Contacts of the helix formed by residues 101 - 114 (chain O) in PDB entry 2J28
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 GLY 101 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A C 4.9 1.0 + - - -
49A C 3.5 11.4 + - - -
68O LYS* 3.5 34.5 - - - +
100O HIS* 1.3 80.5 - - - +
102O ARG* 1.3 55.8 + - - +
103O VAL* 3.4 0.6 - - - +
105O ALA* 2.6 40.1 + - - +
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Residues in contact with ARG 102 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A C 3.1 29.5 + - - +
50A A 4.6 5.6 - - - +
29O HIS 5.5 0.9 - - - +
30O ARG* 2.8 37.5 + - + +
31O THR 2.6 31.1 + - - -
32O PRO* 4.3 5.8 - - - +
33O ARG* 3.2 21.7 - - - +
34O HIS 3.9 5.5 + - - +
35O ILE* 4.1 10.4 - - + +
66O GLY 4.0 4.3 + - - -
67O ASN* 3.7 14.3 + - - +
68O LYS* 3.7 28.8 - - + +
71O ALA* 3.1 21.2 - - + +
101O GLY* 1.3 67.2 - - - -
103O VAL* 1.3 70.4 + - + +
105O ALA* 2.8 5.9 + - - +
106O LEU 2.8 18.4 + - - -
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Residues in contact with VAL 103 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A U 4.4 9.2 - - - +
49A C 4.2 13.0 - - - +
28O VAL* 3.8 29.3 - - + +
29O HIS 4.3 9.6 - - - +
30O ARG* 4.6 10.5 - - + +
35O ILE* 4.2 1.5 - - - +
95O SER 4.9 4.7 - - - +
97O PHE* 4.1 19.1 - - + -
98O GLN 3.1 27.1 - - - +
99O TYR* 5.0 6.0 - - + -
100O HIS* 3.9 10.1 - - + +
101O GLY 4.5 0.7 - - - +
102O ARG* 1.3 75.9 - - + +
104O GLN* 1.3 68.2 + - - +
106O LEU* 2.9 12.6 + - - +
107O ALA* 3.3 8.7 + - - +
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Residues in contact with GLN 104 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99O TYR* 3.5 39.0 + - + +
100O HIS* 2.8 50.8 + - - +
101O GLY 3.4 0.8 + - - -
103O VAL* 1.3 80.8 - - - +
105O ALA* 1.3 57.6 + - - +
107O ALA* 2.9 14.7 - - - +
108O ASP* 2.5 36.9 - - - +
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Residues in contact with ALA 105 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68O LYS* 4.0 14.4 - - + +
71O ALA* 3.9 8.1 - - + -
72O ALA* 4.1 9.9 - - + +
100O HIS 4.0 0.4 + - - -
101O GLY 2.6 27.1 + - - +
102O ARG* 2.8 12.9 + - - +
104O GLN* 1.3 69.3 - - - +
106O LEU* 1.3 65.2 - - - +
107O ALA 3.0 0.2 + - - -
108O ASP* 2.8 14.1 - - - +
109O ALA* 2.7 26.0 + - - +
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Residues in contact with LEU 106 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O LEU* 5.7 4.5 - - + -
28O VAL* 3.4 33.9 - - + -
35O ILE* 3.3 33.2 - - + -
36O TYR 3.7 10.8 - - - +
37O ALA* 4.2 5.2 - - + -
71O ALA* 3.5 13.6 - - - +
74O VAL* 3.7 17.7 - - + -
75O GLY* 3.7 15.0 - - - -
78O VAL* 4.6 9.6 - - + -
93O ASP* 4.8 2.5 - - - +
102O ARG 2.8 9.5 + - - -
103O VAL 3.3 9.4 - - - +
105O ALA* 1.3 70.2 - - - +
107O ALA* 1.3 54.4 + - - +
109O ALA* 2.9 2.9 - - - +
110O ALA* 2.7 39.8 + - + +
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Residues in contact with ALA 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93O ASP* 3.8 15.6 + - - +
99O TYR* 2.9 38.6 - - + +
103O VAL 3.3 3.2 + - - +
104O GLN 2.9 11.8 + - - +
105O ALA 3.0 0.6 + - - -
106O LEU* 1.3 75.2 - - - +
108O ASP* 1.3 66.3 + - - +
109O ALA 2.8 5.5 + - - -
110O ALA* 2.8 15.2 + - - +
111O ARG* 2.9 13.8 + - - +
117O PHE* 3.9 12.7 - - + -
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Residues in contact with ASP 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72O ALA* 5.9 0.5 - - - +
99O TYR* 5.2 0.2 - - - -
104O GLN* 2.5 39.5 + - - +
105O ALA* 2.8 26.4 - - - +
107O ALA* 1.3 74.6 - - - +
109O ALA* 1.3 51.4 + - - +
111O ARG* 3.4 21.7 + - - +
112O GLU* 2.6 42.3 + - + +
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Residues in contact with ALA 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72O ALA* 3.2 33.7 - - - +
75O GLY* 3.5 11.9 - - - -
76O LYS* 3.8 7.1 + - - -
105O ALA 2.7 14.4 + - - +
106O LEU 2.9 14.4 - - - +
107O ALA 2.8 0.8 + - - -
108O ASP* 1.3 75.5 + - - +
110O ALA* 1.3 56.6 + - - +
112O GLU* 2.8 44.3 + - - +
113O ALA 3.7 1.6 + - - -
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Residues in contact with ALA 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O LEU* 5.8 3.1 - - + -
75O GLY* 3.3 22.1 - - - +
78O VAL* 5.5 3.6 - - + -
79O ALA* 3.8 10.1 - - + +
93O ASP* 5.4 0.4 - - - +
106O LEU* 2.7 22.1 + - + +
107O ALA 2.8 7.6 + - - +
109O ALA* 1.3 72.4 - - - +
111O ARG* 1.3 59.2 + - - +
113O ALA 3.6 0.9 + - - -
114O GLY 2.8 25.1 + - - +
115O LEU* 3.9 14.5 - - + +
117O PHE* 3.9 16.6 - - + -
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Residues in contact with ARG 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2376B A 2.7 64.3 + - - -
99O TYR* 3.8 11.9 + - - -
107O ALA* 2.9 12.3 + - - +
108O ASP* 3.4 20.1 + - - +
110O ALA* 1.3 74.8 - - - +
112O GLU* 1.3 65.9 + - - +
113O ALA 2.8 8.5 + - - +
114O GLY 3.2 13.4 - - - +
115O LEU 4.5 7.1 - - - +
116O GLN* 5.0 0.4 - - - +
117O PHE* 2.8 54.1 + - + +
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Residues in contact with GLU 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72O ALA* 4.2 9.7 - - - +
76O LYS* 3.7 27.3 - - + +
105O ALA 4.9 0.3 - - - +
108O ASP* 2.6 27.2 + - + +
109O ALA* 2.8 36.2 + - - +
111O ARG* 1.3 73.3 - - - +
113O ALA* 1.3 57.3 + - + +
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Residues in contact with ALA 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O LYS* 4.6 15.9 - - + +
79O ALA* 4.4 12.3 - - + -
80O GLU* 5.7 1.1 - - + +
109O ALA 3.7 0.4 + - - -
110O ALA 3.6 5.1 + - - +
111O ARG 2.8 6.5 + - - +
112O GLU* 1.3 79.5 - - + +
114O GLY* 1.3 58.5 + - - +
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Residues in contact with GLY 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79O ALA* 4.4 1.5 - - - +
110O ALA 2.8 21.2 + - - +
111O ARG* 3.2 10.0 - - - +
113O ALA* 1.3 81.5 - - - +
115O LEU* 1.3 83.7 + - - +
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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