Contacts of the helix formed by residues 102 - 113 (chain I) 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 ARG 102 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101I SER* 1.3 73.9 - - - +
103I ALA* 1.3 62.0 + - - +
105I LEU* 3.4 6.7 + - - +
106I GLN* 3.3 39.4 + - - +
125I THR* 3.5 29.1 + - - +
129I GLU* 3.8 18.2 + - - -
139I VAL* 3.7 19.3 - - + +
140I GLU 3.0 8.3 + - - -
141I ASP* 3.1 56.7 + - + +
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Residues in contact with ALA 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101I SER* 3.0 10.9 - - - +
102I ARG* 1.3 79.6 - - - +
104I GLN* 1.3 63.2 + - - +
106I GLN* 3.0 27.8 + - - +
107I GLU* 3.1 22.8 + - + +
141I ASP 5.7 0.6 + - - -
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Residues in contact with GLN 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82I ALA* 3.1 45.1 + - + +
99I LYS 4.6 0.7 - - - +
100I ILE* 3.1 24.4 - - + +
101I SER* 3.0 33.8 + - - +
103I ALA* 1.3 79.3 - - - +
105I LEU* 1.3 56.4 + - - +
107I GLU* 2.8 36.5 + - - +
108I ILE* 2.8 18.8 + - + +
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Residues in contact with LEU 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I LEU* 3.5 33.0 - - + -
100I ILE* 3.9 11.2 - - + -
101I SER 3.3 10.2 + - - +
102I ARG* 3.6 8.5 - - - +
103I ALA 3.3 0.6 - - - -
104I GLN* 1.3 78.3 - - - +
106I GLN* 1.3 53.2 + - - +
108I ILE* 3.7 4.4 - - + +
109I ALA* 2.7 36.5 + - - +
125I THR* 4.0 14.6 - - + +
128I ILE* 4.0 10.3 - - + +
129I GLU* 3.2 34.5 - - + -
132I ALA* 4.9 2.2 - - + -
139I VAL* 3.2 37.0 - - + -
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Residues in contact with GLN 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I ARG* 3.3 25.6 + - - +
103I ALA* 3.0 18.9 + - - +
105I LEU* 1.3 77.5 - - - +
107I GLU* 1.3 54.2 + - + +
109I ALA* 3.3 2.8 + - - +
110I GLN* 2.8 34.7 + - - +
121I ILE* 5.5 9.9 - - + +
125I THR* 3.8 24.6 + - + +
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Residues in contact with GLU 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103I ALA* 3.2 16.8 - - + +
104I GLN* 2.8 32.2 + - - +
106I GLN* 1.3 76.1 - - + +
108I ILE* 1.3 58.0 + - + +
110I GLN* 3.3 8.3 + - - +
111I THR* 2.9 30.4 + - - -
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Residues in contact with ILE 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I ALA* 4.9 4.3 - - - +
78I LEU* 3.5 50.5 - - + +
79I LEU* 3.3 31.9 - - + -
82I ALA* 4.1 13.0 - - + -
100I ILE* 4.7 0.2 - - + -
104I GLN* 2.8 18.0 + - + +
105I LEU* 3.7 8.7 - - + +
107I GLU* 1.3 75.0 - - + +
109I ALA* 1.3 61.0 + - - +
111I THR* 3.0 6.9 + - - -
112I LYS* 2.8 30.4 + - + +
128I ILE* 3.2 21.8 - - + -
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Residues in contact with ALA 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I LEU 2.7 21.5 + - - +
106I GLN* 3.4 6.5 - - - +
108I ILE* 1.3 72.0 - - - +
110I GLN* 1.3 57.6 + - - +
112I LYS* 3.7 1.3 - - - +
113I ALA* 2.8 28.2 + - - +
116I MET* 4.5 1.0 - - - +
121I ILE* 4.7 1.6 - - + +
124I MET* 3.7 17.6 - - + +
125I THR* 3.4 36.1 - - - +
128I ILE* 3.0 13.3 - - + +
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Residues in contact with GLN 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I GLN 2.8 17.6 + - - +
107I GLU* 3.3 10.1 - - - +
109I ALA* 1.3 75.6 - - - +
111I THR* 1.3 65.3 + - - +
113I ALA* 3.0 23.0 - - - +
121I ILE* 5.3 11.3 - - - +
124I MET* 5.3 1.3 - - - +
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Residues in contact with THR 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I THR* 3.1 29.3 + - - +
73I PRO* 4.9 4.7 - - + -
78I LEU* 4.2 14.0 - - + +
107I GLU 2.9 17.0 + - - -
108I ILE* 3.0 10.4 + - - -
110I GLN* 1.3 80.4 - - - +
112I LYS* 1.3 61.2 + - - +
113I ALA 3.3 0.3 + - - -
114I ALA* 4.2 7.6 + - - +
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Residues in contact with LYS 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059B G 3.9 10.5 - - - -
1060B U 3.2 24.2 + - - -
55I PRO* 5.4 1.2 - - - +
72I THR* 3.1 32.4 + - + +
73I PRO 2.9 30.6 + - - +
74I PRO* 3.9 0.4 - - - +
75I ALA* 4.1 5.4 - - - +
78I LEU* 3.6 15.5 - - + -
108I ILE* 2.8 24.0 + - + +
111I THR* 1.3 72.8 - - - +
113I ALA* 1.3 54.9 + - - +
114I ALA 3.1 2.9 - - - -
115I ASP* 2.7 40.5 + - - +
116I MET* 2.9 38.6 + - + -
128I ILE* 4.1 0.2 - - + -
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Residues in contact with ALA 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I ALA 2.8 15.8 + - - +
110I GLN* 3.0 29.6 - - - +
111I THR 3.2 0.4 - - - -
112I LYS* 1.3 74.8 - - - +
114I ALA* 1.3 63.3 + - - +
116I MET* 3.0 22.6 + - - +
124I MET* 3.6 27.7 - - + +
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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