Contacts of the helix formed by residues 102 - 112 (chain A) in PDB entry 1F9N
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 ASN 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A ALA* 3.8 21.4 - - + +
98A THR* 3.5 8.5 - - - +
99A MET* 3.2 38.2 + - - +
100A PRO 2.8 23.0 + - - -
101A GLY* 1.3 79.9 - - - +
103A ALA* 1.3 66.8 + - - +
104A GLN 3.5 1.8 - - - -
105A ALA* 3.6 10.4 + - - +
106A ILE* 3.2 28.7 + - + +
125A ASP 3.3 1.2 + - - -
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Residues in contact with ALA 103 (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 THR* 3.4 6.8 + - - +
102A ASN* 1.3 75.4 - - - +
104A GLN* 1.3 68.2 + - - +
106A ILE* 3.0 3.3 + - - -
107A GLY* 2.7 23.7 + - - -
123A CYS* 4.0 3.1 - - - -
124A GLY 3.8 6.3 - - - +
125A ASP 3.4 17.0 + - - +
126A ASP 4.0 2.5 - - - -
127A THR 3.6 22.7 - - - +
128A ILE* 3.5 29.2 - - + +
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Residues in contact with GLN 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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101A GLY* 6.2 2.0 - - - -
102A ASN 3.5 1.3 - - - +
103A ALA* 1.3 77.6 - - - +
105A ALA* 1.3 61.9 - - - +
107A GLY* 3.5 2.3 + - - -
108A ALA* 3.3 17.8 + - - +
123A CYS* 3.6 29.9 + - - +
124A GLY 3.5 17.1 + - - +
125A ASP* 4.8 1.5 + - - +
104F GLN* 5.7 4.9 - - - +
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Residues in contact with ALA 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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68A GLN* 4.2 6.3 + - - +
102A ASN* 3.6 10.8 + - - +
103A ALA 3.2 0.8 - - - -
104A GLN* 1.3 75.8 - - - +
106A ILE* 1.3 62.1 + - + +
108A ALA* 2.9 29.2 + - - +
109A LEU* 3.2 11.1 + - - +
101F GLY* 5.2 15.7 - - - +
104F GLN* 5.9 10.3 - - + +
125F ASP* 5.9 3.6 - - - +
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Residues in contact with ILE 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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76A LEU* 4.2 19.7 - - + -
79A ALA* 4.3 22.9 - - + -
80A LEU* 4.5 17.9 - - + +
83A ALA* 4.5 13.0 - - + -
98A THR* 3.6 28.3 - - + -
102A ASN* 3.2 19.2 + - + +
103A ALA 3.0 3.5 + - - +
105A ALA* 1.3 77.2 - - + +
107A GLY* 1.3 61.9 + - - +
109A LEU* 3.3 11.3 + - + +
110A MET* 3.2 30.8 + - + +
128A ILE* 3.8 15.0 - - + -
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Residues in contact with GLY 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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103A ALA 2.7 11.1 + - - -
104A GLN 4.0 0.4 - - - -
106A ILE* 1.3 78.4 - - - +
108A ALA* 1.3 60.2 + - - +
110A MET* 3.6 10.6 + - - +
111A ASP* 3.4 28.2 + - - +
121A THR* 4.1 3.8 + - - -
123A CYS* 3.5 28.7 - - - -
128A ILE* 4.1 6.9 - - - +
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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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68A GLN* 4.1 19.3 - - - +
104A GLN 3.3 10.8 + - - +
105A ALA* 2.9 14.9 + - - +
107A GLY* 1.3 77.3 - - - +
109A LEU* 1.3 62.6 + - - +
111A ASP* 3.2 16.5 + - - +
112A ASN* 3.3 20.6 + - - +
125F ASP* 6.1 0.9 - - - +
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Residues in contact with LEU 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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68A GLN* 3.9 47.3 - - + +
72A PRO* 4.2 10.4 - - + +
75A LYS* 3.7 48.2 - - + +
76A LEU* 3.8 17.3 - - + -
79A ALA* 4.5 10.1 - - + -
105A ALA* 3.2 9.0 + - + +
106A ILE* 3.3 11.4 + - - +
108A ALA* 1.3 78.4 - - - +
110A MET* 1.3 62.5 + - - +
112A ASN* 3.2 18.6 + - - +
113A LEU* 3.5 13.8 - - - +
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Residues in contact with MET 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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76A LEU* 4.4 17.0 - - + -
96A LEU* 4.0 12.3 - - + -
106A ILE* 3.2 17.0 + - + +
107A GLY* 3.8 10.8 - - - +
108A ALA 3.2 0.8 - - - -
109A LEU* 1.3 78.3 - - - +
111A ASP* 1.3 64.7 + - - +
113A LEU* 3.1 26.7 + - + +
114A ASP 3.6 1.2 + - - -
115A TRP* 5.6 2.7 - - + -
118A MET* 3.6 29.6 - - + +
121A THR* 5.1 3.4 - - + -
128A ILE* 3.8 35.7 - - + -
130A ILE* 3.3 36.6 - - + -
145A LEU* 4.5 14.8 - - + -
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Residues in contact with ASP 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 GLY 3.4 14.1 + - - +
108A ALA* 3.2 12.1 + - - +
110A MET* 1.3 75.7 - - - +
112A ASN* 1.3 64.3 + - - +
113A LEU 3.1 3.6 + - - -
114A ASP* 3.6 15.7 + - - +
118A MET* 5.5 2.2 - - - +
120A GLY* 5.9 0.3 - - - -
121A THR* 3.1 30.6 + - - +
97C LYS* 5.8 7.0 + - - -
126C ASP* 5.4 4.5 - - - +
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Residues in contact with ASN 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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68A GLN* 3.0 44.5 - - - +
69A ARG* 3.9 26.3 + - - +
72A PRO* 4.1 12.3 - - + +
108A ALA* 3.4 15.5 + - - +
109A LEU* 3.2 11.4 + - - +
110A MET 3.1 1.0 - - - -
111A ASP* 1.3 81.7 + - - +
113A LEU* 1.3 61.1 + - - +
114A ASP* 5.0 1.4 - - - +
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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