Contacts of the helix formed by residues 106 - 118 (chain A) in PDB entry 3NJ8
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 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LEU* 4.7 0.7 - - - -
80A ASP 4.4 2.0 - - - -
83A PHE* 3.7 21.3 - - + -
84A ASP* 3.3 19.9 + - - -
85A LYS 3.4 24.2 - - - +
86A PRO* 3.4 4.5 - - - +
89A VAL* 3.8 14.1 - - + -
105A TYR* 1.3 84.6 - - + +
107A ILE* 1.3 61.2 + - - +
109A GLU* 2.7 33.4 + - - +
110A VAL* 2.9 31.5 + - - +
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Residues in contact with ILE 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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79A LEU* 4.2 17.0 - - + -
80A ASP 4.4 2.4 + - - +
81A ALA* 4.0 17.5 - - + +
83A PHE 3.3 21.4 + - - +
84A ASP* 3.6 4.0 + - - +
106A THR* 1.3 72.8 - - - +
108A LYS* 1.3 67.5 + - - +
109A GLU 2.9 0.7 + - - -
110A VAL* 3.0 8.1 + - - +
111A ALA* 2.9 22.9 + - - +
156A SER* 4.2 11.4 - - - +
159A SER* 3.2 48.2 - - - +
160A LEU* 4.3 12.3 - - + +
163A HIS* 3.7 15.7 - - + -
164A PHE* 4.4 9.5 - - + -
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Residues in contact with LYS 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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84A ASP 3.0 21.6 + - - +
85A LYS* 3.2 48.2 - - + +
86A PRO* 5.0 6.3 - - + -
87A GLU* 4.5 3.5 + - - +
106A THR* 4.8 0.7 - - - +
107A ILE* 1.3 74.6 - - - +
109A GLU* 1.3 60.9 + - + +
111A ALA* 3.8 1.9 + - - +
112A VAL* 3.2 30.9 + - + +
163A HIS* 3.4 33.4 + - + +
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Residues in contact with GLU 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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86A PRO* 3.3 33.2 - - + +
104A GLY* 3.2 41.4 + - - +
105A TYR 3.4 1.2 + - - -
106A THR* 2.7 35.0 + - - +
107A ILE 3.0 0.8 - - - -
108A LYS* 1.3 77.5 - - + +
110A VAL* 1.3 67.6 + - - +
112A VAL* 3.0 9.9 + - - +
113A LYS* 3.0 25.9 + - + +
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 3.6 36.8 - - + -
77A TYR* 4.1 12.6 - - + -
78A PRO 3.5 23.8 - - - +
79A LEU* 3.8 19.1 - - + -
104A GLY 4.0 7.2 + - - +
105A TYR 4.2 0.7 - - - -
106A THR 2.9 17.5 + - - +
107A ILE* 3.5 5.2 - - - +
109A GLU* 1.3 73.4 - - - +
111A ALA* 1.3 60.4 + - - +
113A LYS* 2.9 10.8 + - - +
114A VAL* 2.8 35.1 + - + +
164A PHE* 3.9 7.0 - - + -
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Residues in contact with ALA 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 ILE 2.9 15.6 + - - +
108A LYS 3.9 4.9 - - - +
110A VAL* 1.3 76.0 - - - +
112A VAL* 1.3 62.7 + - + +
114A VAL* 4.1 1.1 - - - +
115A LYS* 3.4 18.2 + - - +
163A HIS* 3.4 34.1 - - + +
164A PHE* 3.8 28.0 - - + -
167A ILE* 3.7 10.8 - - - +
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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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108A LYS* 3.2 22.7 + - + +
109A GLU* 3.0 12.2 + - - +
111A ALA* 1.3 74.8 - - - +
113A LYS* 1.3 60.9 + - + +
115A LYS* 2.8 28.0 + - - +
116A GLN* 2.9 34.7 + - + +
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Residues in contact with LYS 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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77A TYR* 4.1 25.5 - - + -
78A PRO* 5.0 7.2 - - + +
103A ASP* 3.2 32.4 + - - -
104A GLY* 3.6 22.9 + - - +
109A GLU* 3.0 14.4 + - + +
110A VAL* 2.9 10.7 + - - +
112A VAL* 1.3 74.5 - - + +
114A VAL* 1.3 53.1 + - - +
116A GLN* 3.3 17.5 + - - +
117A ASP* 2.7 45.4 + - - +
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Residues in contact with VAL 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 PHE* 3.8 24.7 - - + -
77A TYR* 3.6 32.3 - - + -
110A VAL* 2.8 21.8 + - + +
111A ALA 4.1 5.2 - - - +
113A LYS* 1.3 74.8 - - - +
115A LYS* 1.3 57.8 + - - +
118A LEU* 2.8 39.3 + - + -
119A GLY 3.1 6.5 + - - +
121A ILE* 3.9 28.5 - - + -
164A PHE* 4.3 8.1 - - + -
167A ILE* 4.5 7.2 - - + -
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Residues in contact with LYS 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 ALA 3.4 11.4 + - - +
112A VAL* 2.8 11.9 + - - +
114A VAL* 1.3 76.2 - - - +
116A GLN* 1.3 66.5 - - + +
119A GLY* 3.3 25.7 + - - +
120A ASN* 2.9 34.3 + - - +
167A ILE* 3.8 28.9 - - + -
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Residues in contact with GLN 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* 2.9 35.2 + - + +
113A LYS* 3.5 19.9 - - - +
115A LYS* 1.3 80.1 - - + +
117A ASP* 1.3 68.8 + - - +
119A GLY 4.8 0.3 + - - -
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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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77A TYR* 2.7 38.3 + - - +
113A LYS* 2.7 22.3 + - - +
116A GLN* 1.3 82.2 - - - +
118A LEU* 1.3 70.7 + - + +
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Residues in contact with LEU 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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11A THR* 4.2 21.8 - - + -
37A ARG* 3.8 29.4 + - - +
39A ALA* 3.8 29.6 - - + -
74A ALA* 4.1 32.8 - - + +
77A TYR* 4.3 8.3 - - + +
114A VAL* 2.8 25.2 + - + +
117A ASP* 1.3 91.7 - - + +
119A GLY* 1.3 67.0 + - - +
120A ASN 4.4 2.4 - - - +
121A ILE* 5.8 0.2 - - + -
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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