Contacts of the helix formed by residues 131 - 146 (chain J) in PDB entry 2ABJ
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 131 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22J THR* 3.1 33.4 + - + +
23J PHE* 4.9 0.5 - - - -
130J PHE* 1.3 76.7 - - - +
132J LYS* 1.3 62.7 + - - +
133J GLU* 3.0 22.9 + - - +
134J GLU* 3.2 24.7 + - + +
135J LEU 3.1 18.0 + - - -
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Residues in contact with LYS 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J ASN* 5.9 1.1 - - - +
115J MET* 3.4 44.9 - - + +
116J ASP* 3.6 30.9 + - - +
119J TYR* 3.7 39.9 - - + +
120J ARG* 5.2 5.9 - - - +
130J PHE* 3.5 11.3 + - + -
131J ASP* 1.3 73.2 + - - +
133J GLU* 1.3 61.0 + - + +
135J LEU 3.5 0.5 + - - -
136J LEU* 3.1 26.9 + - - +
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Residues in contact with GLU 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J ASN* 2.6 33.8 + - - +
131J ASP* 3.0 10.5 + - - +
132J LYS* 1.3 77.0 - - + +
134J GLU* 1.3 61.3 + - - +
136J LEU* 3.5 11.8 + - - +
137J GLU* 3.0 28.9 + - - +
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Residues in contact with GLU 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J THR* 4.2 2.7 - - + +
23J PHE* 3.5 27.4 - - + +
24J LYS* 3.8 21.3 + - + +
25J ALA* 2.7 37.0 + - - +
26J LYS* 4.4 1.2 + - - +
131J ASP* 3.2 30.5 + - + +
133J GLU* 1.3 75.8 - - - +
135J LEU* 1.3 60.4 + - - +
137J GLU* 3.4 4.7 + - - +
138J CYS* 3.0 31.9 + - - -
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Residues in contact with LEU 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J PHE* 3.8 23.5 - - + -
56J LEU* 4.1 17.7 - - + -
115J MET* 3.7 15.0 - - + -
118J MET* 3.6 26.2 - - + -
130J PHE* 3.5 26.9 - - + -
131J ASP 3.1 10.8 + - - +
132J LYS 3.9 6.1 - - - +
133J GLU 3.4 0.2 - - - -
134J GLU* 1.3 72.9 - - - +
136J LEU* 1.3 61.2 + - - +
138J CYS* 3.2 1.8 + - - +
139J ILE* 2.9 39.0 + - + +
162J PRO* 5.2 0.4 - - + -
181J LEU* 3.8 26.9 - - + -
183J VAL* 4.6 0.7 - - + -
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Residues in contact with LEU 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J LEU* 5.6 0.7 - - + -
108J LEU* 4.0 17.0 - - + -
111J PRO* 3.7 32.3 - - + -
112J ASN* 3.5 33.7 - - - +
115J MET* 3.9 16.3 - - + -
132J LYS 3.1 17.7 + - - +
133J GLU* 3.7 15.7 - - - +
134J GLU 3.3 0.2 - - - -
135J LEU* 1.3 76.5 - - - +
137J GLU* 1.3 56.4 - - - +
139J ILE* 3.2 8.9 + - + +
140J GLN* 2.9 45.4 + - + +
381J ILE* 5.5 3.6 - - + -
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Residues in contact with GLU 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J ALA* 3.5 25.8 - - + -
133J GLU 3.0 18.1 + - - +
134J GLU* 3.8 1.8 - - - +
136J LEU* 1.3 75.4 - - - +
138J CYS* 1.3 57.6 - - - +
140J GLN* 3.3 4.6 + - - +
141J GLN* 2.9 60.4 + - + +
384J SER* 2.9 25.5 + - - -
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Residues in contact with CYS 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J PHE* 4.1 10.5 - - + -
25J ALA* 3.8 22.7 - - - -
28J LEU* 3.9 24.9 - - - -
56J LEU* 3.7 24.1 - - + +
69J PRO* 4.0 16.2 - - - -
71J ILE* 4.1 4.3 - - - +
134J GLU 3.0 17.4 + - - -
135J LEU* 3.5 10.3 - - - +
137J GLU* 1.3 75.7 - - - +
139J ILE* 1.3 60.8 + - - +
141J GLN* 3.5 3.1 + - - +
142J LEU* 3.1 22.2 + - - +
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Residues in contact with ILE 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56J LEU* 4.7 1.3 - - + -
96J LEU* 5.2 4.9 - - + -
108J LEU* 5.0 9.2 - - + -
115J MET* 3.8 30.1 - - + -
135J LEU* 2.9 31.5 + - + +
136J LEU* 3.6 8.3 - - + +
138J CYS* 1.3 72.1 - - - +
140J GLN* 1.3 61.9 + - - +
142J LEU* 3.1 8.9 + - + +
143J VAL* 2.9 31.4 + - + +
160J ILE* 3.9 33.4 - - + -
162J PRO* 4.0 20.6 - - + -
183J VAL* 4.0 22.4 - - + -
185J LEU* 5.8 0.4 - - + -
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Residues in contact with GLN 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J LEU* 4.1 24.8 - - + +
136J LEU* 2.9 35.6 + - + +
137J GLU* 3.5 11.0 - - - +
139J ILE* 1.3 76.3 - - - +
141J GLN* 1.3 58.1 + - - +
143J VAL* 3.4 2.6 + - - -
144J LYS* 2.8 26.6 + - - +
381J ILE* 4.2 15.6 - - - +
382J VAL 4.0 4.0 + - - -
383J LEU* 3.2 28.3 - - - +
384J SER* 2.8 53.2 + - - +
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Residues in contact with GLN 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J ALA* 5.7 0.2 - - + -
28J LEU* 3.7 26.7 - - + -
71J ILE* 3.8 7.6 - - + +
137J GLU* 2.9 43.7 + - + +
138J CYS 3.7 5.4 - - - +
139J ILE 3.3 0.2 - - - -
140J GLN* 1.3 76.0 - - - +
142J LEU* 1.3 55.7 + - - +
144J LYS* 3.5 29.5 + - - +
145J LEU* 3.0 28.6 + - - +
384J SER* 4.0 14.8 - - - -
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Residues in contact with LEU 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54J HIS* 3.7 32.8 - - + +
55J MET* 3.8 10.8 - - - +
56J LEU* 3.9 9.2 - - + +
71J ILE* 3.6 24.6 - - + +
138J CYS 3.1 12.8 + - - +
139J ILE* 3.1 10.4 + - - +
141J GLN* 1.3 75.2 - - - +
143J VAL* 1.3 59.5 + - - +
145J LEU* 3.3 3.8 + - - +
146J ASP* 3.0 25.9 + - - +
183J VAL* 3.8 42.4 - - + +
185J LEU* 3.8 24.0 - - + -
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Residues in contact with VAL 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98J ALA* 4.0 21.8 - - + -
106J ILE* 4.5 0.2 - - + -
108J LEU* 5.2 4.3 - - + -
139J ILE* 2.9 22.0 + - + +
140J GLN* 3.9 4.0 - - - +
142J LEU* 1.3 71.7 - - - +
144J LYS* 1.3 55.6 + - - +
146J ASP 3.2 0.7 - - - -
147J GLN* 2.7 38.5 + - - +
150J VAL* 4.3 12.8 - - + -
158J LEU* 4.4 4.0 - - + -
160J ILE* 4.0 21.1 - - + -
185J LEU* 3.9 31.6 - - + -
383J LEU* 4.2 20.9 - - + -
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Residues in contact with LYS 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J GLN 2.8 19.5 + - - +
141J GLN* 3.6 30.9 + - - +
143J VAL* 1.3 76.9 - - - +
145J LEU* 1.3 61.2 + - - +
147J GLN* 3.1 36.5 - - - +
383J LEU* 3.8 18.6 - - + +
384J SER 3.4 24.8 + - - +
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Residues in contact with LEU 145 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J VAL* 4.3 20.4 - - + -
32J PRO* 5.4 7.6 - - + -
54J HIS* 3.8 34.1 + - + +
71J ILE* 3.6 30.1 - - + -
141J GLN 3.0 17.4 + - - +
142J LEU 3.7 4.7 - - - +
143J VAL 3.3 0.2 - - - -
144J LYS* 1.3 77.9 - - - +
146J ASP* 1.3 60.0 + - - +
147J GLN* 3.4 1.1 + - - +
148J GLU 5.4 0.2 + - - -
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Residues in contact with ASP 146 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J THR* 2.8 24.0 + - - +
53J ASP* 3.8 5.8 - - - +
54J HIS* 2.8 51.0 + - - +
142J LEU 3.0 15.6 + - - +
143J VAL 3.2 3.4 - - - -
145J LEU* 1.3 77.8 - - - +
147J GLN* 1.3 56.4 + - - +
148J GLU 3.2 2.7 - - - -
149J TRP* 2.9 45.1 + - + +
150J VAL 4.1 0.9 + - - -
158J LEU* 4.5 3.0 - - - +
185J LEU* 3.8 15.2 - - + +
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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