Contacts of the helix formed by residues 103 - 118 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D PHE* 6.1 0.5 - - - +
22D THR 4.5 4.9 + - - +
57D TRP* 4.6 3.4 - - - -
90D ASP* 3.8 6.6 - - - +
91D ILE* 2.9 52.9 + - + +
100D TYR* 3.1 19.2 + - + +
102D ARG* 1.3 73.9 - - - +
104D PRO* 1.3 62.1 - - - +
105D ARG* 2.9 18.0 + - - +
106D SER* 2.8 47.0 + - - -
107D ILE* 3.0 13.0 + - - +
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Residues in contact with PRO 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D THR* 3.5 16.6 - - - +
23D ASP 3.7 20.2 - - - +
24D THR* 4.0 8.3 - - - +
57D TRP* 4.2 4.5 - - + -
102D ARG 3.0 12.5 - - - +
103D ASP* 1.3 88.5 - - - +
105D ARG* 1.3 56.2 + - - +
107D ILE* 3.4 6.6 + - + +
108D ALA 3.0 22.0 + - - -
366D ASN* 3.8 14.4 - - - +
368D TYR* 3.4 23.0 - - + +
369D LEU* 3.6 27.4 - - + +
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Residues in contact with ARG 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D THR* 5.9 3.8 - - - +
70D ASP* 3.1 32.9 + - - +
73D THR* 3.5 12.3 - - - +
88D ARG* 3.8 13.8 - - - +
89D CYS 4.0 14.5 + - - +
90D ASP* 3.1 31.2 + - - +
103D ASP* 2.9 15.3 + - - +
104D PRO* 1.3 77.0 - - - +
106D SER* 1.3 65.1 - - - +
108D ALA* 3.3 2.6 + - - +
109D LYS* 3.1 36.3 + - + +
229D THR* 4.6 11.5 - - + +
233D ASP* 2.9 37.1 + - - -
368D TYR* 3.9 31.9 - - + -
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Residues in contact with SER 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D ASP* 4.6 7.7 + - - +
91D ILE 3.9 1.2 + - - -
92D LEU* 4.8 1.2 - - - +
99D GLY* 3.8 23.0 - - - -
100D TYR 3.8 14.6 - - - -
103D ASP* 2.8 28.0 + - - -
105D ARG* 1.3 77.3 - - - +
107D ILE* 1.3 51.6 + - - +
109D LYS* 3.0 13.3 + - - +
110D ARG* 2.7 45.3 + - - +
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Residues in contact with ILE 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D TYR 5.0 0.7 - - - +
101D ASP 3.6 25.1 - - - +
102D ARG* 4.4 6.5 - - - +
103D ASP 3.0 14.8 + - - +
104D PRO* 3.5 9.0 - - + +
106D SER* 1.3 77.8 - - - +
108D ALA* 1.3 62.1 + - - +
110D ARG* 3.4 13.7 + - - +
111D ALA* 3.1 19.9 + - - +
369D LEU* 4.1 19.3 - - + -
372D ALA* 4.7 2.5 - - + -
433D VAL* 3.6 19.7 - - + +
434D PHE* 3.5 46.2 - - + -
438D ALA* 4.7 5.8 - - + -
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D PRO 3.0 14.0 + - - +
105D ARG 3.6 8.5 - - - +
106D SER 3.2 0.2 - - - -
107D ILE* 1.3 77.2 - - - +
109D LYS* 1.3 62.9 + - - +
111D ALA* 3.4 2.0 + - - -
112D GLU* 3.1 16.5 + - - +
228D MET* 3.5 26.3 - - + +
229D THR* 3.5 18.3 + - - +
232D ALA* 5.9 0.2 - - + -
368D TYR* 3.9 28.3 - - + +
372D ALA* 4.7 3.1 - - - -
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Residues in contact with LYS 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ASP* 4.3 6.1 + - - -
90D ASP* 3.1 38.0 + - - +
105D ARG* 3.1 35.2 + - + +
106D SER* 3.0 12.0 + - - +
108D ALA* 1.3 73.4 - - - +
110D ARG* 1.3 65.7 + - - +
112D GLU* 2.9 8.2 + - - +
113D ASP* 2.9 31.4 + - - +
229D THR* 4.0 20.2 - - + +
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Residues in contact with ARG 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D GLN* 5.9 0.2 - - - +
99D GLY 3.1 24.2 + - - -
100D TYR 3.9 3.7 + - - -
101D ASP* 3.0 34.3 + - - +
106D SER* 2.7 25.3 + - - +
107D ILE* 3.5 13.3 - - - +
109D LYS* 1.3 72.1 - - - +
111D ALA* 1.3 62.3 + - - +
113D ASP* 3.1 13.3 + - - +
114D TYR* 3.0 23.6 + - - +
431D GLY 5.5 2.1 - - - +
432D GLY 3.5 19.2 + - - -
433D VAL* 3.0 37.2 + - + +
435D THR* 3.5 19.6 - - - +
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ILE 3.1 9.5 + - - +
108D ALA 3.5 9.0 - - - +
110D ARG* 1.3 81.3 - - - +
112D GLU* 1.3 61.2 + - - +
114D TYR* 3.6 3.0 + - - +
115D LEU* 3.2 15.6 + - - +
228D MET* 4.2 14.4 - - + -
372D ALA* 4.2 7.9 - - + -
375D LEU* 3.7 18.9 - - + +
376D MET* 4.0 13.9 - - - -
433D VAL* 3.7 22.4 - - + +
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Residues in contact with GLU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ALA 3.1 16.2 + - - +
109D LYS* 2.9 11.2 + - - +
111D ALA* 1.3 72.8 - - - +
113D ASP* 1.3 65.7 + - - +
115D LEU* 3.3 19.4 + - - +
116D ARG* 3.5 28.6 + - - +
123D THR* 4.9 4.3 - - - +
124D VAL* 4.0 22.5 + - + +
227D THR* 3.8 13.7 + - - -
228D MET* 3.9 26.1 + - + +
229D THR* 3.1 38.9 + - - +
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Residues in contact with ASP 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D LYS* 2.9 24.9 + - - +
110D ARG* 3.3 12.3 - - - +
112D GLU* 1.3 72.8 - - - +
114D TYR* 1.3 51.1 + - - +
115D LEU 3.0 3.8 - - - -
116D ARG* 3.0 31.1 + - - +
117D ALA* 2.8 34.1 + - - +
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Residues in contact with TYR 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D ARG 3.0 15.6 + - - +
111D ALA 3.7 4.5 - - - +
113D ASP* 1.3 75.0 - - - +
115D LEU* 1.3 61.8 + - - +
117D ALA* 3.7 11.0 - - + -
118D THR* 3.1 41.0 + - + +
376D MET* 4.3 12.1 - - + -
379D LEU* 3.6 31.2 - - + -
383D LYS* 3.1 27.1 - - - +
430D ALA* 3.6 18.5 - - + +
431D GLY* 3.1 43.3 - - - +
433D VAL* 4.2 9.4 - - + -
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Residues in contact with LEU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ALA 3.2 12.6 + - - +
112D GLU* 3.3 13.5 - - - +
113D ASP 3.0 1.0 + - - -
114D TYR* 1.3 78.3 - - - +
116D ARG* 1.3 60.2 + - - +
118D THR* 3.0 19.2 + - - +
119D GLY 3.5 3.1 + - - -
120D ILE* 3.8 4.2 + - + -
121D ALA* 3.2 54.5 - - + +
122D ASP 4.1 2.0 - - - -
123D THR* 3.7 14.8 - - - +
124D VAL* 3.8 26.2 - - + -
274D LEU* 3.8 7.4 - - + -
375D LEU* 4.4 1.8 - - + -
379D LEU* 3.3 39.5 - - + -
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Residues in contact with ARG 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D GLU* 3.5 28.2 + - - +
113D ASP* 3.0 33.2 + - - +
115D LEU* 1.3 78.4 - - - +
117D ALA* 1.3 58.2 + - - +
119D GLY* 3.0 19.2 + - - -
121D ALA 3.4 5.6 - - - -
122D ASP* 3.3 50.8 + - + +
123D THR* 4.7 6.5 - - - +
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Residues in contact with ALA 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ASP 2.8 16.0 + - - +
114D TYR* 3.7 13.9 - - + +
115D LEU 3.2 0.2 - - - -
116D ARG* 1.3 74.4 - - - +
118D THR* 1.3 58.2 + - + +
119D GLY* 2.9 10.1 + - - -
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Residues in contact with THR 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D TYR* 3.1 48.4 + - + +
115D LEU* 3.0 13.7 + - - +
117D ALA* 1.3 74.5 - - + +
119D GLY* 1.3 52.0 + - - +
120D ILE* 2.7 46.6 + - + +
379D LEU* 4.9 0.5 - - - +
383D 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