Contacts of the helix formed by residues 120 - 135 (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 ASP 120 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082B U 5.1 2.6 + - - -
119I ALA* 1.3 81.4 - - - +
121I ILE* 1.3 67.4 + - + +
122I GLU* 3.1 22.1 - - - +
123I ALA* 2.8 45.6 + - - +
124I MET* 3.2 21.0 + - - +
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Residues in contact with ILE 121 (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* 5.5 9.6 - - + +
109I ALA* 4.7 1.3 - - + +
110I GLN* 5.3 10.8 - - - +
120I ASP* 1.3 72.6 - - + +
122I GLU* 1.3 86.7 + - + +
124I MET* 3.2 19.2 + - + +
125I THR* 2.7 42.7 + - - +
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Residues in contact with GLU 122 (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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120I ASP* 3.1 28.8 - - - +
121I ILE* 1.3 106.3 - - + +
123I ALA* 1.3 62.8 + - - +
125I THR* 3.5 6.5 - - - -
126I ARG* 2.9 33.9 + - - +
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Residues in contact with ALA 123 (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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1080B A 5.0 0.2 + - - -
1081B U 3.9 30.7 + - - +
1082B U 4.7 1.3 - - - +
118I GLY* 4.2 6.7 - - - -
119I ALA 4.2 1.1 - - - +
120I ASP* 2.8 31.8 + - - +
122I GLU* 1.3 78.9 - - - +
124I MET* 1.3 62.0 - - - +
126I ARG* 3.3 19.9 + - - +
127I SER* 3.0 25.4 + - - -
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Residues in contact with MET 124 (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* 3.7 19.3 - - + +
110I GLN* 5.3 0.7 - - - +
113I ALA* 3.6 41.7 - - + +
116I MET* 4.2 12.4 - - + +
118I GLY* 3.7 33.2 - - - +
119I ALA 4.9 1.8 - - - +
120I ASP* 3.2 20.4 + - - +
121I ILE* 3.2 19.0 + - + +
123I ALA* 1.3 76.8 - - - +
125I THR* 1.3 66.4 + - - +
127I SER* 2.9 19.6 + - - +
128I ILE* 3.2 15.4 + - - +
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Residues in contact with THR 125 (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* 3.5 20.8 + - - +
105I LEU* 4.0 22.2 - - + +
106I GLN* 3.8 24.0 + - + +
109I ALA* 3.4 13.1 - - - +
121I ILE* 2.7 28.7 + - - +
122I GLU* 3.5 8.1 - - - -
124I MET* 1.3 73.8 - - - +
126I ARG* 1.3 57.8 + - - +
128I ILE* 3.4 5.2 + - - +
129I GLU* 3.0 40.7 + - - +
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Residues in contact with ARG 126 (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 4.5 1.4 + - - -
1080B A 2.5 65.5 + - - -
1081B U 2.5 34.9 + - - -
122I GLU* 2.9 21.3 + - - +
123I ALA* 3.7 15.6 + - - +
125I THR* 1.3 75.3 - - - +
127I SER* 1.3 64.5 + - - +
128I ILE 3.1 1.1 - - - -
129I GLU* 3.6 20.8 - - + +
130I GLY* 3.1 16.8 + - - -
133I ARG* 4.8 6.8 + - - +
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Residues in contact with SER 127 (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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1058B U 5.0 2.3 + - - -
1059B G 3.2 52.3 + - - +
1080B A 4.5 7.5 + - - -
1081B U 4.4 18.7 + - - -
116I MET* 4.5 8.4 - - - +
117I THR* 5.6 2.6 - - - +
118I GLY 5.7 1.7 + - - -
123I ALA 3.0 16.3 + - - -
124I MET* 2.9 12.3 + - - -
126I ARG* 1.3 75.2 - - - +
128I ILE* 1.3 61.6 + - - +
130I GLY 3.2 8.8 + - - -
131I THR* 3.4 6.1 - - - +
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Residues in contact with ILE 128 (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 4.4 0.7 - - - +
75I ALA* 4.6 3.6 - - + -
79I LEU* 3.7 27.4 - - + -
105I LEU* 4.0 12.6 - - + +
108I ILE* 3.2 22.9 - - + +
109I ALA* 3.0 42.8 - - + +
112I LYS* 4.1 0.4 - - + -
116I MET* 3.4 27.6 - - + -
124I MET 3.2 5.6 + - - +
125I THR 3.5 7.9 - - - +
127I SER* 1.3 73.3 - - - +
129I GLU* 1.3 65.0 + - - +
130I GLY 3.0 1.6 - - - -
131I THR* 2.5 32.4 + - - +
132I ALA* 2.9 4.7 + - - +
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Residues in contact with GLU 129 (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* 3.8 19.1 + - - -
105I LEU* 3.2 26.5 - - + +
125I THR* 3.0 41.7 + - - +
126I ARG* 3.7 19.9 - - + +
127I SER 3.3 0.6 - - - -
128I ILE* 1.3 76.6 - - - +
130I GLY* 1.3 62.6 + - - +
132I ALA* 3.1 9.8 + - - +
133I ARG* 2.9 62.6 + - - +
139I VAL* 5.0 6.2 - - + +
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Residues in contact with GLY 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1059B G 3.4 20.2 - - - -
1060B U 3.7 6.7 - - - -
1079B C 3.9 9.4 - - - +
1080B A 5.9 0.4 - - - -
1088B A 3.6 2.8 + - - +
126I ARG 3.1 11.5 + - - -
127I SER 3.2 0.4 + - - -
128I ILE 3.0 1.0 - - - -
129I GLU* 1.3 78.1 - - - +
131I THR* 1.3 52.9 + - - +
133I ARG* 3.6 13.1 + - - +
134I SER* 2.8 30.7 + - - -
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Residues in contact with THR 131 (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 3.3 19.7 - - - +
1060B U 3.1 35.9 - - + -
1062B G 4.1 2.4 + - - -
75I ALA* 3.8 15.1 - - + +
76I ALA* 4.9 5.2 - - - -
79I LEU* 2.7 20.3 - - - +
127I SER 3.4 10.5 - - - +
128I ILE* 2.5 19.1 + - - +
130I GLY* 1.3 73.8 - - - +
132I ALA* 1.3 58.6 + - - +
134I SER* 3.0 8.7 + - - -
135I MET* 3.0 32.2 + - - +
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Residues in contact with ALA 132 (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* 3.3 28.0 - - + -
100I ILE* 5.8 0.7 - - + -
105I LEU* 4.9 0.4 - - + -
128I ILE 2.9 5.1 + - - +
129I GLU* 3.4 13.0 - - - +
131I THR* 1.3 81.5 + - - +
133I ARG* 1.3 57.4 + - - +
134I SER 3.0 0.2 - - - -
135I MET* 2.9 17.8 + - - -
137I LEU* 3.0 40.6 + - + +
139I VAL* 4.4 13.0 - - + -
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Residues in contact with ARG 133 (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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1079B C 4.7 13.6 + - - -
92I PRO* 3.9 0.9 - - - +
93I ASN* 3.0 40.8 + - - +
126I ARG* 4.8 7.5 + - - +
129I GLU* 2.9 69.7 + - + +
130I GLY* 3.8 11.6 - - - +
131I THR 3.3 0.2 - - - -
132I ALA* 1.3 76.8 - - + +
134I SER* 1.3 60.0 + - - +
135I MET 3.2 0.2 - - - -
136I GLY* 3.9 6.2 + - - +
137I LEU 4.4 6.3 - - - +
139I VAL* 6.2 3.8 - - + +
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Residues in contact with SER 134 (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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1062B G 3.0 38.7 + - - +
1063B G 2.6 22.8 - - - +
1077B A 5.9 2.3 + - - -
1088B A 2.7 30.5 + - - -
92I PRO* 2.8 20.0 - - - +
93I ASN* 5.1 1.1 - - - -
130I GLY 2.8 10.8 + - - -
131I THR 3.0 6.7 + - - -
133I ARG* 1.3 78.5 - - - +
135I MET* 1.3 53.9 + - - +
136I GLY 3.5 0.4 - - - -
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Residues in contact with MET 135 (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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1062B G 4.8 0.4 - - - +
1063B G 3.7 26.2 - - - -
76I ALA* 3.0 39.7 - - + +
79I LEU* 3.2 31.9 - - - -
80I LYS* 3.4 24.9 - - + +
85I ILE* 4.6 3.4 - - + -
88I GLY* 3.6 6.7 - - - -
89I SER* 3.1 25.3 + - - -
97I VAL* 3.9 2.8 - - - +
131I THR* 3.0 12.8 + - - +
132I ALA 2.9 8.8 + - - +
134I SER* 1.3 79.7 - - - +
136I GLY* 1.3 60.9 + - - +
137I LEU* 3.4 23.6 - - + +
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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