3.5 29.0 + - - +
123F THR* 4.9 4.3 - - - +
124F VAL* 4.0 22.5 + - + +
227F THR* 3.8 13.7 + - - -
228F MET* 3.9 24.8 + - + +
229F THR* 3.1 40.4 + - - +
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Residues in contact with ASP 113 (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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109F LYS* 2.9 24.8 + - - +
110F ARG* 3.3 11.7 - - - +
112F GLU* 1.3 72.9 - - - +
114F TYR* 1.3 51.9 + - - +
115F LEU 3.0 4.5 - - - -
116F ARG* 3.0 30.7 + - - +
117F ALA* 2.8 33.4 + - - +
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Residues in contact with TYR 114 (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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110F ARG 3.0 14.7 + - - +
111F ALA 3.7 4.7 - - - +
113F ASP* 1.3 75.7 - - - +
115F LEU* 1.3 61.3 + - - +
117F ALA* 3.7 11.0 - - + -
118F THR* 3.1 40.8 + - + +
376F MET* 4.3 11.4 - - + -
379F LEU* 3.6 31.2 - - + -
383F LYS* 3.1 26.7 - - - +
430F ALA* 3.6 18.9 - - + +
431F GLY* 3.1 43.1 - - - +
433F VAL* 4.2 10.1 - - + -
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Residues in contact with LEU 115 (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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111F ALA 3.2 12.6 + - - +
112F GLU* 3.3 14.4 - - - +
113F ASP 3.0 0.8 + - - -
114F TYR* 1.3 78.6 - - - +
116F ARG* 1.3 61.4 + - - +
118F THR* 3.0 18.6 + - - +
119F GLY 3.5 2.9 + - - -
120F ILE* 3.8 4.2 + - + -
121F ALA* 3.2 53.7 - - + +
122F ASP 4.1 1.8 - - - -
123F THR* 3.7 15.5 - - - +
124F VAL* 3.8 26.2 - - + -
274F LEU* 3.8 8.1 - - + -
375F LEU* 4.4 1.1 - - + -
379F LEU* 3.3 40.4 - - + -
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Residues in contact with ARG 116 (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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112F GLU* 3.5 29.2 + - - +
113F ASP* 3.0 32.6 + - - +
115F LEU* 1.3 77.8 - - - +
117F ALA* 1.3 58.4 + - - +
119F GLY* 3.0 18.5 + - - -
121F ALA 3.4 5.8 - - - +
122F ASP* 3.3 48.9 + - + +
123F THR* 4.7 6.5 - - - +
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Residues in contact with ALA 117 (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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113F ASP 2.8 16.0 + - - +
114F TYR* 3.7 14.1 - - + +
115F LEU 3.2 0.2 - - - -
116F ARG* 1.3 73.6 - - - +
118F THR* 1.3 59.5 + - + +
119F GLY* 2.9 9.7 + - - -
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Residues in contact with THR 118 (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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114F TYR* 3.1 47.0 + - + +
115F LEU* 3.0 14.2 + - - +
117F ALA* 1.3 74.1 - - + +
119F GLY* 1.3 51.9 + - - +
120F ILE* 2.7 47.4 + - + +
379F LEU* 4.9 0.2 - - - +
383F LYS* 4.8 9.2 - - + -
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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