Contacts of the helix formed by residues 103 - 118 (chain C) in PDB entry 1F1H
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C PHE* 6.0 0.9 - - - +
22C THR 4.7 3.1 + - - +
57C TRP* 4.4 4.0 - - - -
89C CYS 5.6 0.2 - - - +
90C ASP* 3.7 5.1 - - - -
91C ILE* 2.8 42.4 + - + +
100C TYR* 3.1 29.2 + - + +
101C ASP 3.4 0.2 - - - -
102C ARG* 1.3 73.9 - - - +
104C PRO* 1.3 72.3 - - - +
105C ARG* 2.9 17.5 + - - +
106C SER* 2.9 24.0 + - - +
107C ILE* 3.0 24.5 + - - +
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Residues in contact with PRO 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C THR* 3.6 16.2 - - + +
23C ASP 3.5 24.2 - - - +
24C THR* 4.1 4.9 - - - +
57C TRP* 3.9 5.2 - - + -
102C ARG 3.2 11.1 - - - +
103C ASP* 1.3 90.3 - - - +
105C ARG* 1.3 60.8 + - - +
107C ILE* 3.5 3.6 + - + +
108C ALA 3.1 17.0 + - - -
366C ASN* 3.8 19.7 - - - +
368C TYR* 3.3 26.0 - - + +
369C LEU* 3.8 21.8 - - + +
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Residues in contact with ARG 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C PHE* 6.5 0.2 - - - +
22C THR* 5.9 2.9 - - - +
70C ASP* 3.1 34.5 + - - +
73C THR* 3.5 13.1 - - - +
88C ARG* 3.8 13.6 - - - +
89C CYS 3.8 16.3 + - - +
90C ASP* 3.0 34.7 + - - +
103C ASP* 2.9 11.7 + - - +
104C PRO* 1.3 76.0 - - - +
106C SER* 1.3 66.3 + - - +
108C ALA* 3.2 3.5 + - - +
109C LYS* 3.1 34.5 + - + +
229C THR* 4.3 9.1 - - + +
233C ASP* 2.9 37.2 + - - -
368C TYR* 3.9 29.1 - - + -
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ASP* 4.4 9.6 + - - +
91C ILE 3.9 8.3 + - - -
92C LEU* 4.6 1.2 - - - +
99C GLY* 3.9 15.4 - - - -
100C TYR 3.9 13.2 - - - -
103C ASP* 2.9 30.6 + - - -
105C ARG* 1.3 77.4 - - - +
107C ILE* 1.3 57.1 + - - +
109C LYS* 3.1 13.4 + - - +
110C ARG* 2.9 39.6 + - - +
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Residues in contact with ILE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C TYR 5.1 0.7 - - - +
101C ASP 3.5 25.1 - - - +
102C ARG 4.7 3.6 - - - +
103C ASP 3.0 18.6 + - - +
104C PRO* 3.5 10.3 - - + +
106C SER* 1.3 76.5 - - - +
108C ALA* 1.3 61.9 + - - +
110C ARG* 3.4 13.0 + - - +
111C ALA* 3.1 18.5 + - - +
369C LEU* 3.8 22.7 - - + -
372C ALA* 4.5 5.2 - - + -
433C VAL* 3.6 19.3 - - + +
434C PHE* 3.7 46.7 - - + -
438C ALA* 4.7 6.5 - - + -
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Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PRO 3.1 14.2 + - - +
105C ARG 3.2 7.6 + - - +
107C ILE* 1.3 76.5 - - - +
109C LYS* 1.3 62.7 + - - +
111C ALA 3.3 1.2 + - - -
112C GLU* 3.1 19.2 + - - +
228C MET* 3.3 26.4 - - + +
229C THR* 3.5 15.7 - - + +
232C ALA* 5.8 0.4 - - + -
368C TYR* 4.0 28.9 - - + +
372C ALA* 4.4 5.8 - - - +
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Residues in contact with LYS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ASP* 3.8 9.7 + - - -
90C ASP* 3.1 38.9 + - - +
105C ARG* 3.1 34.3 + - - +
106C SER* 3.1 11.9 + - - +
108C ALA* 1.3 74.1 - - - +
110C ARG* 1.3 60.1 + - + +
112C GLU* 3.0 7.6 + - - +
113C ASP* 2.9 36.8 + - - +
229C THR* 4.0 18.8 - - + +
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Residues in contact with ARG 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLN* 3.7 15.1 - - - +
99C GLY* 2.8 29.3 + - - -
100C TYR 4.5 1.8 - - - -
101C ASP* 2.9 36.7 + - - +
106C SER* 2.9 22.3 + - - +
107C ILE* 3.6 11.7 - - - +
108C ALA 3.3 0.2 - - - -
109C LYS* 1.3 76.2 - - + +
111C ALA* 1.3 56.3 + - - +
113C ASP* 3.4 12.8 + - - +
114C TYR* 2.9 30.5 + - - +
431C GLY 5.5 2.1 - - - +
432C GLY 3.2 18.7 + - - -
433C VAL* 3.1 37.9 + - + +
435C THR* 4.0 6.9 - - - +
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Residues in contact with ALA 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ILE 3.1 12.7 + - - +
108C ALA 3.6 8.3 - - - +
110C ARG* 1.3 76.3 - - - +
112C GLU* 1.3 66.2 + - - +
114C TYR* 3.9 4.3 - - - +
115C LEU* 3.2 15.8 + - - +
228C MET* 4.1 13.2 - - + -
372C ALA* 4.2 10.1 - - + -
375C LEU* 3.7 18.8 - - + +
376C MET* 4.1 12.8 - - + -
433C VAL* 4.0 19.5 - - + +
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Residues in contact with GLU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ALA 3.1 17.8 + - - +
109C LYS* 3.0 9.9 + - - +
111C ALA* 1.3 73.2 - - - +
113C ASP* 1.3 66.2 + - - +
115C LEU* 3.2 20.9 + - - +
116C ARG* 3.4 31.7 + - - +
122C ASP 5.2 0.2 - - - +
123C THR* 5.1 1.7 - - - +
124C VAL* 3.4 29.4 + - + +
227C THR* 4.2 11.7 + - - -
228C MET* 3.8 19.9 + - + -
229C THR* 3.1 37.4 + - - +
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Residues in contact with ASP 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LYS* 2.9 20.0 + - - +
110C ARG* 3.5 15.0 - - - +
112C GLU* 1.3 76.5 - - - +
114C TYR* 1.3 58.4 + - - +
116C ARG* 3.0 31.7 + - - +
117C ALA* 2.8 28.0 + - - +
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Residues in contact with TYR 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ARG 2.9 18.0 + - - +
111C ALA 3.9 3.8 - - - +
113C ASP* 1.3 72.8 - - - +
115C LEU* 1.3 65.6 + - - +
117C ALA* 3.7 10.7 - - + +
118C THR* 3.1 41.7 + - + +
376C MET* 4.1 17.3 - - + -
379C LEU* 3.7 33.0 - - + -
383C LYS* 3.3 33.5 + - + +
430C ALA* 3.7 12.4 - - + +
431C GLY* 3.4 37.2 - - - +
433C VAL* 4.3 9.6 - - + -
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Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C ALA 3.2 11.9 + - - +
112C GLU* 3.2 14.0 + - - +
113C ASP 3.1 0.8 - - - -
114C TYR* 1.3 74.9 - - - +
116C ARG* 1.3 61.4 + - - +
118C THR* 2.9 20.8 + - - +
119C GLY 3.4 3.3 + - - -
120C ILE* 3.8 5.4 + - + -
121C ALA* 3.3 48.6 - - + +
122C ASP 4.2 2.5 - - - +
123C THR 3.9 12.1 - - - +
124C VAL* 3.7 26.7 - - + -
274C LEU* 3.9 12.6 - - + -
375C LEU* 4.4 3.4 - - + -
379C LEU* 3.4 38.4 - - + -
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Residues in contact with ARG 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C GLU* 3.4 26.0 + - - +
113C ASP* 3.0 41.9 + - - +
115C LEU* 1.3 78.1 - - - +
117C ALA* 1.3 59.7 - - - +
119C GLY* 2.8 22.0 + - - -
121C ALA 3.5 5.4 - - - -
122C ASP* 3.3 50.3 + - + +
123C THR* 5.0 4.6 - - - +
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Residues in contact with ALA 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ASP 2.8 14.8 + - - +
114C TYR* 3.7 14.1 - - + +
115C LEU 3.4 0.4 - - - -
116C ARG* 1.3 77.8 - - - +
118C THR* 1.3 62.1 + - + +
119C GLY 3.3 0.9 + - - -
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Residues in contact with THR 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C TYR* 3.1 47.9 + - + +
115C LEU* 2.9 17.7 + - - +
117C ALA* 1.3 76.1 - - + +
119C GLY* 1.3 57.5 + - - +
120C ILE* 3.0 37.8 + - + +
379C LEU* 5.0 0.7 - - - +
383C LYS* 5.0 7.9 - - + -
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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