Contacts of the helix formed by residues 102 - 111 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C ALA* 3.8 20.1 - - + +
98C THR* 3.8 5.4 - - - +
99C MET* 3.4 15.4 + - - +
100C PRO 3.1 22.8 + - - -
101C GLY* 1.3 80.4 + - - +
103C ALA* 1.3 65.5 + - - +
104C GLN 3.4 2.0 - - - -
105C ALA* 3.4 12.6 + - - +
106C ILE* 2.9 32.5 + - + +
66D ALA* 3.3 34.9 + - - +
68D GLN* 5.3 1.2 - - - +
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Residues in contact with ALA 103 (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 THR* 3.4 9.5 + - - +
102C ASN* 1.3 77.3 - - - +
104C GLN* 1.3 61.2 + - - +
106C ILE* 3.2 1.7 + - - -
107C GLY* 2.9 21.5 + - - -
123C CYS* 3.9 2.1 - - + -
124C GLY 3.0 26.0 - - - +
125C ASP* 4.3 0.4 - - - +
126C ASP* 3.1 20.4 - - - +
127C THR 3.5 10.5 - - - +
128C ILE* 3.4 25.7 - - + +
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Residues in contact with GLN 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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101C GLY* 6.1 2.7 - - - -
102C ASN 3.4 0.6 - - - +
103C ALA* 1.3 78.2 - - - +
105C ALA* 1.3 63.1 + - - +
107C GLY* 3.3 1.0 + - - -
108C ALA* 3.1 22.5 + - - +
123C CYS* 3.2 39.2 + - - +
124C GLY* 3.7 13.3 + - - +
125C ASP* 4.3 7.6 - - + +
101D GLY* 4.4 21.8 - - - +
104D GLN* 6.5 1.1 - - + -
105D ALA* 6.3 4.5 - - + -
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Residues in contact with ALA 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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101C GLY 5.6 0.9 - - - +
102C ASN* 3.4 17.1 + - - +
103C ALA 3.2 0.4 - - - -
104C GLN* 1.3 78.5 - - - +
106C ILE* 1.3 67.5 + - + +
108C ALA* 3.2 9.0 + - - +
109C LEU* 3.1 27.6 + - + +
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Residues in contact with ILE 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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76C LEU* 4.0 8.1 - - + -
79C ALA* 3.3 45.3 - - + +
80C LEU* 3.5 26.0 - - + -
83C ALA* 5.0 5.4 - - + -
96C LEU* 4.6 2.5 - - + -
98C THR* 4.5 10.5 - - + -
102C ASN* 2.9 23.1 + - + +
103C ALA* 4.5 0.2 - - - -
105C ALA* 1.3 76.9 - - + +
107C GLY* 1.3 64.3 + - - +
109C LEU* 3.0 10.6 + - - +
110C MET* 2.9 30.0 + - + +
128C ILE* 3.5 23.3 - - + -
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Residues in contact with GLY 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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103C ALA 2.9 10.9 + - - -
104C GLN 3.7 0.4 - - - -
106C ILE* 1.3 76.5 - - - +
108C ALA* 1.3 62.5 + - - +
110C MET* 2.9 26.3 + - - +
111C ASP* 3.0 18.0 + - - +
121C THR* 4.1 6.5 + - - -
123C CYS* 3.6 26.7 - - - -
128C ILE* 3.8 0.6 - - - +
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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 GLN 3.1 12.2 + - - +
105C ALA* 3.6 9.4 - - - +
107C GLY* 1.3 74.5 - - - +
109C LEU* 1.3 63.1 + - + +
111C ASP* 3.4 15.9 + - - +
112C ASN* 3.1 24.3 + - - +
123C CYS* 5.1 0.2 - - - -
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Residues in contact with LEU 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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68C GLN* 6.1 3.6 - - + -
71C ASN* 6.0 1.6 - - + +
75C LYS* 3.1 58.6 - - + +
76C LEU* 3.5 24.9 - - + +
79C ALA* 3.9 15.3 - - + -
105C ALA* 3.1 16.5 + - + +
106C ILE* 3.0 14.7 + - - +
108C ALA* 1.3 78.3 - - + +
110C MET* 1.3 63.1 + - - +
112C ASN* 3.0 25.8 + - - +
113C LEU* 3.7 10.5 + - - +
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Residues in contact with MET 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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76C LEU* 4.0 16.2 - - + -
80C LEU* 5.9 0.2 - - - -
96C LEU* 4.5 4.9 - - + -
106C ILE* 2.9 19.4 + - + +
107C GLY* 2.9 11.6 + - - +
109C LEU* 1.3 76.0 - - - +
111C ASP* 1.3 62.2 + - - +
113C LEU* 3.2 34.3 + - + +
114C ASP 4.2 1.4 + - - -
115C TRP* 6.0 0.7 - - - -
118C MET* 3.5 25.8 - - + +
121C THR* 4.5 4.7 - - + -
128C ILE* 3.3 49.1 - - + -
130C ILE* 3.8 25.8 - - + -
141C VAL* 6.5 0.2 - - - -
145C LEU* 4.5 17.7 - - - -
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Residues in contact with ASP 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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97B LYS* 5.3 6.9 + - - -
107C GLY 3.0 14.7 + - - +
108C ALA* 3.7 14.0 - - - +
109C LEU 3.1 0.6 - - - -
110C MET* 1.3 75.4 - - - +
112C ASN* 1.3 61.2 + - - +
113C LEU 3.3 1.6 - - - -
114C ASP* 3.5 15.6 + - - +
118C MET* 4.0 5.8 - - - +
120C GLY* 4.7 2.9 - - - -
121C THR* 3.1 41.8 + - - +
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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