Contacts of the helix formed by residues 103 - 118 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21G PHE* 6.0 1.0 - - - +
22G THR 4.7 2.9 + - - +
57G TRP* 4.4 4.3 - - - -
89G CYS 5.6 0.2 - - - +
90G ASP* 3.7 4.7 - - - -
91G ILE* 2.8 42.8 + - + +
100G TYR* 3.1 29.2 + - + +
101G ASP 3.4 0.4 - - - -
102G ARG* 1.3 74.7 - - - +
104G PRO* 1.3 72.2 - - - +
105G ARG* 2.9 17.3 + - - +
106G SER* 2.9 24.8 + - - +
107G ILE* 3.0 24.2 + - - +
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Residues in contact with PRO 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G THR* 3.6 16.6 - - + +
23G ASP 3.5 24.9 - - - +
24G THR* 4.1 5.2 - - - +
57G TRP* 3.9 5.2 - - + -
102G ARG 3.2 10.9 - - - +
103G ASP* 1.3 90.5 - - - +
105G ARG* 1.3 60.6 + - - +
107G ILE* 3.5 4.5 + - + +
108G ALA 3.1 16.6 + - - -
366G ASN* 3.8 18.8 - - - +
368G TYR* 3.3 26.0 - - + +
369G LEU* 3.8 21.9 - - + +
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Residues in contact with ARG 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G THR* 5.9 3.1 - - - +
70G ASP* 3.1 33.9 + - - +
73G THR* 3.5 14.3 - - - +
88G ARG* 3.8 14.0 - - - +
89G CYS 3.8 16.7 + - - +
90G ASP* 3.0 34.6 + - - +
103G ASP* 2.9 11.7 + - - +
104G PRO* 1.3 77.0 - - - +
106G SER* 1.3 66.8 + - - +
108G ALA* 3.2 3.3 + - - +
109G LYS* 3.1 33.3 + - + +
229G THR* 4.3 9.7 - - + +
233G ASP* 2.9 37.6 + - - -
368G TYR* 3.9 27.5 - - + -
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Residues in contact with SER 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90G ASP* 4.4 10.0 + - - +
91G ILE 3.9 8.1 + - - -
92G LEU* 4.6 1.2 - - - +
99G GLY* 3.9 15.1 - - - -
100G TYR 3.9 13.5 - - - -
103G ASP* 2.9 30.1 + - - -
105G ARG* 1.3 77.7 - - - +
107G ILE* 1.3 57.8 + - - +
109G LYS* 3.1 12.8 + - - +
110G ARG* 2.9 39.2 + - - +
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Residues in contact with ILE 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G TYR 5.1 0.9 - - - +
101G ASP 3.5 24.9 - - - +
102G ARG 4.7 3.4 - - - +
103G ASP 3.0 18.8 + - - +
104G PRO* 3.5 9.2 - - + +
105G ARG 3.2 0.2 - - - -
106G SER* 1.3 77.0 - - - +
108G ALA* 1.3 61.2 + - - +
110G ARG* 3.3 12.7 + - - +
111G ALA* 3.1 18.7 + - - +
369G LEU* 3.8 22.0 - - + -
372G ALA* 4.5 4.5 - - + -
433G VAL* 3.6 19.2 - - + +
434G PHE* 3.7 45.5 - - + -
438G ALA* 4.7 7.4 - - + -
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Residues in contact with ALA 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G PRO 3.1 13.8 + - - +
105G ARG 3.2 8.2 + - - +
107G ILE* 1.3 76.9 - - - +
109G LYS* 1.3 62.2 + - - +
111G ALA 3.3 1.2 + - - -
112G GLU* 3.1 19.1 + - - +
228G MET* 3.3 26.5 - - + +
229G THR* 3.5 16.4 - - + +
232G ALA* 5.8 0.2 - - + -
368G TYR* 4.0 28.5 - - + +
372G ALA* 4.4 6.5 - - - -
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Residues in contact with LYS 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G ASP* 3.8 9.5 + - - -
90G ASP* 3.1 38.8 + - - +
105G ARG* 3.1 33.5 + - - +
106G SER* 3.4 11.9 - - - +
108G ALA* 1.3 73.7 - - - +
110G ARG* 1.3 58.9 + - - +
112G GLU* 3.0 8.2 + - - +
113G ASP* 2.9 36.0 + - - +
229G THR* 4.0 19.7 - - + +
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Residues in contact with ARG 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G GLN* 3.7 15.2 - - - +
99G GLY* 2.8 29.3 + - - -
100G TYR 3.9 2.4 + - - -
101G ASP* 2.9 37.2 + - - +
106G SER* 2.9 22.3 + - - +
107G ILE* 3.6 10.5 - - - +
109G LYS* 1.3 75.3 - - - +
111G ALA* 1.3 58.6 + - - +
113G ASP* 3.5 12.6 - - - +
114G TYR* 2.9 29.6 + - - +
431G GLY 5.5 0.5 - - - +
432G GLY 3.2 18.5 + - - -
433G VAL* 3.1 38.7 + - + +
435G THR* 4.0 7.9 - - - +
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Residues in contact with ALA 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G ILE 3.1 13.2 + - - +
108G ALA 3.6 8.7 - - - +
109G LYS 3.2 0.2 - - - -
110G ARG* 1.3 74.0 - - - +
112G GLU* 1.3 64.5 + - - +
114G TYR* 3.6 4.9 + - - +
115G LEU* 3.2 15.9 + - - -
228G MET* 4.1 13.0 - - + -
372G ALA* 4.2 10.3 - - + -
375G LEU* 3.7 18.1 - - + +
376G MET* 4.1 14.1 - - + +
433G VAL* 4.0 19.0 - - + +
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Residues in contact with GLU 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G ALA 3.1 17.3 + - - +
109G LYS* 3.0 10.6 + - - +
111G ALA* 1.3 74.3 - - - +
113G ASP* 1.3 66.8 + - - +
115G LEU* 3.2 20.8 + - - +
116G ARG* 3.4 31.3 + - - +
123G THR* 5.1 2.1 - - - +
124G VAL* 3.4 28.8 + - + +
227G THR* 4.2 11.4 + - - -
228G MET* 3.8 20.5 + - + -
229G THR* 3.1 37.6 + - - +
230G LYS 4.6 0.2 + - - -
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Residues in contact with ASP 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G LYS* 2.9 19.8 + - - +
110G ARG* 3.5 15.3 - - - +
112G GLU* 1.3 76.5 - - - +
114G TYR* 1.3 58.0 + - - +
116G ARG* 3.0 30.2 + - - +
117G ALA* 2.8 27.3 + - - +
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Residues in contact with TYR 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G ARG 2.9 18.3 + - - +
111G ALA 3.9 3.1 - - - +
112G GLU 3.4 0.2 - - - -
113G ASP* 1.3 71.7 - - - +
115G LEU* 1.3 65.7 + - - +
117G ALA* 3.7 11.4 - - + +
118G THR* 3.1 40.8 + - + +
376G MET* 4.1 17.3 - - + -
379G LEU* 3.7 32.3 - - + -
383G LYS* 3.3 33.9 + - + +
430G ALA* 3.7 12.7 - - + +
431G GLY* 3.4 37.5 - - - +
433G VAL* 4.3 9.9 - - + -
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Residues in contact with LEU 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111G ALA 3.2 12.3 + - - +
112G GLU* 3.2 14.0 + - - +
113G ASP 3.1 0.6 - - - -
114G TYR* 1.3 75.1 - - - +
116G ARG* 1.3 62.6 + - - +
118G THR* 2.9 20.4 + - - -
119G GLY 3.4 3.1 + - - -
120G ILE* 3.8 6.1 + - + -
121G ALA* 3.3 49.4 - - + +
122G ASP 4.2 1.8 - - - -
123G THR 3.9 12.1 - - - +
124G VAL* 3.7 26.2 - - + -
274G LEU* 3.9 13.0 - - + -
375G LEU* 4.4 3.1 - - + -
379G LEU* 3.4 38.8 - - + -
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Residues in contact with ARG 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G GLU* 3.4 26.7 + - - +
113G ASP* 3.0 40.9 + - - +
115G LEU* 1.3 77.2 - - - +
117G ALA* 1.3 59.5 + - - +
119G GLY* 2.8 22.2 + - - -
121G ALA 3.5 5.8 - - - -
122G ASP* 3.3 49.2 + - + +
123G THR* 5.0 4.8 - - - +
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Residues in contact with ALA 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G ASP 2.8 16.1 + - - +
114G TYR* 3.7 15.0 - - + +
115G LEU 3.3 0.2 - - - -
116G ARG* 1.3 76.2 - - - +
118G THR* 1.3 62.1 + - + +
119G GLY* 3.3 0.7 + - - -
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Residues in contact with THR 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G TYR* 3.1 48.3 + - + +
115G LEU* 2.9 18.2 + - - +
117G ALA* 1.3 75.6 - - + +
119G GLY* 1.3 56.5 + - - +
120G ILE* 3.0 38.5 + - + +
379G LEU* 5.0 0.3 - - - +
383G LYS* 5.0 8.7 - - + -
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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