Contacts of the helix formed by residues 103 - 118 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J PHE* 6.1 0.2 - - - +
22J THR 4.5 4.3 + - - +
57J TRP* 4.6 3.4 - - - -
89J CYS 5.5 0.5 - - - +
90J ASP* 3.8 6.8 - - - +
91J ILE* 2.9 52.2 + - + +
100J TYR* 3.1 19.3 + - + +
102J ARG* 1.3 74.7 - - - +
104J PRO* 1.3 62.4 - - - +
105J ARG* 2.9 18.7 + - - +
106J SER* 2.8 45.2 + - - -
107J ILE* 3.0 13.5 + - - +
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Residues in contact with PRO 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J THR 3.5 15.9 - - - +
23J ASP 3.7 20.4 - - - +
24J THR* 4.0 8.3 - - + +
57J TRP* 4.2 4.7 - - + -
102J ARG 3.0 12.9 - - - +
103J ASP* 1.3 88.8 - - - +
105J ARG* 1.3 55.6 + - - +
107J ILE* 3.4 6.6 + - + +
108J ALA 3.0 22.5 + - - -
366J ASN* 3.8 15.5 - - - +
368J TYR* 3.4 23.0 - - + +
369J LEU* 3.6 27.2 - - + +
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Residues in contact with ARG 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J THR* 5.5 3.8 + - - +
70J ASP* 3.1 32.3 + - - +
73J THR* 3.5 12.7 - - - +
88J ARG* 3.8 13.6 - - - +
89J CYS 4.0 14.9 + - - +
90J ASP* 3.1 31.1 + - - +
103J ASP* 2.9 14.7 + - - +
104J PRO* 1.3 77.0 - - - +
106J SER* 1.3 66.1 + - - +
108J ALA* 3.3 2.6 + - - +
109J LYS* 3.1 36.5 + - + +
229J THR* 4.6 11.3 - - + +
233J ASP* 2.9 37.7 + - - -
368J TYR* 3.9 31.3 - - + -
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Residues in contact with SER 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J ASP* 4.6 7.8 + - - +
91J ILE 3.9 1.6 + - - -
92J LEU* 4.8 0.9 - - - +
99J GLY* 3.8 22.6 - - - -
100J TYR 3.8 15.0 - - - -
103J ASP* 2.8 28.0 + - - -
105J ARG* 1.3 77.1 - - - +
107J ILE* 1.3 52.2 + - - +
109J LYS* 3.0 14.3 + - - +
110J ARG* 2.7 43.9 + - - +
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Residues in contact with ILE 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100J TYR 5.0 0.7 - - - +
101J ASP 3.6 25.8 - - - +
102J ARG* 4.4 5.4 - - - +
103J ASP 3.3 15.0 - - - +
104J PRO* 3.5 9.9 - - + +
106J SER* 1.3 76.1 - - - +
108J ALA* 1.3 61.9 + - - +
110J ARG* 3.5 13.3 - - - +
111J ALA* 3.1 19.6 + - - +
369J LEU* 4.1 20.0 - - + -
372J ALA* 4.7 2.5 - - + -
433J VAL* 3.6 20.3 - - + +
434J PHE* 3.5 45.8 - - + -
438J ALA* 4.7 6.1 - - + -
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Residues in contact with ALA 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104J PRO 3.0 13.8 + - - +
105J ARG 3.6 7.9 - - - +
107J ILE* 1.3 77.1 - - - +
109J LYS* 1.3 63.9 + - - +
111J ALA* 3.4 1.7 + - - -
112J GLU* 3.1 17.0 + - - +
228J MET* 3.5 25.9 - - + +
229J THR* 3.5 19.1 + - + +
368J TYR* 3.9 28.7 - - + +
372J ALA* 4.7 3.1 - - - -
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Residues in contact with LYS 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70J ASP* 4.3 7.2 + - - -
90J ASP* 3.1 36.6 + - - +
105J ARG* 3.1 35.5 + - + +
106J SER* 3.0 11.3 + - - +
108J ALA* 1.3 74.7 - - - +
110J ARG* 1.3 66.4 + - + +
112J GLU* 2.9 8.2 + - - +
113J ASP* 2.9 31.5 + - - +
229J THR* 4.0 20.4 - - + +
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Residues in contact with ARG 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99J GLY* 3.1 24.7 + - - -
100J TYR 3.9 3.5 + - - -
101J ASP* 3.1 34.2 + - - +
106J SER* 2.7 24.7 + - - +
107J ILE* 3.5 12.8 - - - +
109J LYS* 1.3 72.9 - - - +
111J ALA* 1.3 61.8 + - - +
113J ASP* 3.1 13.0 + - - +
114J TYR* 3.0 23.9 + - - +
431J GLY 5.5 2.3 - - - +
432J GLY 3.5 18.4 + - - -
433J VAL* 3.0 38.1 + - + +
435J THR* 3.5 19.4 - - - +
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Residues in contact with ALA 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107J ILE 3.1 10.4 + - - +
108J ALA 3.5 9.0 - - - +
110J ARG* 1.3 81.2 - - - +
112J GLU* 1.3 60.4 + - - +
114J TYR* 3.6 2.8 + - - +
115J LEU* 3.2 15.8 + - - +
228J MET* 4.2 14.6 - - + -
372J ALA* 4.2 8.7 - - + -
375J LEU* 3.7 17.8 - - + +
376J MET* 4.0 13.5 - - - -
433J VAL* 3.7 22.8 - - + +
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Residues in contact with GLU 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J ALA 3.1 16.2 + - - +
109J LYS* 2.9 12.0 + - - +
111J ALA* 1.3 73.7 - - - +
113J ASP* 1.3 65.7 + - - +
115J LEU* 3.3 19.6 + - - +
116J ARG* 3.5 28.4 + - - +
123J THR* 4.9 4.2 - - - +
124J VAL* 4.0 21.3 + - + +
227J THR* 3.8 13.7 + - - -
228J MET* 3.9 25.4 + - + +
229J THR* 3.1 40.0 + - - +
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Residues in contact with ASP 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J LYS* 2.9 24.4 + - - +
110J ARG* 3.1 12.6 + - - +
112J GLU* 1.3 72.8 - - - +
114J TYR* 1.3 52.1 + - - +
115J LEU 3.0 4.3 - - - -
116J ARG* 3.0 30.9 + - - +
117J ALA* 2.8 32.5 + - - +
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Residues in contact with TYR 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J ARG 3.0 14.5 + - - +
111J ALA 3.7 3.8 - - - +
113J ASP* 1.3 74.8 - - - +
115J LEU* 1.3 61.0 + - - +
117J ALA* 3.7 11.2 - - + +
118J THR* 3.1 40.2 + - + +
376J MET* 4.3 11.2 - - + -
379J LEU* 3.6 31.0 - - + -
383J LYS* 3.1 26.7 - - - +
430J ALA* 3.6 18.4 - - + +
431J GLY* 3.1 42.6 - - - +
433J VAL* 4.2 10.1 - - + -
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Residues in contact with LEU 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111J ALA 3.2 11.6 + - - +
112J GLU* 3.3 13.9 - - - +
113J ASP 3.0 1.0 + - - -
114J TYR* 1.3 77.6 - - - +
116J ARG* 1.3 60.6 + - - +
118J THR* 3.0 19.3 + - - -
119J GLY 3.5 2.6 + - - -
120J ILE* 3.8 4.2 + - + -
121J ALA* 3.2 53.5 - - + +
122J ASP 4.1 1.6 - - - -
123J THR* 3.7 15.7 - - - +
124J VAL* 3.8 26.2 - - + -
274J LEU* 3.8 7.2 - - + -
375J LEU* 4.4 2.2 - - + -
379J LEU* 3.2 40.6 - - + -
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Residues in contact with ARG 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J GLU* 3.5 28.5 + - - +
113J ASP* 3.0 32.4 + - - +
115J LEU* 1.3 79.7 - - - +
117J ALA* 1.3 57.6 + - - +
119J GLY* 3.0 19.1 + - - -
121J ALA 3.4 5.2 - - - -
122J ASP* 3.3 50.6 + - + +
123J THR* 4.7 5.9 - - - +
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Residues in contact with ALA 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J ASP 2.8 16.0 + - - +
114J TYR* 3.7 13.9 - - + +
115J LEU 3.2 0.2 - - - -
116J ARG* 1.3 74.6 - - - +
118J THR* 1.3 59.0 + - + +
119J GLY* 2.9 9.6 + - - -
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Residues in contact with THR 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J TYR* 3.1 47.9 + - + +
115J LEU* 3.0 14.7 + - - +
117J ALA* 1.3 74.2 - - + +
119J GLY* 1.3 51.9 + - - +
120J ILE* 2.7 47.1 + - + +
379J LEU* 4.9 0.5 - - - +
383J LYS* 4.8 9.0 - - + -
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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