Contacts of the helix formed by residues 105 - 119 (chain A) in PDB entry 3K9O
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 THR 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A ARG* 5.3 4.5 - - - +
12A GLU* 3.3 20.4 - - + +
15A GLU* 3.6 26.3 + - - +
100A TRP* 5.4 0.9 - - - -
103A ALA 4.1 7.2 - - - +
104A MET* 1.3 78.1 - - - +
106A LEU* 1.3 64.6 + - - +
107A ARG* 3.4 9.4 + - - +
108A THR* 3.1 29.8 + - - +
109A VAL* 3.0 26.3 + - - +
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Residues in contact with LEU 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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9A ILE* 4.4 12.6 - - + -
12A GLU* 2.8 38.1 + - + +
13A PHE* 4.0 14.4 - - - +
16A VAL* 4.2 13.5 - - + -
29A VAL* 5.3 5.2 - - + -
39A LEU* 3.5 26.2 - - + -
60A ILE* 4.3 27.4 - - + -
62A ILE* 4.4 13.0 - - + -
66A TYR* 5.5 2.0 - - + +
71A PRO* 4.7 12.1 - - + -
105A THR* 1.3 72.5 - - - +
107A ARG* 1.3 63.6 + - - +
109A VAL* 3.2 9.7 + - + +
110A LEU* 2.9 29.9 + - + +
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Residues in contact with ARG 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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15A GLU* 4.0 27.4 + - - +
16A VAL* 3.7 20.7 - - + +
19A SER* 4.1 14.0 - - - -
21A GLU* 2.7 39.7 + - - -
27A ILE* 4.0 14.8 - - + -
105A THR* 3.2 10.2 + - - +
106A LEU* 1.3 78.7 - - - +
108A THR* 1.3 67.8 + - - +
110A LEU* 3.2 2.1 + - - +
111A LEU* 2.9 47.7 + - + +
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Residues in contact with THR 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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95A ILE* 4.4 9.6 - - + -
104A MET* 4.6 17.9 - - + -
105A THR* 3.1 28.9 + - - -
107A ARG* 1.3 85.4 + - - +
109A VAL* 1.3 58.8 + - - +
111A LEU* 3.3 6.9 + - - +
112A SER* 2.9 43.2 + - - +
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Residues in contact with VAL 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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60A ILE* 5.9 4.5 - - + -
71A PRO* 4.7 8.7 - - + -
73A VAL* 4.2 20.4 - - + -
93A LEU* 6.3 0.2 - - + -
95A ILE* 4.3 15.9 - - + -
96A LEU* 4.3 13.2 - - + -
100A TRP* 3.7 28.7 - - + -
104A MET* 5.2 1.3 - - + -
105A THR 3.0 17.0 + - - +
106A LEU* 3.5 13.2 - - + +
108A THR* 1.3 77.2 - - - +
110A LEU* 1.3 66.1 + - + +
112A SER* 3.2 1.7 + - - -
113A LEU* 2.9 41.8 + - + +
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Residues in contact with LEU 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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16A VAL* 3.9 29.4 - - + -
27A ILE* 4.1 21.3 - - + -
28A LYS 3.9 17.5 - - - +
29A VAL* 4.6 7.2 - - + -
41A GLY* 4.3 7.4 - - - -
43A ILE* 3.7 17.7 - - + +
58A LEU* 3.7 27.6 - - + -
60A ILE* 4.2 20.0 - - + -
106A LEU* 2.9 23.2 + - + +
107A ARG 3.7 3.1 - - - +
109A VAL* 1.3 80.7 - - + +
111A LEU* 1.3 58.4 + - - +
113A LEU* 3.3 6.0 + - + +
114A GLN* 3.0 23.2 + - - +
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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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21A GLU* 3.9 25.1 - - + +
26A GLN* 5.3 0.7 - - + -
27A ILE* 3.9 21.3 - - + -
107A ARG* 2.9 61.8 + - + +
108A THR* 4.0 4.5 - - - +
110A LEU* 1.3 77.4 - - - +
112A SER* 1.3 57.3 + - - +
114A GLN* 3.3 15.8 + - - +
115A ALA* 2.9 29.2 + - - +
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Residues in contact with SER 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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93A LEU* 4.2 15.0 - - - +
95A ILE* 3.2 29.9 - - - +
108A THR* 2.9 27.2 + - - +
109A VAL 3.6 3.1 - - - -
111A LEU* 1.3 75.8 - - - +
113A LEU* 1.3 59.0 + - - +
115A ALA* 3.3 9.3 + - - +
116A LEU* 2.9 26.0 + - - +
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Residues in contact with LEU 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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43A ILE* 3.8 15.7 - - + +
58A LEU* 3.9 16.4 - - + -
73A VAL* 3.8 29.2 - - + -
75A PHE* 4.4 6.6 - - + -
91A ILE* 3.8 29.8 - - + -
93A LEU* 3.8 22.2 - - + -
96A LEU* 4.5 2.9 - - + -
109A VAL* 2.9 31.3 + - + +
110A LEU* 3.7 7.0 - - + +
112A SER* 1.3 74.8 - - - +
114A GLN* 1.3 64.2 + - - +
116A LEU* 3.1 20.9 + - + +
117A LEU* 3.3 16.8 + - - +
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Residues in contact with GLN 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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26A GLN* 2.8 56.6 + - - +
27A ILE* 4.1 0.9 - - + +
43A ILE* 3.8 16.0 - - + +
44A ALA* 3.0 27.8 + - - +
46A PRO* 3.5 18.7 - - + +
110A LEU 3.0 15.7 + - - +
111A LEU* 3.3 20.4 + - - +
113A LEU* 1.3 74.4 - - - +
115A ALA* 1.3 61.3 + - - +
117A LEU* 3.1 18.7 + - - +
118A ALA 3.4 4.0 + - - -
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Residues in contact with ALA 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 LEU 2.9 18.3 + - - +
112A SER* 3.4 9.9 - - - +
113A LEU 3.2 0.2 - - - -
114A GLN* 1.3 73.9 - - - +
116A LEU* 1.4 60.2 + - - +
118A ALA* 2.9 24.7 + - - +
119A ALA* 3.2 13.0 + - - +
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Residues in contact with LEU 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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75A PHE* 5.5 0.7 - - + -
81A HIS* 2.8 28.1 - - + +
83A ASN* 3.6 39.9 - - + +
84A ILE* 4.7 10.8 - - + -
91A ILE* 4.1 23.3 - - + -
92A CYS 5.0 0.2 - - - +
93A LEU* 4.2 25.4 - - + -
112A SER 2.9 12.9 + - - +
113A LEU* 3.1 20.4 + - + +
115A ALA* 1.4 77.2 - - - +
117A LEU* 1.3 61.2 + - + +
118A ALA 3.0 0.7 + - - -
119A ALA 3.3 23.3 + - - +
121A GLU* 4.5 8.7 - - + -
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Residues in contact with LEU 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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43A ILE* 3.8 20.9 - - + -
44A ALA 4.3 2.9 - - - +
45A GLY* 4.2 4.7 - - - -
46A PRO* 3.5 22.9 - - + -
49A THR* 3.7 8.1 - - - +
51A TYR* 3.3 28.8 - - + -
56A TYR* 4.0 26.7 - - + -
75A PHE* 4.2 13.5 - - + -
79A ILE* 3.5 27.8 - - + -
81A HIS* 4.0 15.4 - - - +
84A ILE* 4.3 3.4 - - + -
113A LEU 3.3 10.7 + - - +
114A GLN 3.1 9.9 + - - +
116A LEU* 1.3 78.8 - - + +
118A ALA* 1.3 61.0 + - - +
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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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46A PRO* 4.2 16.8 - - + -
49A THR* 3.8 17.9 - - + +
114A GLN 3.4 1.8 + - - +
115A ALA* 2.9 17.3 + - - +
117A LEU* 1.3 81.8 - - - +
119A ALA* 1.3 64.5 + - + +
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Residues in contact with ALA 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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115A ALA 3.2 7.5 + - - +
116A LEU* 3.3 21.4 - - - +
117A LEU 3.3 1.0 - - - -
118A ALA* 1.3 85.8 - - + +
120A ALA* 1.3 67.8 + - - +
121A GLU* 3.6 14.7 + - - +
134A TYR* 5.6 0.9 - - - -
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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