Contacts of the helix formed by residues 103 - 118 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21I PHE* 6.1 0.5 - - - +
22I THR* 4.5 4.0 + - - +
57I TRP* 4.6 3.4 - - - -
89I CYS 5.5 0.3 - - - +
90I ASP* 3.8 6.9 - - - +
91I ILE* 2.9 52.0 + - + +
100I TYR* 3.1 19.4 + - + +
102I ARG* 1.3 74.7 - - - +
104I PRO* 1.3 61.9 - - - +
105I ARG* 2.9 18.3 + - - +
106I SER* 2.8 46.7 + - - -
107I ILE* 3.0 12.9 + - - +
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Residues in contact with PRO 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I THR* 3.5 16.2 - - + +
23I ASP 3.7 20.4 - - - +
24I THR* 4.0 8.5 - - - +
57I TRP* 4.2 4.7 - - + -
102I ARG 2.9 12.0 - - - +
103I ASP* 1.3 88.8 - - - +
105I ARG* 1.3 56.5 + - - +
107I ILE* 3.4 5.8 + - + +
108I ALA 3.0 22.7 + - - -
366I ASN* 3.8 14.6 - - - +
368I TYR* 3.4 23.2 - - + +
369I LEU* 3.6 26.4 - - + +
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Residues in contact with ARG 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I THR* 5.5 4.2 + - - +
70I ASP* 3.1 32.9 + - - +
73I THR* 3.5 12.3 - - - +
88I ARG* 3.8 13.8 - - - +
89I CYS 4.0 15.3 + - - +
90I ASP* 3.1 31.3 + - - +
103I ASP* 2.9 14.9 + - - +
104I PRO* 1.3 77.9 - - - +
106I SER* 1.3 65.8 + - - +
108I ALA* 3.3 2.4 + - - +
109I LYS* 3.1 36.1 + - + +
229I THR* 4.6 12.1 - - + +
233I ASP* 2.9 37.3 + - - -
368I TYR* 3.9 30.4 - - + -
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Residues in contact with SER 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90I ASP* 4.6 7.7 + - - +
91I ILE 3.9 1.9 + - - -
92I LEU* 4.8 1.4 - - - +
99I GLY* 3.8 21.8 - - - -
100I TYR 3.8 15.7 - - - -
103I ASP* 2.8 26.8 + - - -
105I ARG* 1.3 77.1 - - - +
107I ILE* 1.3 53.1 + - - +
109I LYS* 3.0 12.7 + - - +
110I ARG* 2.7 45.4 + - - +
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Residues in contact with ILE 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I TYR 5.0 0.7 - - - +
101I ASP 3.6 26.0 - - - +
102I ARG* 4.4 6.1 - - - +
103I ASP 3.3 14.4 - - - +
104I PRO* 3.5 9.4 - - + +
106I SER* 1.3 76.9 - - - +
108I ALA* 1.3 62.8 + - - +
110I ARG* 3.4 13.3 + - - +
111I ALA* 3.1 18.9 + - - +
369I LEU* 4.1 19.5 - - + -
372I ALA* 4.7 2.9 - - + -
433I VAL* 3.6 20.7 - - + +
434I PHE* 3.5 46.0 - - + -
438I ALA* 4.7 5.4 - - + -
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Residues in contact with ALA 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104I PRO 3.0 13.6 + - - +
105I ARG 3.6 7.9 - - - +
106I SER 3.2 0.2 - - - -
107I ILE* 1.3 77.4 - - - +
109I LYS* 1.3 62.5 + - - +
111I ALA* 3.4 2.3 + - - -
112I GLU* 3.1 16.5 + - - +
228I MET* 3.5 26.1 - - + +
229I THR* 3.5 19.0 + - - +
368I TYR* 3.9 28.2 + - + +
372I ALA* 4.7 3.1 - - - -
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Residues in contact with LYS 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I ASP* 4.3 7.0 + - - -
90I ASP* 3.1 37.2 + - - +
105I ARG* 3.1 36.0 + - + +
106I SER* 3.0 11.3 + - - +
108I ALA* 1.3 75.3 - - - +
110I ARG* 1.3 65.9 + - - +
112I GLU* 2.9 8.4 + - - +
113I ASP* 2.9 32.3 + - - +
229I THR* 4.0 20.9 - - + +
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Residues in contact with ARG 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I GLN* 5.9 0.2 - - - +
99I GLY* 3.1 24.5 + - - -
100I TYR 3.9 2.9 + - - -
101I ASP* 3.0 34.4 + - - +
106I SER* 2.7 25.8 + - - +
107I ILE* 3.5 13.3 - - - +
109I LYS* 1.3 72.9 - - - +
111I ALA* 1.3 62.0 + - - +
113I ASP* 3.1 13.8 + - - +
114I TYR* 3.0 24.1 + - - +
431I GLY 5.5 1.9 - - - +
432I GLY 3.5 18.0 + - - -
433I VAL* 3.0 37.9 + - + +
435I THR* 3.5 19.4 - - - +
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Residues in contact with ALA 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I ILE 3.1 10.6 + - - +
108I ALA 3.5 10.3 - - - +
110I ARG* 1.3 80.3 - - - +
112I GLU* 1.3 59.9 + - - +
114I TYR* 3.6 3.1 + - - +
115I LEU* 3.2 15.9 + - - +
228I MET* 4.2 13.2 - - + -
372I ALA* 4.2 8.7 - - + -
375I LEU* 3.7 17.8 - - + +
376I MET* 4.0 13.2 - - - -
433I VAL* 3.7 23.1 - - + +
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Residues in contact with GLU 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I ALA 3.1 16.2 + - - +
109I LYS* 2.9 11.6 + - - +
111I ALA* 1.3 74.1 - - - +
113I ASP* 1.3 67.0 + - - +
115I LEU* 3.3 19.2 + - - +
116I ARG* 3.5 27.3 + - - +
123I THR* 4.9 4.2 - - - +
124I VAL* 4.0 21.5 + - + +
227I THR* 3.8 13.7 + - - -
228I MET* 3.9 25.7 + - + +
229I THR* 3.1 39.4 + - - +
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Residues in contact with ASP 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I LYS* 2.9 24.1 + - - +
110I ARG* 3.1 11.8 + - - +
112I GLU* 1.3 72.4 - - - +
114I TYR* 1.3 50.6 + - - +
115I LEU 3.0 3.8 - - - -
116I ARG* 3.0 31.0 + - - +
117I ALA* 2.8 34.1 + - - +
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Residues in contact with TYR 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I ARG 3.0 14.9 + - - +
111I ALA 3.7 4.0 - - - +
113I ASP* 1.3 75.6 - - - +
115I LEU* 1.3 61.2 + - - +
117I ALA* 3.7 11.2 - - + -
118I THR* 3.1 40.6 + - + +
376I MET* 4.3 10.8 - - + -
379I LEU* 3.6 31.4 - - + -
383I LYS* 3.1 26.7 - - - +
430I ALA* 3.6 19.0 - - + +
431I GLY* 3.1 42.8 - - - +
433I VAL* 4.2 9.4 - - + -
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Residues in contact with LEU 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111I ALA 3.2 12.4 + - - +
112I GLU* 3.3 13.9 - - - +
113I ASP 3.0 0.6 + - - -
114I TYR* 1.3 77.7 - - - +
116I ARG* 1.3 61.2 + - - +
118I THR* 3.0 18.9 + - - -
119I GLY 3.5 2.4 + - - -
120I ILE* 3.8 4.2 + - + -
121I ALA* 3.2 54.4 - - + +
122I ASP 4.1 1.6 - - - -
123I THR* 3.7 15.9 - - - +
124I VAL* 3.8 26.0 - - + -
274I LEU* 3.8 7.6 - - + -
375I LEU* 4.4 1.8 - - + -
379I LEU* 3.3 40.6 - - + -
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Residues in contact with ARG 116 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112I GLU* 3.5 29.2 + - - +
113I ASP* 3.0 33.6 + - - +
115I LEU* 1.3 79.3 - - - +
117I ALA* 1.3 57.8 + - - +
119I GLY* 3.0 19.2 + - - -
121I ALA 3.4 5.6 - - - -
122I ASP* 3.3 50.4 + - + +
123I THR* 4.7 6.3 - - - +
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Residues in contact with ALA 117 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113I ASP 2.8 16.6 + - - +
114I TYR* 3.7 13.9 - - + +
116I ARG* 1.3 73.7 - - - +
118I THR* 1.3 59.3 + - + +
119I GLY* 2.9 9.9 + - - -
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Residues in contact with THR 118 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I TYR* 3.1 47.8 + - + +
115I LEU* 3.0 14.4 + - - +
117I ALA* 1.3 73.3 - - + +
119I GLY* 1.3 52.2 + - - +
120I ILE* 2.7 47.1 + - + +
379I LEU* 4.9 0.5 - - - +
383I 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