Contacts of the helix formed by residues 103 - 118 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21K PHE* 6.1 0.5 - - - +
22K THR 4.5 4.5 + - - +
57K TRP* 4.6 3.4 - - - -
89K CYS 5.5 0.3 - - - +
90K ASP* 3.8 7.1 - - - +
91K ILE* 2.9 52.3 + - + +
100K TYR* 3.1 20.2 + - + +
102K ARG* 1.3 73.6 - - - +
104K PRO* 1.3 62.1 - - - +
105K ARG* 2.9 18.1 + - - +
106K SER* 2.8 47.7 + - - -
107K ILE* 3.0 13.0 + - - +
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Residues in contact with PRO 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K THR 3.5 16.2 - - - +
23K ASP 3.7 20.4 - - - +
24K THR* 4.0 8.3 - - + +
57K TRP* 4.2 4.3 - - + -
102K ARG 2.9 12.3 - - - +
103K ASP* 1.3 88.1 - - - +
105K ARG* 1.3 55.2 + - - +
107K ILE* 3.4 6.2 + - + +
108K ALA 3.0 22.3 + - - -
366K ASN* 3.8 15.0 - - - +
368K TYR* 3.4 23.6 - - + +
369K LEU* 3.6 27.0 - - + +
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Residues in contact with ARG 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K THR* 5.9 3.6 - - - +
70K ASP* 3.1 32.7 + - - +
73K THR* 3.5 12.5 - - - +
88K ARG* 3.8 13.6 - - - +
89K CYS 4.0 15.1 + - - +
90K ASP* 3.1 31.5 + - - +
103K ASP* 2.9 14.7 + - - +
104K PRO* 1.3 77.8 - - - +
106K SER* 1.3 66.4 + - - +
108K ALA* 3.3 2.8 + - - +
109K LYS* 3.1 34.7 + - + +
229K THR* 4.6 11.1 - - + +
233K ASP* 2.9 36.9 + - - -
368K TYR* 3.9 31.3 - - + -
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Residues in contact with SER 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K ASP* 4.6 7.7 + - - +
91K ILE 3.9 1.2 + - - -
92K LEU* 4.8 1.0 - - - +
99K GLY* 3.8 22.5 - - - -
100K TYR 3.8 15.0 - - - -
103K ASP* 2.8 27.2 + - - -
105K ARG* 1.3 76.2 - - - +
107K ILE* 1.3 53.6 + - - +
109K LYS* 3.0 13.3 + - - +
110K ARG* 2.7 44.7 + - - +
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Residues in contact with ILE 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K TYR 5.0 0.7 - - - +
101K ASP 3.6 25.6 - - - +
102K ARG* 4.4 6.1 - - - +
103K ASP 3.0 14.5 + - - +
104K PRO* 3.5 9.6 - - + +
106K SER* 1.3 76.7 - - - +
108K ALA* 1.3 61.5 + - - +
110K ARG* 3.5 12.7 - - - +
111K ALA* 3.1 19.2 + - - +
369K LEU* 4.1 20.0 - - + -
372K ALA* 4.7 2.7 - - + -
433K VAL* 3.6 21.4 - - + +
434K PHE* 3.5 46.2 - - + -
438K ALA* 4.7 5.8 - - + -
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Residues in contact with ALA 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104K PRO 3.0 14.5 + - - +
105K ARG 3.6 8.1 - - - +
106K SER 3.2 0.2 - - - -
107K ILE* 1.3 77.6 - - - +
109K LYS* 1.3 62.4 + - - +
111K ALA* 3.4 1.8 + - - -
112K GLU* 3.1 17.3 + - - +
228K MET* 3.5 27.2 - - + +
229K THR* 3.5 18.8 + - - +
368K TYR* 3.9 28.0 - - + +
372K ALA* 4.7 3.1 - - - -
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Residues in contact with LYS 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70K ASP* 4.3 6.1 + - - -
90K ASP* 3.1 37.5 + - - +
105K ARG* 3.1 36.2 + - + +
106K SER* 3.0 10.9 + - - +
108K ALA* 1.3 75.8 - - - +
110K ARG* 1.3 65.6 + - + +
112K GLU* 2.9 8.3 + - - +
113K ASP* 2.9 31.2 + - - +
229K THR* 4.0 20.0 - - + +
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Residues in contact with ARG 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K GLY* 3.1 24.4 + - - -
100K TYR 3.9 3.5 + - - -
101K ASP* 3.0 34.4 + - - +
106K SER* 2.7 25.3 + - - +
107K ILE* 3.5 13.1 - - - +
109K LYS* 1.3 72.0 - - - +
111K ALA* 1.3 62.8 + - - +
113K ASP* 3.1 13.3 + - - +
114K TYR* 3.0 23.4 + - - +
431K GLY 5.5 1.7 - - - +
432K GLY 3.5 17.8 + - - -
433K VAL* 3.0 38.6 + - + +
435K THR* 3.5 20.0 - - - +
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Residues in contact with ALA 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K ILE 3.1 9.9 + - - +
108K ALA 3.5 9.4 - - - +
110K ARG* 1.3 81.1 - - - +
112K GLU* 1.3 60.0 + - - +
114K TYR* 3.6 2.8 + - - +
115K LEU* 3.2 15.6 + - - +
228K MET* 4.2 13.5 - - + -
372K ALA* 4.2 8.7 - - + -
375K LEU* 3.7 18.4 - - + +
376K MET* 4.0 14.1 - - - -
433K VAL* 3.7 22.8 - - + +
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Residues in contact with GLU 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K ALA 3.1 16.2 + - - +
109K LYS* 2.9 11.2 + - - +
111K ALA* 1.3 72.9 - - - +
113K ASP* 1.3 65.7 + - - +
115K LEU* 3.3 19.6 + - - +
116K ARG* 3.5 28.0 + - - +
123K THR* 4.9 4.0 - - - +
124K VAL* 4.0 22.0 + - + +
227K THR* 3.8 14.4 + - - -
228K MET* 3.9 25.1 + - + +
229K THR* 3.1 39.4 + - - +
375K LEU* 5.4 0.2 - - - -
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Residues in contact with ASP 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K LYS* 2.9 25.7 + - - +
110K ARG* 3.3 12.5 - - - +
112K GLU* 1.3 72.4 - - - +
114K TYR* 1.3 51.9 + - - +
115K LEU 3.0 4.0 - - - -
116K ARG* 3.0 29.8 + - - +
117K ALA* 2.8 33.6 + - - +
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Residues in contact with TYR 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K ARG 3.0 15.8 + - - +
111K ALA 3.7 4.3 - - - +
113K ASP* 1.3 76.2 - - - +
115K LEU* 1.3 60.9 + - - +
117K ALA* 3.7 10.5 - - + -
118K THR* 3.1 39.9 + - + +
376K MET* 4.3 11.4 - - + -
379K LEU* 3.6 31.0 - - + -
383K LYS* 3.1 27.1 - - - +
430K ALA* 3.6 19.5 - - + +
431K GLY* 3.1 42.6 - - - +
433K VAL* 4.2 9.4 - - + -
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Residues in contact with LEU 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111K ALA 3.2 12.4 + - - +
112K GLU* 3.3 13.7 - - - +
113K ASP 3.0 1.0 + - - -
114K TYR* 1.3 78.0 - - - +
116K ARG* 1.3 61.2 + - - +
118K THR* 3.0 18.2 + - - -
119K GLY 3.5 2.9 + - - -
120K ILE* 3.8 4.2 + - + -
121K ALA* 3.2 54.9 - - + +
122K ASP 4.1 1.8 - - - -
123K THR* 3.7 15.7 - - - +
124K VAL* 3.8 25.6 - - + -
274K LEU* 3.8 7.2 - - + -
375K LEU* 4.4 2.0 - - + -
379K LEU* 3.3 40.8 - - + -
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Residues in contact with ARG 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112K GLU* 3.5 27.9 + - - +
113K ASP* 3.0 33.2 + - - +
115K LEU* 1.3 79.8 - - - +
117K ALA* 1.3 57.8 + - - +
119K GLY* 3.0 19.1 + - - -
121K ALA 3.4 5.8 - - - -
122K ASP* 3.3 48.7 + - + +
123K THR* 4.7 6.9 - - - +
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Residues in contact with ALA 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K ASP 2.8 15.6 + - - +
114K TYR* 3.7 14.1 - - + +
115K LEU 3.2 0.2 - - - -
116K ARG* 1.3 73.9 - - - +
118K THR* 1.3 60.0 + - + +
119K GLY* 2.9 10.1 + - - -
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Residues in contact with THR 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114K TYR* 3.1 49.0 + - + +
115K LEU* 3.0 14.6 + - - +
117K ALA* 1.3 74.2 - - + +
119K GLY* 1.3 51.5 + - - +
120K ILE* 2.7 47.3 + - + +
379K LEU* 4.9 0.5 - - - +
383K LYS* 4.8 8.5 - - + -
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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