Contacts of the helix formed by residues 109 - 120 (chain C) in PDB entry 1DXO
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 PRO 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLU* 3.2 10.3 - - - +
10C ALA* 4.0 19.3 - - + +
42C TYR* 5.6 3.4 - - + +
101C PHE* 3.5 23.3 - - + -
102C PRO* 3.8 9.6 - - + +
104C GLN* 3.4 29.6 - - - +
108C VAL* 1.3 87.3 - - + +
110C ALA* 1.3 66.5 + - - +
111C ILE* 4.1 19.1 - - + -
112C LEU* 2.8 9.1 + - + -
113C LYS 2.8 19.9 + - - -
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Residues in contact with ALA 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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48A PRO* 3.9 11.2 - - + +
49A ILE* 5.1 1.3 - - + -
110A ALA* 3.5 16.5 - - + +
113A LYS* 4.1 9.4 - - - +
114A GLY* 3.4 31.0 - - - +
117A GLU* 3.0 24.7 + - - +
48C PRO* 4.1 2.0 - - - +
108C VAL 3.5 0.8 + - - -
109C PRO* 1.3 69.9 - - - +
111C ILE* 1.3 57.3 + - - +
113C LYS* 3.0 5.2 + - - -
114C GLY* 2.8 27.9 + - - -
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Residues in contact with ILE 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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49A ILE* 3.7 25.2 - - + +
10C ALA* 4.0 17.9 - - + -
41C LEU* 3.5 47.1 - - + +
42C TYR* 3.6 42.4 - - + +
46C PHE* 4.0 21.8 - - + +
48C PRO* 4.0 12.1 - - + +
109C PRO* 3.1 8.6 - - + +
110C ALA* 1.3 78.6 - - - +
112C LEU* 1.3 59.4 + - - +
114C GLY 3.9 0.4 + - - -
115C TRP* 3.3 16.3 + - - +
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Residues in contact with LEU 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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8C VAL* 3.9 17.3 - - + +
10C ALA* 4.0 22.0 - - + -
41C LEU* 3.6 20.2 - - + -
99C PHE* 4.1 17.3 - - + -
100C GLN 5.3 1.3 - - - +
101C PHE* 4.3 24.2 - - + -
108C VAL* 4.3 8.7 - - + -
109C PRO* 2.8 12.0 + - + +
111C ILE* 1.3 76.8 - - - +
113C LYS* 1.3 68.1 + - - +
114C GLY 3.2 1.3 - - - -
115C TRP* 3.1 23.6 + - + -
116C PHE* 3.1 29.9 + - + -
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Residues in contact with LYS 113 (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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104A GLN 2.9 25.9 + - - -
105A TRP* 3.7 23.8 - - - -
107A GLY* 3.8 5.8 - - - -
108A VAL 2.4 34.7 + - - +
110A ALA* 3.9 19.1 - - + +
113A LYS* 5.0 5.8 - - + -
108C VAL* 3.7 20.5 - - + +
109C PRO 2.8 12.0 + - - +
110C ALA* 3.5 11.7 - - - +
112C LEU* 1.3 76.4 - - - +
114C GLY* 1.3 61.7 + - - +
116C PHE* 3.2 14.4 + - + +
117C GLU* 3.1 39.8 + - - +
175C ILE* 4.9 4.9 - - + -
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Residues in contact with GLY 114 (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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110A ALA* 3.3 10.0 - - - +
48C PRO* 3.1 32.1 - - - -
110C ALA 2.8 12.1 + - - -
113C LYS* 1.3 76.4 - - - +
115C TRP* 1.3 57.6 + - - +
117C GLU* 3.7 4.8 - - - +
118C ARG* 2.9 36.0 + - - +
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Residues in contact with TRP 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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6C LEU* 4.7 7.0 - - + -
8C VAL* 3.9 21.8 - - + -
41C LEU* 3.5 25.4 - - + +
46C PHE* 3.4 31.8 - + + -
87C GLU* 3.0 35.7 + - + +
91C LEU* 4.3 17.3 - - + -
99C PHE* 3.5 23.8 - + - -
111C ILE 3.3 15.0 + - - +
112C LEU* 3.1 23.9 + - + +
114C GLY* 1.3 77.3 - - - +
116C PHE* 1.3 84.0 + + - +
119C VAL* 2.9 49.5 + - + +
120C PHE* 3.7 20.4 - + - -
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Residues in contact with PHE 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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105A TRP* 3.6 15.5 + - + -
99C PHE* 3.3 47.8 - + - -
108C VAL* 4.6 11.4 - - + -
112C LEU* 3.1 31.8 + - + -
113C LYS* 3.4 13.5 - - + +
115C TRP* 1.3 83.5 - + - +
117C GLU* 1.3 60.8 + - + +
120C PHE* 2.9 66.6 + + + +
144C LEU* 6.0 1.6 - - + -
171C ILE* 5.6 4.3 - - + -
175C ILE* 3.7 36.1 - - + -
176C LEU* 4.6 5.2 - - + -
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Residues in contact with GLU 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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104A GLN* 2.8 38.5 + - - +
105A TRP* 3.8 22.7 - - + +
109A PRO* 3.5 4.7 - - - +
110A ALA* 3.0 33.2 + - - +
301A FAD 3.9 14.9 - - + +
48C PRO 4.3 2.6 - - - +
50C ILE* 3.5 26.2 + - + +
67C TYR* 4.1 8.0 - - - -
113C LYS* 3.1 26.8 + - - +
114C GLY* 3.2 5.4 + - - +
116C PHE* 1.3 75.9 - - - +
118C ARG* 1.3 60.3 + - - +
120C PHE 4.8 2.8 - - - +
121C ILE* 4.2 4.3 - - - +
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Residues in contact with ARG 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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46C PHE* 4.1 14.8 - - + -
47C ASN* 3.0 36.0 + - - +
48C PRO 4.3 2.7 - - - +
49C ILE 3.6 15.7 - - - -
50C ILE* 3.5 19.3 - - + +
53C LYS 5.2 0.4 + - - -
54C ASP* 2.5 47.4 + - - +
67C TYR* 4.1 4.0 - - - -
81C SER* 4.4 4.4 + - - -
83C ASP* 2.4 38.8 + - - -
84C ILE* 3.3 33.2 - - + +
114C GLY 2.9 17.0 + - - +
115C TRP 4.5 0.7 - - - +
117C GLU* 1.3 78.9 - - - +
119C VAL* 1.3 60.2 + - - +
121C ILE* 3.1 24.4 - - - +
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Residues in contact with VAL 119 (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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46C PHE* 4.4 7.6 - - + -
84C ILE* 4.1 11.2 - - + +
87C GLU* 3.6 35.7 - - + -
88C GLN* 3.0 30.3 + - + +
91C LEU* 3.7 28.9 - - + -
115C TRP* 2.9 40.1 + - + +
118C ARG* 1.3 75.5 - - - +
120C PHE* 1.3 63.7 + - + +
121C ILE 2.8 9.9 + - - -
124C PHE* 3.3 4.0 - - + -
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Residues in contact with PHE 120 (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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105A TRP* 3.5 27.9 + + + -
301A FAD 6.0 0.7 - - - +
91C LEU* 3.4 28.9 - - + -
99C PHE* 4.7 2.9 - + - -
115C TRP* 3.7 17.3 - + - -
116C PHE* 2.9 51.3 + + + +
117C GLU 4.8 2.2 - - - +
119C VAL* 1.3 75.0 - - + +
121C ILE* 1.3 65.6 + - - +
124C PHE* 5.1 0.2 - + - -
125C ALA* 3.7 15.7 - - + -
126C TYR* 3.7 4.3 - - - -
137C PHE* 4.5 3.1 - + - -
175C ILE* 3.6 23.8 - - + -
176C LEU* 4.9 1.8 - - + -
179C CYS* 3.6 25.4 - - - -
181C PHE* 4.4 19.3 - + - -
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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