Contacts of the helix formed by residues 104 - 123 (chain A) in PDB entry 3OAN
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 GLN 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASN* 3.5 10.4 - - - +
102A VAL* 3.5 0.9 - - - +
103A LYS* 1.3 98.1 + - - +
105A LYS* 1.3 67.6 + - - +
106A ALA* 4.0 11.4 - - + +
107A ASP* 3.1 27.4 + - - +
108A GLY 3.1 16.6 + - - -
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Residues in contact with LYS 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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80A ASP 4.7 15.5 - - - -
82A GLU* 4.0 25.3 - - + +
83A ASN* 3.9 22.3 - - + +
103A LYS 4.3 0.2 + - - -
104A GLN* 1.3 74.3 - - - +
106A ALA* 1.3 57.4 + - - +
108A GLY* 3.0 4.0 + - - -
109A ARG* 3.0 48.3 + - - +
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Residues in contact with ALA 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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104A GLN* 3.2 10.1 - - + +
105A LYS* 1.3 78.4 - - - +
107A ASP* 1.3 58.4 + - - +
109A ARG* 3.4 26.5 + - - +
110A ARG* 3.0 51.8 + - - +
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Residues in contact with ASP 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 3.8 6.4 - - + -
16A GLU* 4.3 28.4 - - + +
102A VAL* 3.7 15.7 - - + -
103A LYS* 4.3 6.4 + - - +
104A GLN* 3.1 37.8 + - - +
106A ALA* 1.3 77.1 - - - +
108A GLY* 1.3 57.8 + - - +
110A ARG* 2.9 27.0 + - - +
111A LEU* 2.9 28.4 + - - +
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Residues in contact with GLY 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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82A GLU 3.3 24.0 - - - -
85A ILE* 3.7 7.5 - - - +
102A VAL* 3.4 14.3 - - - +
104A GLN 3.1 6.6 + - - -
105A LYS 3.0 5.4 + - - -
107A ASP* 1.3 76.5 - - - +
109A ARG* 1.3 56.4 + - - +
111A LEU* 3.4 4.0 + - - +
112A VAL* 3.0 33.9 + - - +
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Residues in contact with ARG 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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76A PRO* 6.3 0.7 - - - -
82A GLU* 3.1 44.1 + - + +
105A LYS* 3.0 30.9 + - - +
106A ALA* 3.8 31.4 - - - +
108A GLY* 1.3 74.1 - - - +
110A ARG* 1.3 54.5 + - - +
112A VAL* 3.4 6.7 + - - +
113A GLY* 2.8 32.9 + - - -
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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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14A PHE* 4.1 19.1 - - + -
16A GLU* 5.4 3.8 + - - -
106A ALA* 3.0 36.1 + - - +
107A ASP* 2.9 45.5 + - - +
109A ARG* 1.3 75.4 - - - +
111A LEU* 1.3 56.3 + - - +
113A GLY* 3.3 1.5 + - - -
114A ALA* 2.8 34.6 + - + +
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Residues in contact with LEU 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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14A PHE* 3.7 40.0 - - + -
38A LEU* 3.8 25.1 - - + -
40A LEU* 5.2 5.4 - - + -
52A VAL* 5.5 1.1 - - + -
85A ILE* 4.0 26.0 - - + -
87A TRP* 4.5 13.5 - - + -
100A ILE* 4.2 11.2 - - + -
102A VAL* 5.0 4.7 - - + -
107A ASP 2.9 14.0 + - - +
108A GLY* 3.6 9.2 - - - +
109A ARG 3.3 0.4 - - - -
110A ARG* 1.3 76.8 - - - +
112A VAL* 1.3 57.4 + - - +
114A ALA* 3.3 0.9 + - - -
115A VAL* 2.9 50.9 + - + +
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Residues in contact with VAL 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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74A TYR* 3.7 26.6 - - - +
75A GLN* 4.8 1.1 - - + -
76A PRO* 4.0 21.5 - - + -
85A ILE* 3.6 26.0 - - + -
108A GLY 3.0 21.5 + - - +
109A ARG* 3.7 6.7 - - - +
111A LEU* 1.3 74.5 - - - +
113A GLY* 1.3 63.6 + - - +
115A VAL* 3.4 4.2 + - - +
116A ALA* 3.0 26.4 + - + +
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Residues in contact with GLY 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 ARG 2.8 20.1 + - - -
110A ARG* 3.7 1.6 - - - -
112A VAL* 1.3 74.6 - - - +
114A ALA* 1.3 56.6 + - - +
116A ALA* 3.3 4.5 + - - +
117A ASP* 2.9 41.2 + - - +
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Residues in contact with ALA 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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13A LEU* 4.1 20.8 - - + +
14A PHE* 4.4 8.3 - - + -
40A LEU* 3.7 17.2 - - + +
110A ARG* 2.8 21.1 + - + +
111A LEU 3.8 3.1 - - - +
113A GLY* 1.3 70.7 - - - +
115A VAL* 1.3 59.9 + - - +
117A ASP* 3.9 8.0 - - - +
118A ALA* 2.9 29.5 + - - +
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Residues in contact with VAL 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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40A LEU* 4.1 16.2 - - + -
68A VAL* 4.1 15.2 - - + +
74A TYR* 3.4 44.6 - - + -
87A TRP* 4.0 18.8 - - + -
111A LEU* 2.9 39.3 + - + +
112A VAL* 4.0 4.3 - - - +
114A ALA* 1.3 74.6 - - - +
116A ALA* 1.3 52.0 + - - +
118A ALA* 3.2 4.3 + - - +
119A GLN* 2.8 36.9 + - - +
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Residues in contact with ALA 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 VAL* 3.0 21.5 + - + +
113A GLY* 3.7 4.7 - - - +
115A VAL* 1.3 77.4 - - - +
117A ASP* 1.3 65.0 + - - +
119A GLN* 3.3 14.8 + - - +
120A GLN* 3.1 23.7 + - - +
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Residues in contact with ASP 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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42A ARG* 5.1 0.8 + - - -
113A GLY* 2.9 25.7 + - - +
114A ALA* 3.9 6.9 + - - +
116A ALA* 1.3 75.2 - - - +
118A ALA* 1.3 67.1 + - - +
120A GLN* 3.4 8.2 + - - +
121A ALA* 3.2 21.8 + - - +
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Residues in contact with ALA 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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13A LEU* 3.9 22.9 - - + +
40A LEU* 4.5 1.8 - - + -
42A ARG* 4.4 11.1 + - - +
47A LYS 4.8 0.3 - - - +
50A VAL* 4.1 22.5 - - + +
68A VAL* 5.6 1.1 - - + -
114A ALA 2.9 19.0 + - - +
115A VAL* 3.4 7.0 - - - +
117A ASP* 1.3 76.5 - - - +
119A GLN* 1.3 61.9 + - + +
121A ALA* 3.2 4.9 + - - +
122A MSE 3.0 27.2 + - - +
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Residues in contact with GLN 119 (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 VAL* 3.8 16.4 - - + -
69A VAL 2.8 27.6 + - - +
70A LYS* 3.6 16.5 + - + +
72A PHE 2.9 23.4 + - - +
73A LYS* 5.4 0.3 - - - -
74A TYR* 3.5 17.8 + - - -
115A VAL* 2.8 23.0 + - - +
116A ALA* 3.6 14.4 - - - +
118A ALA* 1.3 74.1 - - - +
120A GLN* 1.3 60.3 + - - +
122A MSE 3.2 25.7 + - - +
123A GLU* 3.4 15.0 - - - +
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Residues in contact with GLN 120 (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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116A ALA 3.1 12.6 + - - +
117A ASP* 3.7 11.9 - - - +
118A ALA 3.3 0.2 - - - -
119A GLN* 1.3 76.0 - - - +
121A ALA* 1.3 63.1 + - - +
123A GLU* 3.3 28.0 + - - +
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Residues in contact with ALA 121 (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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42A ARG* 3.7 23.6 - - - +
47A LYS* 4.3 28.9 - - + +
117A ASP 3.2 7.8 + - - +
118A ALA 3.2 9.4 + - - +
120A GLN* 1.3 77.0 - - - +
122A MSE 1.3 63.6 + - - +
123A GLU 3.4 5.2 + - - -
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Residues in contact with MSE 122 (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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47A LYS 3.5 20.6 - - - +
48A GLY* 3.4 31.4 - - - +
50A VAL* 3.8 21.5 - - + +
68A VAL* 3.4 41.7 - - - +
70A LYS* 3.8 38.6 + - + +
118A ALA 3.0 16.0 + - - +
119A GLN* 3.2 19.9 + - - +
121A ALA* 1.3 76.6 - - - +
123A GLU* 1.3 64.7 + - - +
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Residues in contact with GLU 123 (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 LYS* 3.6 36.0 - - - +
119A GLN 3.4 14.0 - - - +
120A GLN* 3.4 22.9 - - - +
121A ALA 3.2 6.6 - - - -
122A MSE 1.3 81.8 - - - +
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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