Contacts of the helix formed by residues 103 - 118 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A PHE* 6.0 0.9 - - - +
22A THR 4.7 3.1 + - - +
57A TRP* 4.4 4.3 - - - -
89A CYS 5.6 0.2 - - - +
90A ASP* 3.7 5.2 - - - -
91A ILE* 2.8 42.7 + - + +
100A TYR* 3.1 28.2 + - + +
102A ARG* 1.3 74.1 - - - +
104A PRO* 1.3 72.1 - - - +
105A ARG* 2.9 17.5 + - - +
106A SER* 2.9 24.3 + - - +
107A ILE* 3.0 23.8 + - - +
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Residues in contact with PRO 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 3.6 16.2 - - + +
23A ASP 3.5 25.1 - - - +
24A THR* 4.1 4.9 - - - +
57A TRP* 3.9 5.2 - - + -
102A ARG 3.2 11.0 - - - +
103A ASP* 1.3 90.4 - - - +
105A ARG* 1.3 60.8 + - - +
107A ILE* 3.5 4.7 + - + +
108A ALA 3.1 16.6 + - - -
366A ASN* 3.8 19.7 - - - +
368A TYR* 3.3 25.3 - - + +
369A LEU* 3.8 22.1 - - + +
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Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 5.9 2.9 - - - +
70A ASP* 3.1 34.1 + - - +
72A SER* 5.4 0.2 + - - -
73A THR* 3.5 13.5 - - - +
88A ARG* 3.8 12.9 - - - +
89A CYS 3.8 16.3 + - - +
90A ASP* 3.0 34.2 + - - +
103A ASP* 2.9 12.3 + - - +
104A PRO* 1.3 76.4 - - - +
106A SER* 1.3 66.6 + - - +
108A ALA* 3.2 3.5 + - - +
109A LYS* 3.1 34.8 + - + +
229A THR* 4.3 10.5 - - + +
233A ASP* 2.9 37.6 + - - -
368A TYR* 3.9 27.9 - - + -
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Residues in contact with SER 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ASP* 4.4 10.0 + - - +
91A ILE 3.9 8.3 + - - -
92A LEU* 4.6 0.9 - - - +
99A GLY* 3.9 14.8 - - - -
100A TYR 3.9 13.5 - - - -
103A ASP* 2.9 29.5 + - - -
105A ARG* 1.3 77.5 - - - +
107A ILE* 1.3 57.9 + - - +
109A LYS* 3.1 13.1 + - - +
110A ARG* 2.9 38.7 + - - +
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Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TYR 5.1 0.7 - - - +
101A ASP 3.5 24.2 - - - +
102A ARG* 4.7 3.4 - - - +
103A ASP 3.0 19.7 + - - +
104A PRO* 3.5 9.2 - - + +
105A ARG 3.2 0.2 - - - -
106A SER* 1.3 77.0 - - - +
108A ALA* 1.3 63.0 + - - +
110A ARG* 3.4 12.8 + - - +
111A ALA* 3.1 18.2 + - - +
369A LEU* 3.8 22.7 - - + -
372A ALA* 4.5 5.2 - - + -
433A VAL* 3.6 18.8 - - + +
434A PHE* 3.7 46.7 - - + -
438A ALA* 4.7 7.2 - - + -
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PRO 3.1 14.2 + - - +
105A ARG 3.2 8.0 + - - +
107A ILE* 1.3 76.0 - - - +
109A LYS* 1.3 62.8 + - - +
111A ALA 3.3 1.2 + - - -
112A GLU* 3.1 18.7 + - - +
228A MET* 3.3 26.6 - - + +
229A THR* 3.5 15.7 - - + +
368A TYR* 4.0 28.9 - - + +
372A ALA* 4.4 5.8 - - - -
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Residues in contact with LYS 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ASP* 3.8 9.7 + - - -
90A ASP* 3.1 39.8 + - - +
105A ARG* 3.1 33.9 + - - +
106A SER* 3.4 11.9 - - - +
108A ALA* 1.3 74.7 - - - +
110A ARG* 1.3 59.7 + - + +
112A GLU* 3.0 7.5 + - - +
113A ASP* 2.9 36.4 + - - +
229A THR* 4.0 20.2 - - + +
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Residues in contact with ARG 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLN* 3.7 15.9 - - - +
99A GLY* 2.8 29.1 + - - -
100A TYR 3.9 2.4 + - - -
101A ASP* 2.9 36.9 + - - +
106A SER* 2.9 23.5 + - - +
107A ILE* 3.6 11.0 - - - +
108A ALA 3.3 0.2 - - - -
109A LYS* 1.3 76.3 - - + +
111A ALA* 1.3 57.7 + - - +
113A ASP* 3.4 12.4 + - - +
114A TYR* 2.9 30.0 + - - +
431A GLY 5.5 1.9 - - - +
432A GLY 3.2 18.3 + - - -
433A VAL* 3.1 39.1 + - + +
435A THR* 4.0 7.5 - - - +
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Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ILE 3.1 13.9 + - - +
108A ALA 3.6 8.5 - - - +
109A LYS 3.2 0.2 - - - -
110A ARG* 1.3 74.5 - - - +
112A GLU* 1.3 64.4 + - - +
114A TYR* 3.6 4.3 + - - +
115A LEU 3.2 15.9 + - - -
228A MET* 4.1 12.8 - - + -
372A ALA* 4.2 10.5 - - + -
375A LEU* 3.7 19.1 - - + +
376A MET* 4.1 13.7 - - + -
433A VAL* 4.0 19.0 - - + +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ALA 3.1 17.6 + - - +
109A LYS* 3.0 9.9 + - - +
111A ALA* 1.3 73.6 - - - +
113A ASP* 1.3 66.3 + - - +
115A LEU* 3.2 20.5 + - - +
116A ARG* 3.4 31.2 + - - +
123A THR* 5.1 2.1 - - - +
124A VAL* 3.4 29.0 + - + +
227A THR* 4.2 11.7 + - - -
228A MET* 3.8 20.9 + - + -
229A THR* 3.1 38.1 + - - +
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Residues in contact with ASP 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LYS* 2.9 19.7 + - - +
110A ARG* 3.5 14.7 - - - +
112A GLU* 1.3 75.9 - - - +
114A TYR* 1.3 57.8 + - - +
116A ARG* 3.0 31.8 + - - +
117A ALA* 2.8 27.0 + - - +
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Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ARG 2.9 18.3 + - - +
111A ALA 3.9 3.4 - - - +
112A GLU 3.4 0.2 - - - -
113A ASP* 1.3 73.6 - - - +
115A LEU* 1.3 64.8 + - - +
117A ALA* 3.7 10.7 - - + +
118A THR* 3.1 42.2 + - + +
376A MET* 4.1 16.8 - - + -
379A LEU* 3.7 33.0 - - + -
383A LYS* 3.3 33.9 + - + +
430A ALA* 3.7 12.8 - - + +
431A GLY* 3.4 37.2 - - - +
433A VAL* 4.3 9.9 - - + -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ALA 3.2 12.1 + - - +
112A GLU* 3.2 14.0 + - - +
113A ASP 3.1 0.6 - - - -
114A TYR* 1.3 75.5 - - - +
116A ARG* 1.3 62.2 + - - +
118A THR* 2.9 21.1 + - - +
119A GLY 3.4 3.1 + - - -
120A ILE* 3.8 5.6 + - + -
121A ALA* 3.3 50.5 - - + +
122A ASP 4.2 1.8 - - - +
123A THR* 3.9 11.9 - - - +
124A VAL* 3.7 25.8 - - + -
274A LEU* 3.9 13.2 - - + -
375A LEU* 4.4 3.6 - - + -
379A LEU* 3.4 38.6 - - + -
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Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU* 3.4 25.6 + - - +
113A ASP* 3.0 41.6 + - - +
115A LEU* 1.3 77.8 - - - +
117A ALA* 1.3 59.5 - - - +
119A GLY* 2.8 21.5 + - - -
121A ALA 3.5 6.5 - - - -
122A ASP* 3.3 48.2 + - + +
123A THR* 5.0 5.3 - - - +
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ASP 2.8 16.0 + - - +
114A TYR* 3.7 14.4 - - + +
115A LEU 3.4 0.2 - - - -
116A ARG* 1.3 77.7 - - - +
118A THR* 1.3 60.6 + - + +
119A GLY* 3.3 1.0 + - - -
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Residues in contact with THR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TYR* 3.1 47.9 + - + +
115A LEU* 2.9 17.7 + - - +
117A ALA* 1.3 76.3 - - + +
119A GLY* 1.3 57.6 + - - +
120A ILE* 3.0 37.8 + - + +
379A LEU* 5.0 0.3 - - - +
383A LYS* 5.0 8.1 - - + -
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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